3659 results for "RNA AND sequencing OR transcriptome"

in 289.41 milliseconds.

• Pooled Single-Cell RNA-Seq of iPSC-Derived Neural Stem Cells from ADHD and Control Individuals

  This dataset contains FASTQ files from pooled single-cell RNA sequencing (scRNA-seq) of neural stem cells (NSCs) derived from induced pluripotent stem cells (iPSCs). The iPSCs were reprogrammed using the non-integrative Sendai virus system (CytoTune-iPS 2.0), introducing OCT3/4, SOX2, KLF4, and cMYC. Donor somatic cells included keratinocytes, PBMCs, and lymphoblastoid cell lines from individuals with ADHD and age-matched healthy controls (6–18 years). iPSCs underwent standard quality control, including immunocytochemistry, qRT-PCR, mycoplasma testing, and SNP genotyping. NSCs were produced via neural induction and validated by qRT-PCR and immunostaining for PAX6, SOX2, NESTIN, TUJ1, and FOXG1. Sequencing was performed on the Illumina NovaSeq 6000.

  Dataset EGAD00001015644

• Single-cell RNA sequencing on 11,138 single T cells from 12 colon and rectal cancer (CRC) patients

  Deep single-cell RNA sequencing data for 11,138 T cells from tumour, adjacent normal tissue and peripheral blood of treatment-naive CRC patients. The DATA ACCESS AGREEMENT is provided at https://github.com/zhangyybio/single-T-cell-data-access. Applicants can request access to the data by directly downloading it or by sending an email to cancerpku@pku.edu.cn. The process that is used to approve an application includes verifying the institution, participants and research purposes of the application. In general this process will take about two weeks. In principal, any academic research institutions complying with the laws and bioethic regulation policies of China will be approved.

  Dataset EGAD00001003910

• Bulk RNAseq FASTQ files of WNT7B reporter PDAC organoids (P28 and P40) sorted by mNeonGreen high and low

  This dataset contains raw FASTQ files from bulk RNA sequencing of two patient-derived PDAC organoid lines (P28 and P40) carrying a WNT7B reporter knock-in. Organoids were sorted into mNeonGreen high (WNT-high) and low (WNT-low) populations, with three biological replicates per sorted population. RNA was extracted using the Qiagen QiaSymphony SP system, and libraries were prepared with the Illumina Truseq stranded polyA kit. Sequencing was performed on an Illumina NextSeq2000 platform using single-end 50bp reads. Quality control was conducted with FastQC, and reads were trimmed with TrimGalore as appropriate. Data are controlled-access and intended for transcriptomic analysis of WNT7B expression-dependent transcriptional programs in PDAC organoids.

  Dataset EGAD50000002218

• Single cell RNAseq FASTQ files of three PDAC organoid lines (P28, P40, P47) using SORT-seq

  This dataset contains raw FASTQ files from single cell RNA sequencing of three patient-derived pancreatic ductal adenocarcinoma (PDAC) organoid lines (P28, P40, P47) cultured under standard conditions. For each line, single cells were FACS sorted into 384-well capture plates, with each well containing a 50nl droplet of barcoded primers. Plates were processed following an adapted SORT-seq protocol, and cDNA libraries were generated using CEL-Seq2 with TruSeq small RNA primers (Illumina). Sequencing was performed on an Illumina NextSeq500 platform using paired-end reads (read 1: 26 cycles, index read: 6 cycles, read 2: 60 cycles). Data are controlled-access and intended for single cell transcriptomic analysis of PDAC organoid heterogeneity and WNT pathway activity.

  Dataset EGAD50000002220

• Use of new methodologies to achieve a thorough molecular characterization in pediatric acute leukemia

  In childhood leukemia, a better genetic characterization is needed to define new clinic-biological entities, refine the risk-stratification of patients and help to reduce the toxicity by applying a risk-directed therapy. This project aims to obtain information that will allow us to personalize the management of pediatric patients with leukemia as much as possible, so that we can offer a complete diagnosis, a sensitive follow-up and a more targeted treatment to the real risk of each case. The use of massive genome analysis technologies such as transcriptome sequencing (RNA-Sequencing) will allow a comprehensive biological characterization of pediatric leukemia patients, especially those cases that we have not been able to characterize by conventional diagnostic techniques. We believe that the RNA-Seq technique will allow us to identify new biomarkers that will be useful for: 1) defining new biological entities with their own clinical behavior; 2) refining the stratification of patients into risk groups; 3) finding targets for a better follow-up of MRD and 4) identifying therapeutic targets for the application of targeted therapies to reduce toxicity. PI: Camós-Guijosa, Mireia; Vega-García, Nerea Funding: PI21/00213 Instituto de Salud Carlos III (ISCIII)

  Study EGAS50000000701

• Single-cell RNA sequencing of control and Notch inhibitor treated HCC PDX model

  We generated single-cell RNA-seq data for anti-Notch2 (n=3), anti-JAG1 (n=1) and anti-gD (n=4) treated LIV78 tumors. NCR nude mice bearing similarly sized LIV78 tumors (volumes between 300-900mm3) were injected intravenously with 30mg/kg body weight of either anti-Notch2, anti-Jag1 or anti-gD control antibody 72hrs prior to tumor harvest and tumor cell isolation. Following the depletion of CD45+ and Ter119+ cells, the samples were processed for single-cell RNA-seq (scRNAseq) as described previously (Long et al., 2019) using the Chromium Single Cell 3’ Library and Gel bead kit v2, following the manufacturer’s manual. cDNAs and libraries were prepared following the manufacturer’s manual (10X Genomics). Libraries were profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified using Kapa Library Quantification Kit (Kapa Biosystems, Wilmington, MA). Each library was sequenced in one lane of HiSeq 2500 (Illumina) following the manufacturer’s sequencing specification (10X Genomics) to produce the resulting FASTQ files.

  Dataset EGAD50000000738

• Single cell RNA-seq and ATAC-seq of CD4+ T cells from blood and tumor of NSCLC patients

  This dataset contains fastq files for paired blood-tumor scRNA-seq samples from 5 NSCLC patients and paired blood-tumor scATAC-seq samples from 2 NSCLC patients, both sequenced with NovaSeq or Illumina HiSeq - Rapid Run.

  Dataset EGAD50000000424

• RNAseq from a study of MYC, BCL2 and BCL6 rearrangements in non-Hodgkin lymphoma.

  Paired-end ribodepletion RNAseq performed on 257 samples of Burkitt lymphoma, diffuse large B cell lymphoma, follicular lymphoma, and high-grade B cell lymphoma with MYC and BCL2 or BCL6 rearrangements. RNA was derived from either fresh frozen or formalin fixed/paraffin embedded (FFPE) tissues. Sequencing was performed on Illumina HiSeqX or NovaSeqX instruments.

  Dataset EGAD50000000496

• Bulk RNA-sequencing data from five lines of human iPSC-derived (hiPSC-derived) astrocytes, both alone and in co-culture with neurons, to define the molecular response of astrocytes to misfolded alpha-synuclein.

  Samples were derived from five lines of human iPSC-derived (hiPSC-derived) astrocytes, both alone and in co-culture with neurons +/- alpha-synuclein oligomer treatment. Paired-end FASTQ files for each of the samples are provided.

  Dataset EGAD50000001109

• 10Xchromium 3' RNA-seq of 21 samples from human embryonic heart

  21 samples were taken from human embryonic heart of PCW 5.5-14 of a total of 13 fetuses. Samples were subject to 10Xgenomics chromium single cell 3' sequencing version 2 or 3. Data was analyzed using STARSolo version 2.7.10a, using human genome GRCh38.p12 and transcript annotations from ENSEMBL release 93 from reference package GRCh38-3.0.0 as available from 10Xgenomics.

  Dataset EGAD50000001499

• Differentiation-associated ISG expression of NK cells in chronic viral hepatitis

  Little is known about the effects of ISGs on NK cell responses in chronic viral hepatitis. Here, we determined the expression, regulation and function of ISGs in NK cells with respect to phenotype and function, we performed high-throughput single cell RNA sequencing of circulating CD3-CD56+ NK cells from healthy donors (HD) and patients with chronic HBV or HCV infections.

  Dataset EGAD50000001623

• Sequence-based gene expression in uterine and ovarian carcinosarcomas

  Gynecologic carcinosarcomas (CS), including more generally uterine (endometrial) and less frequently ovarian localization, are histologically defined as biphasic neoplasms composed of carcinomatous (C) epithelial and sarcomatous (S) malignant components. We report a comprehensive analysis of 20 patients of macro-dissected samples of C and S components through RNA sequencing.

  Dataset EGAD00001009099

• 10X 3' V2 data of single immune cells in hepatocellular carcinoma

  The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites. This is the droplet data of this study

  Dataset EGAD00001005961

• single-cell transcriptomics data from immune cells

  Smart-seq2 protocol was used to perform single cell RNA-sequencing on 465 immune cells. The immune cells analysed include 215 HLA-DQ2: gluten-(DQ2.5-glia-α1, -α2, -ω1, and -ω2) tetramer-sorted T cells, 247 transglutaminase 2 (TG2)-positive plasma cells from intestinal biopsy or peripheral blood from celiac disease patients, and 3 unassigned cells in 3 batches.

  Dataset EGAD00001004081

• Cell type-specific transcriptomics of esophageal adenocarcinoma

  3' mRNA-Seq obtained from distinct isolated cell types (epithelia cells,immune cells, fibroblasts) of endoscopically obtained esophageal adenocarcinoma tissue as well as normal esophageal mucosa. Libraries for RNA-sequencing were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina according to the low input protocol. Libraries were sequenced on a HiSeq 4000 (Illumina) by 1x 50 bases.

  Dataset EGAD00001005508

• Bulk RNA sequencing of human T and B cells before and after interleukin-2 immunotherapy

  Bulk RNA sequencing of flow cytometry sorted human CD4+ regulatory T (Treg), CD4+ conventional T (Tcon), CD8+ T, and CD19+ B cells from systemic lupus erythematosus patients collected at baseline (day 0, before interleukin-2 immunotherpay), day 5 (after 1 treatment cycle of interleukin-2 immunotherapy), and day 68 (after 4 treatment cycles of interleukin-2 immunotherapy). The dataset comprises files from the above-mentioned 4 immune cell subsets, collected at 3 time points (day 0, day 5, and day 68) of 12 systemic lupus erythematosus patients. Due to technical reasons, day 5 samples of patient SLE_012 could not be processed and are thus missing. The complete dataset totals in 140 raw sequencing files (fastq format).

  Dataset EGAD50000000661

• RNAseq data

  RNAseq FASTq files from 797 tumors from AVANT. Sequencing libraries were generated with the TruSeq Stranded Total RNA kit (Illumina) following ribosomal RNA (rRNA) depletion with the Ribo-Zero Gold kit (Illumina). The libraries were sequenced on the HiSeq4000 (Illumina) with a sequencing protocol of 75 bp paired-end sequencing. Note: 10 samples used in the original publication were excluded from this upload due to regulations from the Human Genetics Resources Administration of China (HGRAC).

  Dataset EGAD00001009728

• Single Cell Transcriptomic Analysis of Cellular Heterogeneity in Human Colorectal Tumours

  1,591 single cells from 11 colorectal cancer patients were profiled using Fluidigm based single cell RNA-seq protocol to characterized cellular heterogeneity of colorectal cancer. 630 single cells from 7 cell lines were profiled similarly to benchmark de novo cell type identification algorithms.

  Dataset EGAD00001002727

• Single cell characterization of arrested B-lymphoid differentiation and leukemic cell states in ETV6-RUNX1-positive pediatric leukemia

  Leukemic bone marrow in primary ETV6-RUNX1 positive acute lymphoblastic leukemia samples (Six diagnostic and two 15 days after treatment) using Chromium 3' single cell RNA-seq. Samples sequenced on 1-3 lanes and raw fastq files provided for each sample.

  Dataset EGAD00001006074

• Tumor-resident T-cell regulate responses to checkpoint blockade immunotherapies

  In cancer models, CD103+CD8 TRM cells are implicated in the response to anti-PD-1 immunotherapy, and a subset of CD4 TRM cells expressing the integrin CD49a is required for response to anti-CTLA-4 immunotherapy. We performed single-cell RNA sequencing on tumour-infiltrating T lymphocytes (TILs) isolated from colon carcinoma et unsupervised analyses reveal several TRM populations.

  Study EGAS50000000826

• Differentiation-associated ISG expression of NK cells in chronic viral hepatitis

  Little is known about the effects of ISGs on NK cell responses in chronic viral hepatitis. Here, we determined the expression, regulation and function of ISGs in NK cells with respect to phenotype and function, we performed high-throughput single cell RNA sequencing of circulating CD3-CD56+ NK cells from healthy donors (HD) and patients with chronic HBV or HCV infections.

  Study EGAS00001007771

• scCRISPRi/a-seq Control and IFN treated iPS derived human GPC/OPCs

  Datasets consists of 2 batches of human glial progenitors (iPS), cells were sequenced as controls and IFN treated. Using the 10Genomics platform from the samples 2 libraries were built forgene expression libraries (scRNA-seq) and captured guides sequencing library (gRNA) on a set of Multiple Sclerosis associated SNPs. Batch one includes KRAB and P300 perturbed cells in 2 rounds sequenced RNA libraries for Ctrl and IFN and 1 round of capture guides for Ctrl and IFN. Batch 2 includes 1 round of both RNA expresison library and captures guides for KRAB and P300 perturbations in Ctrl and IFN treated cells.

  Dataset EGAD50000002053

• single cell RNA-seq data of circulating tumor cells from three small cell lung cancer patients

  This dataset contains raw 10x Genomics single-cell RNA sequencing data from a total of eight runs of circulating tumor cells from three small cell lung cancer patients. Each run represented by four FASTQ files (R1, R2, I1, I2) generated using the Illumina NextSeq 2000 platform. These files include read pairs as well as sample and cellular barcode indices. Circulating tumor cells were enriched from the blood of three SCLC patients using the CTC-iChip followed by magnetic depletion of RBCs. The enriched samples were processed with the 10x Genomics Chromium platform (Chromium GEM-X Single Cell 3' Kit v4) and sequenced on a NextSeq 2000 system.

  Dataset EGAD50000002035

• Mapping_genetic_variants_underlying_gene_regulation_in_inflammed_intestinal_cell_types_to_identify_novel_IBD_drug_targets

  Biopsies from the terminal ileum and rectum of individuals with Crohn's disease are digested on ice to single cells and processed for single-cell RNA-sequencing (10X Genomics and Illumina) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001003770

• Extensive patient-to-patient single nuclei transcriptome heterogeneity in pheochromocytomas and paragangliomas

  Pheochromocytomas (PC) and paragangliomas (PG) are rare neuroendocrine tumors of varied genetic makeup, associated with high cardiovascular morbidity and a variable risk of malignancy. We focused on PCPG tumors with germline SDHB and RET mutations, representing distinct prognostic groups with worse or better prognoses, respectively. We applied single-nuclei RNA sequencing (snRNA-seq) on tissue samples from 11 patients.

  Study EGAS00001006230

• Whole Exome and Transcriptome Sequencing in Sporadic ALS

  Amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease, is a fatal and devastating neurodegenerative disorder that causes the progressive death of upper and lower motor neurons. Although many efforts have been done to elucidate molecular factors involved in the onset and progression of the disorder, the causes of ALS are yet unknown and undefined. Transcriptome studies, based mostly on microarrays, have revealed multiple perturbations of the motor neuron function, supporting the current idea that several cellular events contribute to the pathobiology of the disease, including mitochondrial dysfunction, enhanced apoptosis, glutamate-mediated excitotoxicity, free radical injury, protein misfolding, abnormal calcium metabolism and altered axonal transport. In the present study, we have deeply sequenced the whole transcriptome of ventral horns of the human lumbar spinal cord from matched control and ALS post-mortem donors. Whole exome sequencing from the same donors has also been performed to exclude known genetic variants associated to the familiar form of ALS. In addition, to characterize the ALS transcriptome we have sequenced the RNA fraction at low molecular weight in the same tissues and individuals. Genomic and transcriptomic reads have been generated using the Illumina HiSeq2000 sequencer.

  Study phs000747

• Integrative analysis reveals a macrophage-predominant, immunosuppressive immune microenvironment and subtype-specific therapeutic vulnerabilities in advanced salivary gland cancer

  Background Salivary gland cancers (SGC) are rare and heterogeneous malignant tumors. Advanced SGC lack established treatment options and show poor response to immunotherapy. Here, an integrative multi-omics analysis in a large cohort of advanced SGC revealed insights into the tumor immune microenvironment (TIM) and distinct mechanisms of immune evasion. Methods A total of 104 patients with recurrent/metastatic SGC from the DKTK MASTER program were included in this study. Whole-exome or whole-genome sequencing and RNA-sequencing was performed on fresh frozen tumor tissue. The tumor immune microenvironment was analyzed using CIBERSORT deconvolution analysis and immune gene expression scores in bulk RNA-sequencing data. Single-nuclei sequencing and immunohistochemistry analyses were performed in selected samples. Results were validated in bulk RNA-sequencing data of a previously published independent dataset. Results Bulk transcriptome analysis revealed an immune-deserted TIM in the majority of advanced SGC samples. Immune exclusion was most prominent in adenoid cystic carcinoma (ACC) subgroup 1 exhibiting a downregulation of the antigen processing machinery. Only a small subset of advanced SGC, including few adenoid cystic carcinoma, exhibited T-cell inflammation, which was correlated with tumor mutational burden in Non-ACC samples. Subtype specific expression of immune checkpoints as well as cancer testis antigens were identified with prominent expression of VTCN1 in luminal cells within ACC. Single-cell RNA-sequencing and bulk RNA-seq deconvolution analysis validated immune cell exclusion and revealed a TIM that was dominated by M2 macrophages across SGC subtypes. Among evaluable patients treated with immune checkpoint inhibitors, a high T-cell to macrophage ratio was associated with clinical benefit. Conclusions These data support biomarker-based development of immune-checkpoint inhibition and the development of novel immune-checkpoint inhibitors and cellular therapies in SGC.

  Study EGAS50000000809

• Genetic and Epigenetic Determinants of Pediatric Obesity-Associated Asthma

  Fifty-nine obese and sixty-one normal-weight asthmatic children of African American or Hispanic background, age 7-11 years, with well controlled asthma, were recruited from clinics affiliated with Children's Hospital at Montefiore, Bronx, New York, USA. We isolated CD4+ T cells (Th cells) from a fasting sample of peripheral blood and conducted genome-wide assays of gene expression by Directional Transcriptome Sequencing (RNA-seq), DNA methylation by HELP-tagging, and examined genetic polymorphisms and single nucleotide polymorphisms (SNPs), informative about ancestry, by array-based genotyping using Multi-Ethnic Genotyping Array.

  Study phs001812

• LCM-RNAseq on human lung macrophages

  In the reported study, we employed Laser Capture Microdissection (LCM) for the transcriptome profiling of lung macrophages cells populations as a function of location within the healthy tissue. In detail, macrophage mini-bulks (100 cells each) were collected by LCM from 4 healthy human donors in 5 different locations of the airways (a total of 20 biopsies), including parenchyma (L1 – lower left lobe (LLL); L6 – 80% distance from LLL tip), trachea (L2), bronchi (L3 – 1st/2nd generation; L5 – 3rd/4th generation) and processed for RNA-seq.

  Dataset EGAD00001008694

• Next Generation Sequencing Characterization of Hematopoietic Stem and Progenitors Cells in Human Systemic Lupus Eryhtematosus

  This dataset contains RNA-sequencing of Bone marrow-derived CD34+ cells from Healthy Controls (n=2) and SLE patients (n=8). SLE patients are divided into two categories based on severity: patients with moderate/mild disease (n=3) and patients with severe disease (n=5). Libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Single-end 75-bp mRNA sequencing was performed on Illumina NextSeq 500. The raw fastq files are uploaded.

  Dataset EGAD00001005052

• mRNA capture sequencing and RT-qPCR for the detection of pathognomonic, novel and secondary fusion transcripts in formalin-fixed paraffin-embedded tissue: a sarcoma showcase

  RNA sequencing is widely used to study gene abundance patterns, but less frequently to assess structural alterations such as fusion transcripts. In this study, we assess the performance of messenger RNA (mRNA) capture sequencing to identify fusion transcripts in formalin-fixed paraffin-embedded (FFPE) tissue of different types of sarcoma, followed by orthogonal confirmation using RT-qPCR. To validate our workflow, we used the TruSight RNA Pan-Cancer Panel to analyze a first cohort of 6 positive control tumors for which the diagnostic workup demonstrated the presence of a specific chromosomal rearrangement. Fusion transcript calling by FusionCatcher confirmed all known aberrations and enabled the identification of both fusion gene partners and breakpoints. Next, whole transcriptome TruSeq RNA Exome sequencing was applied to a second cohort of 17 patients, diagnosed with fusion gene-negative alveolar rhabdomyosarcoma (ARMS) or undifferentiated round cell sarcoma (URCS), for whom fluorescence in situ hybridization (FISH) did not identify the classical pathognomonic rearrangements. Remarkably, for 6 out of 17 patients, mRNA capture sequencing readily detected a pathognomonic fusion transcript, i.e. PAX3-FOXO1 in 2 ARMS patients, and EWSR1-FLI1, EWSR1-ERG or EWSR1-NFATC2 in 4 URCS patients. These data show that RNA capture sequencing may enhance the detection rate of pathognomonic fusion genes in sarcoma. For the 11 patients with no known pathognomonic fusion transcript, 11 newly identified fusion transcripts were confirmed by RT-qPCR, including COPS3-TOM1L2, NCOA1-DTNB, WWTR1-LINC01986, PLAA-MOB3B, AP1B1-CHEK2 and BRD4-LEUTX fusion transcripts in ARMS patients. Additionally, recurrently detected secondary fusion transcripts in two patients diagnosed with EWSR1-NFATC2-positive sarcoma were confirmed (COPS4-TBC1D9, PICALM-SYTL2, SMG6-VPS53 and UBE2F-ALS2). Our results provide new insights into the underlying genetic causes of these malignancies.

  Study EGAS00001005202

• Single-cell RNA-seq of immune cells from human tumor fragments after 48 hour culture ex vivo (Kaptein et al., 2024)

  Single-cell RNA-seq profiling of immune cells from human ovarian carcinoma, renal carcinoma and melanoma samples after 48h of ex vivo culture using the patient-derived tumor fragment platform (5 samples total). Samples were cultured in various conditions, including: untreated, CD8-IL2v-treated, CD8-IL2v + LCKi -treated, aPD1-treated, CD8-IL2v + aPD1 -treated, Untargeted IL2-treated, aCD3-treated and aCD3 + CD8-IL2-treated . FASTQ files contain gene expression data, feature barcode antibody capture or TCR data on immune cells from all conditions combined per patient.

  Dataset EGAD50000000377

• RNA-seq datatset of primary human thymocyte subsets

  FASTQ-files of RNA-seq experiments of 8 primary human thymocyte subsets, isolated by flow-cytometry (FACS) from neonatal thymus biopsies. All samples were sorted to be negative for the expression of the lineage surface markers CD11c, CD19, CD56, CD141 and CD303 and additionally had the following surface phenotypes: DN1 (CD4-CD8-CD7+CD1a-CD161-CD38-); DN2 (CD4-CD8-CD7+CD1a-CD161-CD38+CD3-TCRab-); DN3 (CD4-CD8-CD7+CD1a+); ISP (CD4+CD8-CD3-TCRab-CD1a+); DPE (CD4+CD8+TCRab-CD69-); DPL (CD4+CD8+TCRab+CD69+); SP4 (CD4+CD8-); SP8 (CD4-CD8+). Samples were sorted from 2-4 pediatric patients undergoing heart surgery.

  Dataset EGAD50000001599

• BLUEPRINT release August 2016, RNA-Seq for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell, on genome GRCh38

  RNA-Seq data for 6 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 24 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002339

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (RNA-Seq for CD14-positive, CD16-negative classical monocyte, on genome GRCh37)

  RNA-Seq data for 197 CD14-positive, CD16-negative classical monocyte sample(s). 197 run(s), 197 experiment(s), 197 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_rnaseq_analysis_sanger_20160816

  Dataset EGAD00001002674

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (RNA-Seq for CD4-positive, alpha-beta T cell, on genome GRCh37)

  RNA-Seq data for 212 CD4-positive, alpha-beta T cell sample(s). 212 run(s), 212 experiment(s), 212 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_rnaseq_analysis_sanger_20160816

  Dataset EGAD00001002671

• BLUEPRINT release January 2015, RNA-Seq for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell

  RNA-Seq data for 5 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 23 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001165

• BLUEPRINT release August 2014, RNA-Seq for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell

  RNA-Seq data for 4 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 22 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001000903

• BLUEPRINT release August 2015, RNA-Seq for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell, on genome GRCh38

  RNA-Seq data for 5 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 23 run(s), 5 experiment(s), 5 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001534

• Counts: Brain transcriptome of hereditary cerebral haemorrhage with amyloidosis–Dutch type (HCHWA-D)

  These are the log2CPM (log2 counts per million) fragments per gene counts associated with the BAM files in EGAD00001003806, in tab separated format. Counts for 36 postmortem brain samples from 9 non-demented control subjects and 9 Hereditary cerebral hemorrhage with amyloidosis-Dutch type subjects are included (1 Frontal cortex sample and 1 Occipital cortex sample per subject). RNA samples were depleted for ribosomal RNA with the Ribo Zero Gold Human kit (Illumina) and strand specific RNA-Seq libraries were generated. Paired-end sequencing was performed on a HiSeq2500 Illumina system (2x50bp reads). Alignments were performed using GSNAP v2014-12-23 with setting "--npaths 1" on GRCh38 reference genome without the alternative contigs. Fragment per gene counting was performed using HTSeq-count v0.6.1p1 with setting "--stranded reverse". The gene annotation used for quantification were UCSC RefSeq genes for GRCh38 downloaded on 2015-07-13.

  Dataset EGAD00010001457

• RNA-Seq of human longitudinal whole blood samples from PCR-positive and PCR-negative recent household contacts of COVID-19 index cases.

  Little is known about the transcriptomic profile of individuals who are exposed to SARS-CoV-2 yet resist becoming PCR positive. To investigate this, longitudinal whole-blood samples were taken (0, 7, 14, and 28 days after enrolment) from PCR positive and PCR negative SARS-CoV-2-naïve household contacts who were recently exposed to a COVID-19 index. Samples were also taken from pre- and post-pandemic unexposed controls. Total RNA was extracted from PAXgene tubes before undergoing poly(A) selection followed by globin and rRNA depletion. DNA libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. All samples were then sequenced across 2 flowcells of an Illumina HiSeq 4000.

  Dataset EGAD50000000684

• Single-cell RNA sequence analysis of iPS cell-derived cardiomyocytes treated with S-RBD-sfGFP or GFP

  To determine the transcriptional response in human cardiomyocytes treated with SARS-CoV-2 spike receptor-binding domain (S-RBD-sfGFP), human cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs) were replated on day 21 after differentiation and treated with S-RBD-sfGFP or control-GFP for 48 hours on day 26-28. iPSC-CMs were dissociated and the single cell suspension was analyzed by single cell RNA-sequence.

  Study JGAS000620

• Transcriptome alterations underlying metabolic dysfunction and liver disease in myotonic dystrophy type 1

  Myotonic dystrophy type 1 (DM1) is a multisystem disorder affecting various organs, including the skeletal muscles, eyes, heart, central nervous system, and endocrine system. Liver dysfunction and lipid metabolism abnormalities are frequently observed in DM1 but are not fully understood. To explore the molecular basis of these abnormalities, transcriptome analysis was performed on postmortem liver samples from DM1 patients DM1 patients (n = 11) and disease control patients (n = 9) using bulkRNA sequencing (RNA-seq) on the MGI DNBSEQ-G400RS. Differential gene expression and alternative splicing analyses revealed significant transcriptomic changes associated with lipid metabolism, liver fibrosis, and glucose homeostasis. Interestingly, transcriptome changes in DM1 livers also revealed partial resolution of sexual dimorphism in gene expression, along with unique sex-specific pathway alterations. A correlation between serum GGT levels and splicing abnormalities in DM1 patients was identified, suggesting a link between transcriptomic changes and clinical outcomes. This dataset provides valuable insights into the molecular mechanisms underlying DM1-related liver dysfunction and metabolic abnormalities.

  Study JGAS000814

• Manchester Eye Tissue Repository Genome-Transcriptome Project

  The Manchester Eye Tissue Repository Genome-Transcriptome (METR-GT) Project comprises whole genome sequencing data and paired short read, high-depth bulk-RNA sequencing data from the neurosensory retina (NSR) and the retinal pigment epithelium (RPE) from 201 unrelated individuals that donated eye-tissue post-mortem. None of the individuals included in the cohort had phenotypic presentation, assessed post-mortem, consistent with late-stage AMD or monogenic ophthalmic disorders. In this dataset we include WGS fastq files, WGS VCF files (at an individual level and an aggregate VCF that has undergone variant-level quality control), RNASeq BAM files of the NSR and RPE, gene expression quantification files of the NSR and RPE (including raw gene counts generated by RNASeQC and estimated TPM and FPKM values generated by RSEM). Additionally, we have included the output files from eQTL mapping in both tissues, generated by tensorQTL and instances of aberrant gene expression events generated by the OUTRIDER module of the DROP pipeline.

  Dataset EGAD50000002082

• Ischemia Reperfusion Responses in Human Lung Transplants at the Single Cell Resolution

  Ischemia reperfusion is an unavoidable step of organ transplantation. Development of therapeutics for lung injury during transplantation has proved challenging; understanding lung injury from human data at the single cell resolution is required to accelerate the development of therapeutics. Donor lung biopsies from six human lung transplant cases were collected at the end of cold preservation and 2-hour reperfusion and underwent single cell RNA sequencing.

  Dataset EGAD50000000704

• scRNAseq of co-culture of human organoids with polarized pro-inflammatory or anti-inflammatory macrophages

  In order to know if the mechanisms we identified in mice – demonstrating that macrophages are able to orchestrate the intestinal regenerative process – are conserved in humans we develop a co-culture system with human intestinal organoids and human polarized macrophages. We co-culture human organoids with pro-inflammatory or anti-inflammatory macrophages for 48h. On day 3 cells were collected to perform single cell RNA sequencing.

  Dataset EGAD50000000675

• RNA sequencing of NK cells in human lung

  The dataset contains RNAseq data from 5 subsets of NK cells isolated from human lung: 1) CD69+CD49a+CD103+CD16-CD56bright NK cells 2) CD69+CD49a+CD103-CD16-CD56bright NK cells 3) CD69+CD49a-CD103-CD16-CD56bright NK cells 4) CD69-CD49a-CD103-CD16-CD56bright NK cells 5) CD56dimCD16+NKG2A+CD57- NK cells The dataset contains paired data for the subsets from 2 donors with 2 biological replicates/donor and subset.

  Dataset EGAD00001004850

• Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases. Cancer Discovery doi: 10.1158/2159-8290. PMID: 30787016 PMCID: PMC6497554

  The BAM files for WES and RNA seq used in the article "Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases." on cancer Discovery 2019. PMID: 30787016 PMCID: PMC6497554. Authors : Grant M Fischer, ..., Michael A Davies.

  Dataset EGAD00001005046

• RNA-seq of cells cultured in vitro

  This dataset includes 90 samples profiled by high-throughput Illumina sequencing, in bam format, aligned to GRCh37. Normal human CD34+ cord blood (CB), bone marrow (BM), or post-natal thymus (PNT) cells were transduced with various combinations of T-ALL oncogenes and cultured in vitro.

  Dataset EGAD00001009750

• Genomic Data for Integrative Profiling of T790M Negative EGFR Mutated NSCLC

  Contains WES and RNA-seq for the 59 patients with first- and second-generation EGFR TKI-resistant metastatic EGFR-mutated NSCLC.

  Dataset EGAD00001010272

• TRACERx NSCLC - Multiregion RNA sequencing data from the 421 cohort

  RNAseq data from the TRACERx 421 cohort

  Dataset EGAD00001009862

• Smartseq2 data of single immune cells in hepatocellular carcinoma

  The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites. This dataset is part of Smartseq2 data

  Dataset EGAD00001005960

• Prognostic and immunomodulatory consequences of ERV expression in ovarian cancer

  The dataset contains transcriptional data obtained using total RNA sequencing on a Illumina machin. 59 samples are from the Hammersmith Hospital (HH) cohort of human primary ovarian tumours and 20 samples are from ovarian cancer cell lines Kuramochi (3 replicates) and Ovsaho (2 replicates) treated with 1 uM DNMTi guadecitabine or vehicle, at an early (day 5) or late (day 8) timepoint.

  Dataset EGAD00001006589

• The BNT162b2 mRNA COVID-19 vaccine induces long-term effects on both adaptive and innate immune responses

  This dataset contains bulk RNA sequencing at different timepoints post-BNT162b2 mRNA COVID-19 vaccination. Stimulation experiments were performed at each of the timepoints (RPMI, Influenza, R848 and Influenza stimuli), resulting in 242 libraries distributed over 4 stimulations and 4 timepoints. Libraries were sequenced on the DBNSEQ platform.

  Dataset EGAD00001011042

• Single-cell RNA and TCR sequencing of 37 PBMC pools of advanced HCC patients.

  scRNAseq and scTCRseq of serial peripheral blood mononuclear cell (PBMC) samples (n=72) taken at various timepoints before and during treatment (Week 0 (W0), Week 3 (W3), Week 6 (W6)). PBMC samples were pooled together into 37 pools, loading 2 or three samples per lane in the 10X Genomics chip, in equal proportions, according to a pre-designed pooling matrix.

  Dataset EGAD00001011345

• Genetic investigation of 12q-amplified osteosarcomas

  Further investigation and characterisation of 12q-amplified low- and high-grade osteosarcomas with MDM2 and/or CDK4 amplification focusing on SV, copy number and gene fusion analyses. In total, 25 cases (33 samples total due to multi-sampling) were included, with some form of sequencing data available for 27 samples. Mate-pair whole genome sequencing (Illumina) is available for 19 samples, longread whole genome sequencing (PacBio HiFi) on 10 samples and RNA-sequencing (Illumina Truseq) on 21 samples. Data is available as BAM files.

  Dataset EGAD50000000707

• SLAMF7 Regulates Synovial Macrophages in Rheumatoid Arthritis

  The purpose of this study was to characterize the role of SLAMF7 on human macrophages. RNA-sequencing was performed on myeloid populations from blood of healthy controls or rheumatoid arthritis patients, or synovial fluid of rheumatoid arthritis patients, based on high or low expression of SLAMF7. Then, monocyte-derived macrophages from healthy controls were left untreated, or stimulated with anti-SLAMF7 or recombinant SLAMF7 protein, and transcriptional profile was defined after SLAMF7 engagement.

  Study phs002771

• Single-cell RNA sequencing of pediatric Hodgkin Lymphoma to study the inhibition of T cell subtypes

  Here, we applied single-cell RNA-sequencing (scRNA-seq) on isolated HRS cells and the immune cells from the same pediatric classical Hodgkin Lymphoma (cHL) tumors. Specifically, 13 cHL patients and 3 reactive lymph node control samples were included in this cohort. This allowed us to identify genes of cell surface proteins that are consistently overexpressed in HRS cells and can potentially be used as targets for antibody-drug conjugates or CAR T cells. Finally, we identify potential interactions by which HRS cells inhibit T cells, among which the Galectin-1/CD69 and HLA-DRA/LAG3 interactions. However, high levels of inter-patient heterogeneity of the interaction strength were observed. In conclusion, this study identifies new potential therapeutic targets for cHL and highlights the importance of studying heterogeneity when identifying therapy targets.

  Dataset EGAD50000000626

• Bulk-tissue RNA-sequencing paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen tissues from 4 post-mortem neuropathologically-confirmed control individuals ( anterior prefrontal cortex & cerebellar cortex – 4 individuals, putamen- 3 individuals)

  Profiling of paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen samples by bulk-tissue RNA-sequencing. Samples were derived from 4 post-mortem neuropathologically-confirmed control individuals ( anterior prefrontal cortex – 4 individuals, cerebellar cortex – 4 individuals, putamen- 3 individuals). Paired-end FASTQ files for each of the human samples are provided. Fastp (v 0.20.0), a fast all-in-one FASTQ pre-processor, was used for adapter trimming, read filtering and base correction. Fastp default settings were used for quality filtering and base correction. Further details on parameters used are available here: https://github.com/RHReynolds/RNAseqProcessing .

  Dataset EGAD00001009264

• Induction of trained immunity by influenza vaccine: impact on COVID-19

  Cryopreserved PBMCs from 10 individuals before and after vaccination were used to perform single cell RNA sequencing. Equal number of cells per individual were pooled together (5 individuals per pool) and single-cell RNA sequencing was performed in paired-end mode on NovaSeq 6000 (Illumina) with a depth of 50,000 reads per cell. DNA was isolated from PBMCs and then used for genotyping by Illumina GSA Beadchip. This dataset contains the fastq sequence files, genotypes of the donors used for demultiplexing the pools and files indicating the linkages between individuals, pools and fastq files. The number of samples listed by EGA does not match the actual number of samples due to limitations on the upload scheme used.

  Dataset EGAD00001007827

• Single cell ATAC seq component of ATAC-RNA multiome analysis of a four weeks post conception embryo head

  Four single-cell ATAC libraries were generated from an unbiased sample of cells of a human four weeks post conception embryo using the 10X Chromium Single-Cell Instrument and NextGEM Single Cell Multiome ATAC+Gene Expression kit (10X Genomics) according to the manufacturer’s protocol.

  Dataset EGAD50000001502

• 4_eCLIP_NOVA1_NOVA2_RBFOX2

  eCLIP of NOVA1, NOVA2 and RBFOX2 from iPSC-derived motor neurons in 2 control lines. Per line and RNA-binding protein input and IP samples and analysis including bigWig files and peak files.

  Dataset EGAD00001008428

• Human tumor single-cell

  We profiled 11 patient tumor samples by single-cell and single-nuclei RNA-seq using 10X Chromium 3'. These include samples from the following entities: WNT-subtype medulloblastoma (N=3), embryonal tumors with multilayered rosettes (N=3), and atypical teratoid-rhabdoid tumors (N=5). The BAM files are provided.

  Dataset EGAD00001005129

• RNAseq in ASD patients and controls

  RNA sequences of a total of 24 samples, including 13 unrelated ASD patients (13 males) and 11 adult individuals of Spanish origin as controls (4 males, 7 females). The RNAseq study was conducted on a HiSeq 4000 (Illumina) and paired-end sequences were obtained (fastq files).

  Dataset EGAD00001008160

• Advanced iPSC-CMs maturation by integrating maturation medium, nanopatterning, and electrical stimulation

  RNA seq of iPSC-derived cardiomyocytes cultured in lipid-enriched maturation medium (MM), in MM on nanopattern-surfaces (NP) and under the influence of MM, NP and electrical Stimulation (ES, 2Hz, 14 days). 9 Samples from 3 Independent batches/differentiations of cardiomyocytes from 2 different iPSC-lines (iWTD2.1 and isWT7.22).

  Dataset EGAD00001011289

• Colon Cancer Organoid Cultures and Tumors RNASeq Data

  Four micrograms of total RNA was used for cDNA library construction using the KAPA Stranded mRNA-Seq Kit (KR0960-v3.15), following manufacturer's protocol. The adaptor-ligated libraries were enriched by 6 cycles of polymerase chain reaction (PCR). Libraries were sequenced using the Novaseq 6000 with paired end 151bp reads.

  Dataset EGAD00001005753

• CITE-seq data of primary acute myeloid leukemia patient samples with complex karyotype

  In this study, we aimed to assess RNA expression and surface antigen expression of acute myeloid leukemia with complex karyotype (CK-AML) at the single-cell level. For this purpose, we performed cellular indexing of transcriptomes and epitopes (CITE-seq) of primary leukemia samples from four CK-AML patients.

  Dataset EGAD00001011171

• Bulk RNA Seq in FAP Adenoma

  Bulk RNASeq data of Duodenal organoids, sorted ILC3 and duodenal tissue

  Dataset EGAD00001015488

• RNA-sequencing of human skin samples obtained from SSc patients and healthy controls.

  Patient information SSc patients were recruited at the Department of Rheumatology of the Leiden University Medical Center (Leiden, The Netherlands). All patients met the American Rheumatism Association classification criteria for SSc (Subcommittee for scleroderma criteria 1980), and were classified according to LeRoy and Medsger criteria as either limited or diffuse cutaneous disease (LeRoy EC, Black C, Fleischmajer R, Jablonska S, Krieg T, Medsger TA Jr, Rowell N 1988). Institutional review board approval and written informed consent was obtained before patients entered this study. Two 4 mm skin biopsies were taken from a standardized location on the most proximal part of the lower arm, distal from the elbow. In 10 patients the skin biopsy came from a clinically affected area and in 4 patients the skin was locally unaffected. One sample was used for RNA sequencing and one sample was used for immunohistochemistry. Skin biopsies from healthy individuals were commercially sourced (Tissue Solutions, UK) and collected from donors undergoing skin resection surgery and after informed consent. To match the healthy skin with patients as much as possible, skin biopsies from healthy controls were also taken from a similar position (the under-arm (for 4 controls) and leg (for 2 controls)). Healthy skin donors were selected to match the age and sex of the SSc patient cohort. Biopsies from patients and controls were equally treated and were both stored at -80°C until RNA isolation was performed. RNA from frozen skin biopsies was isolated using RNeasy kit from fibrous tissue (Qiagen, the Netherlands). RNA quantity was determined by using SimplyNano 2000 and quality was assessed on Tapestation (Agilent, the Netherlands). All samples included in the study had a RIN score above 7.0. Transcriptome characterisation and analysis RNA sequencing was performed using polyA selection and a stranded protocol using Ion Torrent next generation sequencing technology (Service XS, The Netherlands). The Ion PI Template OT2 200 Kit v3 and Ion PI Sequencing 200 Kit v3 were used according to the manufacturer’s instructions. 20 samples were run on 11 PI chips. PI chip analyses, base calling and quality checks were performed using the Torrent Server Suite. An average of 42 million 100 bp reads was generated per sample. Following quality control, reads were aligned to the human genome (Homo sapiens GRh38.78) using Bowtie2 and STAR (Dobin et al. 2013; Langmead and Salzberg 2012). Reads were first aligned with STAR. For the unmapped reads from STAR, a second alignment step was performed using bowtie2 (local very sensitive options)

  Dataset EGAD00001003832

• Single-cell Kinnex sequencing of Alzheimer's disease isoform profile

  Alzheimer’s disease (AD) is the most common cause of dementia, yet its molecular causes remain incompletely understood. RNA diversity in part arising from dysregulated splicing may contribute to AD pathogenesis; however, the ability to interrogate the resulting full-length isoforms in single brain cells has been technologically limited. Here we report the use of PacBio Kinnex long-read sequencing combined with 10X Genomics single-cell preparations to identify both annotated and unannotated RNA isoforms. Eight AD and seven non-diseased post-mortem human brains yielded ~70,000 single nuclei showing diverse, differentially expressed, and switched transcripts in multiple genes. Cell-type-specific isoform expression and variants with intra-exonic junctions associated with reverse transcriptase-mediated somatic gene recombination were also detected. Novel isoforms, including CHI3L1 and SEPTIN4, were altered in AD. Kinnex sequencing of RNA isoforms from single nuclei detected vast isoform diversity amongst brain cell types, representing an under-explored element in AD and other brain disorders.

  Study EGAS50000001476

• ICARUS-BREAST01 Dataset

  A phase II clinical trial (NCT04965766) of patritumab deruxtecan in 99 breast cancer patients. Whole-exome sequencing (WES) is available for 43 tumor samples and 43 blood samples collected at entry into the trial. RNA-squencing is available for 44 samples comprising 22 samples collected at entry into the trial and 22 samples collected during treatment (cycle 1 day 3, cycle 1 day 19, or cycle 2 day 3) from 22 patients.

  Dataset EGAD50000000773

• Transcriptomic data in 46,XX, 46,XY, 47,XXY, 47,XYY individuals

  This dataset contains paired-end (151x2) RNA sequencing data (fastq files) from 25 human blood samples, some with sex chromosome aneuploidies. Data were generated using Illumina technology (Novaseq 6000) and a median of approximately 174 million pairs of reads per sample were obtained using two sequencing batchs. Samples come from: six 46,XX individuals, six 46,XY individuals, nine 47,XXY individuals, and four 47,XYY individuals.

  Dataset EGAD00001011202

• Next Generation Sequencing Characterization of Tregs in Human Peripheral Blood during Autoimmunity

  Tregs were sorted as CD4+CD25+CD127- cells from peripheral blood of 14 healthy individuals, 8 patients with mild/severe rheumatoid arthritis, 1 patient with systemic lupus erythematosus/rheumatoid arthritis, 2 patients with ulcerative colitis and 2 patients with Chrohn's disease. RNA was extracted and polyA libraries were prepared using the Illumina Truseq sample preparation kit v.2. Single-end 75bp sequencing was performed on NextSeq500.

  Dataset EGAD00001005446

• Dataset RNA-Seq of tumors for ImmuNEO already used in study EGAS00001004813

  Sequencing data of 20 tumor runs (different tumors), which were uploaded to EGAS00001004813 and used in the ImmuNeo publication. The sequencing was always paired and run on Illumina HiSeq sequencers.

  Dataset EGAD00001009670

• Single cell sequencing on whole bone marrow of NBM and AML

  To generate a cellular taxonomy of the human NBM and AML, representing both rare hematopoietic stem/progenitor cells (HSPCs) and stromal niche populations, allowing assessment of their cellular diversity and predicted intercellular signaling, we performed single cell RNA sequencing (scRNAseq) on viably frozen bone marrow (BM) aspirates from four healthy donors and 6 NPM1+ AML patients at diagnosis

  Dataset EGAD00001011057

• BrainSpan Atlas of the Human Brain

  The NIH-funded BrainSpan (www.brainspan.org) and PsychENCODE (www.psychencode.org). Consortia sought to generate and analyze multi-dimensional genomics data from the developing and adult human brain in healthy and disease states. One of the main goals has been to perform large-scale and integrated analysis of the genome, transcriptome, and epigenome of the human brain to broaden our understanding of human neurodevelopment. This dataset consists of sixteen regions, including eleven neocortical areas, of human donors of both sexes and various ethnic groups. In the first stage of this project, we provide the genome-wide exon-level transcriptome data generated using the Affymetrix GeneChip Human Exon 1.0 ST Arrays, and the genome-wide genotyping data for 2.5 million markers using the Illumina Human Omni 2.5-Quad Bead Chips. In the second stage of this project, we provide whole-genome sequencing data, transcriptome data by mRNA-Seq, small RNA data by smRNA-seq, DNA cytosine methylation by Infinium HumanMethylation450 BeadChip, and epigenomic/epigenetic data by ChIP-Seq for H3K4me3, H3K27me3, H3K27ac and CTCF.

  Study phs000755

• Whole exome and Transcriptome sequencing of treatment-naïve esophageal adenocarcinoma biopsies and matched peripheral blood mononuclear cells

  Exome sequencing was performed on n=28 treatment-naïve esophageal adenocarcinoma (EACs). Three to four biopsies sampling different areas of each tumor were pooled before nucleic acid extractions to mitigate the elevated heterogeneity described for EAC. WES was performed on EAC biopsies at 120X average coverage, with autologous PBMCs used as germline controls at 80X average coverage. Libraries were prepared from 30 ng of input DNA using the SureSelect QXT Human All Exon V7 kit (Agilent Technologies) and sequenced on the NextSeq 550 (Illumina), 2x150 bp. BCL files were demultiplexed to FastQ files using bcl2fastq2 software (Illumina). Three paired end sequencing batches were analyzed independently (Batch1: samples 8, 10, 11, 12, 15, 17, 18; Batch2: samples 20, 24, 25, 26, 27, 29, 30, 31, 33, 34 ; Batch3: samples 35, 37, 39, 40, 41, 43, 45, 48, 54, 55, 57). RNA sequencing was performed on n=26 treatment-naïve esophageal adenocarcinoma (EACs). Three to four biopsies sampling different areas of each tumor were pooled before nucleic acid extractions to mitigate the elevated heterogeneity described for EAC. RNAseq libraries were prepared on 50 ng of total RNA (with RNA integrity index RIN >=7) with the TruSeq Stranded mRNA library preparation kit (Illumina) in accordance with low-throughput protocol. After PCR enrichment (15 cycles) and purification of adapter-ligated fragments, the concentration and length of DNA fragments were measured using D1000 Screen Tape System (Agilent), obtaining a median insert size of 311 nucleotides. Then, RNAseq libraries were sequenced using the Illumina NovaSeq platform, 1x100 bp, obtaining on average 100 million single reads per sample.

  Dataset EGAD00001010876

• Whole-genome enzymatic DNA methylation sequencing and single-cell RNA sequencing data from nasal cells of COVID-19 patients

  Nasal swabs were collected from COVID-19 patients during the acute phase of infection as well as 3 and 12-months post-infection. Cells isolated from nasal swabs were subjected to whole-genome enzymatic DNA methylation sequencing (n=33) and scRNA-seq (n=24). For n=12 former COVID-19 pateints, follow-up samples were collected at 3 and 12 months post-infection and subjected to scRNA-seq.

  Dataset EGAD50000000398

• Sequencing data of the ampulla and fimbriae of the fallopian tube in pre-menopausal women

  A total of 10 pre-menopausal patients were recruited for this study. Sequencing of both the fimbriae and ampullary region of the fallopian tubes was performed using 10x Genomics single-cell RNA-seq and ATAC-seq. For one patient, data were sequenced across 4 lanes, while the remaining patients' data were sequenced in 2 lanes each, resulting in a total of 44 sequencing datasets for each platform.

  Dataset EGAD50000000889

• Transcriptomic profiling of myeloid cells from secondary lymphoid organs (lymph nodes and tonsils) from lymphoma patients and controls.

  Despite their recognized impact on the pathogenesis and prognosis of B-cell lymphoma, tumor-associated macrophages (TAM) have not been extensively explored in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). We investigated mononuclear phagocyte (MNP) heterogeneity using single cell RNA sequencing (scRNAseq) in B-cell lymphoma lymph nodes compared to reactive secondary lymphoid organs (lymph nodes and tonsils).

  Study EGAS50000001135

• RNA004 DRS METTL5 variant

  RNA004 is a method for direct RNA sequencing (DRS) that holds promise to enhance the detection of modopathies. To this end, we provide DRS data for a patient sample harboring heterozygous inactivating SNPs for the methyltransferase METTL5, which modifies m6A on 18S rRNA. Companion datasets are 1) EGAS50000001201 for DRS of a healthy control with intact METTL5 and 2) PRJEB74238 for IVT 18S rRNA vector data as unmodified control.

  Study EGAS50000001321

• Pediatric Papillary Thyroid Carcinoma RNA-Seq

  38 PPTCs were sequenced using RNASeq to identify oncogenic variants in driver-unknown tumors and to explore gene expression patterns. RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). Libraries were pooled in equimolar quantities and paired-end sequenced on 2 lanes of a High Throughput Run Mode flowcell with the V4 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol to generate paired-end reads of 126-bases in length.

  Dataset EGAD00001007499

• Gene expression by RNAseq in bronchial biopsies of asthmatics, asthma in remission and healthy subjects

  The study focus was differential expression in bronchial biopsies between persistent asthma, asthma in remission and healthy controls using RNAseq. There were 184 samples that passed QC. RNA samples were processed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA), using an automated procedure in a Caliper Sciclone NGS Workstation (PerkinElmer, Waltham, MA). In this procedure, all cytoplasmic and mitochondria rRNA was removed (RiboZero Gold kit). The obtained cDNA fragment libraries were loaded in pools of multiple samples unto an Illumina HiSeq2500 sequencer using default parameters for paired-end sequencing (2 × 100 bp). Data are available as 221 pairs of FASTQ-files. Note that several samples are associated with multiple sequence runs.

  Dataset EGAD00001005112

• Pathogenesis and Immunity in Endemic Burkitt Lymphoma

  This genomic landscape of Burkitt lymphoma represents a multimodal sequencing of tumors and control tissues and individuals to better understand the etiology, and molecular pathogenesis of Burkitt lymphoma including the roles of the associated Plasmodium falciparum malaria and EBV infections. Comprehensive sequencing set includes genomic, transcriptomic, and epigenomic datasets in concert with variable clinical phenotypes and outcome information such as anatomical presentation site, in-hospital survival rates, and EBV genome type. This deposit includes additional small RNA-seq data from endemic BL (eBL) tumors and RNA-sequencing data from sorted NK cell subsets from the peripheral blood of eBL patients. The additional small RNA-seq data are from tumor specimens from 17 eBL cases, of the previously deposited polyA RNA-seq data from 28 eBL cases (phs1282.V1). The additional RNAseq data from Fluorescence-activated cell sorting (FACS) of NK cell subsets, isolated from the peripheral blood of 7 eBL cases. The additional RNAseq data are from eBL tumor samples of 5 eBL cases, BL cell lines established from these tumor samples and also NSG mouse tumors created by implanting the established BL cell lines into NSG mice. The dataset also includes RNAseq data of the NSG mouse tumors after treatment with Rituximab (RIT) and Phosphate buffered saline (PBS). The fifth batch of data includes mRNA-seq from different passages of a single eBL cell line that have variable EBV phenotypes (low passage with lytic EBV and high passage with latent EBV). This batch also includes lytic and latent lymphoblastoid cell line (LCL) clones from a single blood donor generated through infection with the strain of EBV isolated from the aforementioned eBL cell line. For initial transcriptome analysis see: Kaymaz et al. "Comprehensive Transcriptome and Mutational Profiling of Endemic Burkitt Lymphoma Reveals EBV Type-specific Difference." Molecular Cancer Research, 2017, PMID: 28465297. For initial microRNA analysis see: Oduor et al. "Human and Epstein-Barr Virus miRNA Profiling as Predictive Biomarkers for Endemic Burkitt Lymphoma." Frontiers in Microbiology 8, 2017, PMID: 28400759. For initial NK subsets RNA expression analysis see: Forconi et al. "A new hope for CD56negCD16pos NK cells as unconventional cytotoxic mediators: an adaptation to chronic diseases." Frontiers in Cellular and Infection Microbiology, 2020, PMID: 32373555.For initial eBL cell line and mouse avatar RNA expression analysis see: Saikumar et al. "Endemic Burkitt lymphoma avatar mouse models for exploring inter-patient tumor variation and testing targeted therapies." Life Science Alliance, 2023, PMID: 36878637. For general overview of cohort study see: Buckle et al. "Factors influencing survival among Kenyan children diagnosed with endemic Burkitt lymphoma between 2003 and 2011: A historical cohort study." Int J Cancer. 15:1231, 2016, PMID: 27136063.

  Study phs001282

• TCR- and BCR-sequencing data for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

  Each tumor sample was cut into three pieces, yielding two end-pieces for cryovials and a middle portion placed in 10% buffered formalin. End pieces were homogenized manually and with a paddle blender (Stomacher). All paraffin-embedded blocks, including formalin-fixed tumor samples and molecular-fixed fallopian tubes, were sectioned and stained with hematoxylin and eosin prior to expert histopathological review to confirm the presence of high grade serous carcinoma. Homogenized end pieces were then flash frozen, and RNA was extracted using the miRNeasy Mini kit. Nanodrop was used to assess quality (260/280) and quantity. Total RNA samples were also QC checked using the Caliper HT RNA HiSens assay. Samples ranging from 60-255ng RNA were re-arrayed into a 96-well plate. 5'-RACE PCR was carried out as described in "The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer" (Zhang et al.). Briefly, this involved first round and nested PCR with TRB (TCR beta chain) and IGH (immunoglobulin heavy chain) gene-specific primers. The indexed libraries were sequenced on the Illumina HiSeq platform with paired-end 250bp reads using v2 chemistry reagents.

  Dataset EGAD00001003985

• Covid19 Transcriptomic Data analysis in Irish Population

  The Samples were collected from Saint James's Hospital, Dublin and after informed consent. RNA-Sequencing library preparation was performed using the Illumina TruSeq Stranded Total RNA Library Prep Globin kit (20020612) with an input amount of 100 – 1000 ng. Library preparation was automated and processed using a Hamilton NGS Star. Library quality was assessed using the Roche KAPA Library Quantification Kit (7960298001) and GX Caliper HS Assay (CLS760672, 760517), run on Roche Lightcycler 480 II and Perkin Elmer LabChip GX Touch analyser respectively. Libraries were pooled and sequenced (75bp PE) on an Illumina NovaSeq 6000 instrument using NovaSeq 6000 S2 Reagent Kit v1.5 (20028314) targeting 50M paired reads. Raw data (BCL format) were demultiplexed and converted to FASTQ format using BCL2FastQ (Illumina). Adapters were trimmed using Skewer (PMID: 24925680) and QC assessed using FASTQC. STAR (PMID: 23104886) was used to align reads to the reference genome (GRCh38/hg38) as well as to the transcriptome (GENCODE v. 25). Quality of the RNA alignment was assessed using Picard QC. Gene and isoform quantification was performed using RSEM (PMID: 21816040). The study shares expression data (gene.results) and chimeric.junction.out.

  Study EGAS00001007116

• Long-read single-cell RNA sequencing uncovers cell-type specific transcript regulation in COVID-19

  SARS-CoV-2 infection leads to extensive host transcriptomic changes, but the role of alternative splicing in shaping the immune response remains underexplored. Here, we present the first application of long-read single-cell RNA sequencing on nasopharyngeal swabs from COVID-19 patients and healthy controls to resolve transcript-level changes across cell types. Leveraging the strengths of long-read sequencing, we characterize alterations in both gene and isoform expression within cell populations of the upper respiratory tract—the primary site of SARS-CoV-2 entry. This approach provides new insights into how transcriptional regulation and splicing shape host immune responses to viral infection.

  Study EGAS50000001290

• Sequencing data for oesophageal and related samples - Scott et al (WGS, RNA)

  Data supporting: "Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments" Scott et al. WGS and RNAseq sequencing data Organoid, tumour and normal samples BAM files

  Dataset EGAD00001006738

• Next Generation Sequencing Characterization of Hematopoietic Stem and Progenitors Cells in Human Systemic Lupus Eryhtematosus (2)

  This dataset contains RNA-sequencing of Bone marrow-derived CD34+ cells from Healthy Controls (n=2) and SLE patients (n=10). SLE patients are divided into two categories based on severity: patients with moderate/mild disease (n=4) and patients with severe disease (n=6). Libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Single-end 75-bp mRNA sequencing was performed on Illumina NextSeq 500. The raw fastq files are uploaded.

  Dataset EGAD00001009744

• Single-cell GoT sequencing from CH, MDS and AML patients with CH mutations

  Single-cell targeted amplicon RNA sequencing from CH (n = 3), MDS (n = 6, MDS02 in 2 replicates) and AML (n =1, in 2 replicates) samples with mutations in splicing factors (SF3B1 - n = 8 [2 -CH, 6 MDS], U2AF1 n = 1) or transcription regulators (DNMT3A - CH04). The transcripts are targeted to detect a particular CH mutation in the listed genes. U2AF1 GoT are full-length cDNA, while the rest follow the 10x 3' V3 protocol.

  Dataset EGAD00001011284

• SARS-CoV2 nasal epithelium

  Single cell RNA sequence generated from human primary nasal epithelium differentiated at air-liquid interface. This dataset comprises tissue from two donors, with cultures either unexposed or exposed to SARS-CoV2. Libraries were prepared using the 10X Genomics pipeline as per manufacturer's instructions.

  Dataset EGAD00001008159

• Single-cell atlas of the human healthy airways

  Single cell atlas of human airways from 10 healthy volunteers by 10X Genomics 3’ RNA-seq profiling. 77,969 cells were collected by bronchoscopy at 35 distinct locations, from the nose to the 12th division of the airway tree, either by forceps (46,791 cells), or brush biopsies (31,178 cells).

  Dataset EGAD00001005714

• Evaluation of triple negative breast cancer with heterogeneous immune infiltration

  This dataset contains the raw RNA-seq data (FASTQ files) of the samples used in the study title: "Evaluation of triple negative breast cancer with heterogeneous immune infiltration". The dataset is composed of 3 patients with 6 samples per patient (3 with high TILs and 3 with low TILs).

  Dataset EGAD00001010280

• Human T-bet governs innate and innate-like adaptive IFN-g immunity against mycobacteria.

  We report a patient with mycobacterial disease due to inherited deficiency of the transcription factor T-bet. PBMCs from the patient and his heterozygous father were analyzed with scRNA-seq. these represent 2 single cell RNA samples generated using the 0xGenomics technology and being processed through cell ranger.

  Dataset EGAD00001006623

• RNA-seq dataset of A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories

  Study describing the differentiation trajectory of atypical teratoid rhabdoid tumors (ATRTs) at single-cell level. This study describes how the differentiation trajectory differs per subtype of ATRTs, and how those findings could contribute to develop so-called "maturation therapy" tailored towards ATRTs.

  Dataset EGAD00001015544

• (sn)RNA-seq dataset of Multi-modal analysis of pediatric pilocytic astrocytomas reveals tumor location-associated cellular and transcriptional heterogeneity

  Aim: to comprehensively characterize the cellular and transcriptional landscape of pediatric pilocytic astrocytomas across anatomical tumor locations

  Dataset EGAD00001015705

• RNA-Seq in Patients with Primordial Dwarfism

  Transcriptome studies in patients with rare genetic diseases can potentially aid in the interpretation of likely causal genetic variation through identification of altered transcript abundance and/or structure. RNA-Seq is the most sensitive assay for both investigating transcript structure and abundance The primary aim of this pilot project is to investigate to what degree integrating exome-Seq and RNA-Seq data on the same individual can accelerate the identification of causal alleles for rare genetic diseases. There are two main strands to this: (i) identifying which variants discovered in exome-seq appear to be having a functional impact on transcripts, and (ii) identifying transcript outliers, especially among known causal genes, that may not necessarily have a causal variant identified from exome sequencing. The latter may identify the presence of causal variants that lie far from coding regions (e.g. the formation of cryptic splice sites deep within introns, or loss of long range regulatory elements), which can be confirmed with further targeted genetic assays. Just over 50% of all disease-causing variants recorded in the Human Gene Mutation Database (HGMD) affect transcript structure and abundance (e.g. nonsense SNVs, essential splice site SNVs, frameshifting indels, CNVs). This pilot project will study RNA from lymphoblastoid cell-lines from 12 patients with primordial dwarfism syndromes, for 10 of these samples we have previously generate exome data as part of our collaboration with the group of Prof Andrew Jackson. The two remaining samples are positive controls where the causal mutation is known, and is known to affect transcript structure and/or abundance. Primordial dwarfism is a prime candidate for these RNA-seq studies because all known causal mutations to date have key roles in DNA replication and thus, unsurprisingly, the products of the causal genes are typically ubiquitously expressed. Each RNA will be sequenced, with two technical replicates (independent RT-PCR and libraries) per sample, and each replicate run in 1/2 of a HiSeq lane using 100bp paired reads. Samples preparation was as follows :The cells were grown to confluency, then pellets frozen at -80. RNA samples were prepared using the Qiagen RNeasy kit, then nanodropped and analyzed using the bioanalyzer to determine concentration and purity. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001000640

• Investigating immunopathological signatures associated with COVID-19 severity post Omicron

  The aim of this study was to investigate the type and duration of protective immunity alongside immunopathological signatures associated with COVID-19 severity. RNA sequencing was performed using the Illumina Stranded mRNA Prep Ligation kit to investigate the protein coding transcriptome of PBMC cells. T cell receptor (TCR) repertoire profiling was performed with the TakaraBio SMART-Seq Human TCR (with UMIs) on PBMC cells to investigate the depth and persistence of SARS-CoV-2 targeting TCRs. The cohort (n=20) consisted of 10 non-hospitalised and 10 Hospitalised individuals with samples analysed 3 months post positive SARS-CoV-2 PCR.

  Study EGAS50000000926

• Single Cell Sequencing of Medulloblastoma Samples

  This dataset contains the results of sequencing 9 samples (7 human/PDX, 2 cell lines) of medulloblastoma tumours (or 2 Neural Stem Cell lines). The data was collected to characterize the intratumour heterogeneity of chromothripsis in this tumour type. The 7 tumour samples underwent single cell DNA and RNA sequencing using the 10x CNVkit and 10xRNA protocols, and 1 of the tumour samples as well as the Neural Stem Cell lines underwent StrandSeq sequencing. All experiments were sequenced on Illumina sequencers. The provided files are paired-end fastq files from the sequencing experiments.

  Dataset EGAD50000000909

• Raw molecular data for "Subclonal immune evasion in non-small cell lung cancer"

  Whole exome, RNA sequencing and TCR sequencing of organoid samples derived from TRACERx patients. The dataset also includes whole exome sequencing from the tumour samples from which the organoids were generated, as well as whole exome sequencing from PDX derived from said tumours.

  Dataset EGAD00001015537