7188 results for "({!join from=dataset_studies to=id v=$q1}) OR ("transcriptome" OR "RNA-seq" OR "rna sequencing" OR "rna-sequencing")"

in 125.71 milliseconds.

• scRNA-seq for 4 reactive lymph node and 12 high grade B cell lymphoma samples

  Dataset includes count matrices, barcode tsvs, and features tsv for each sample, generated using Cell Ranger.

  Dataset EGAD50000001386

• Observational study on the immune responses acquired by COVID-19 convalescent individuals

  We performed whole exome sequencing and microarray genotyping analysis of rare disease A two patients. .....

  Study JGAS000563

• irCLIP library generated from HEK293 cells overexpressing 3FLAG-RIG-I gain-of-function variant C268F

  irCLIP library generated from HEK293 cells transfected with either RIG-IWT or RIG-IC268F (n=3).

  Dataset EGAD50000002390

• Triple-negative breast cancer - Visium HD data

  Visium HD aligned reads from patient 1D525, BAM file from 10X spaceranger output directory

  Dataset EGAD50000002284

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0183_002A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0183_002A for Diffuse large B-cell lymphoma patient sample TFRI_Pair_9_DLBCL

  Dataset EGAD00001010232

• RNAseq analysis on metastatic Colorectal Cancer xenografts samples

  Bank of metastatic colorectal cancer (mCRC) of Patient Derived Xenografts (PDXs)

  Dataset EGAD00001009171

• Macrophage response in term and preterm infants

  The data set comprises 48 samples from term and preterm infants. Expression profiles were generated using different stimuli (O2 3%, 21%, 65%; LPS stimulation).

  Dataset EGAD00001006885

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0178_002A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0178_002A for Diffuse large B-cell lymphoma patient sample TFRIPAIR8_DLBCL

  Dataset EGAD00001010231

• MTM-HD - skeletal muscle RNAseq

  MTM-HD - skeletal muscle RNAseq. 57 samples from controls, pre-HD and early-HD patients.

  Dataset EGAD00001009106

• 2_RNAseq_fALS_Ctrl

  iPSC-derived motor neurons form familial ALS and Controls. 2 fALS iPSC lines and 3 Ctrl iPSC lines.

  Dataset EGAD00001008425

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0175_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0175_001 for Triple negative breast cancer patient-derived xenograft SA535X6XB03101

  Dataset EGAD00001011224

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0168_002

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0168_002 for Diffuse large B-cell lymphoma patient sample TFRIPAIR3_DLBCL

  Dataset EGAD00001010227

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0171_002A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0171_002A for Diffuse large B-cell lymphoma patient sample TFRI_Pair_6_DLBCL

  Dataset EGAD00001010230

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0170_002A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0170_002A for Diffuse large B-cell lymphoma patient sample TFRIPAIR5_DLBCL

  Dataset EGAD00001010229

• Bulk tumor RNAseq of bladder cancer patients

  RNAseq fastq files from 611 bulk pre-treatment tumors from two indications: metastatic urothelial bladder cancer patients (IMvigor210) and metastatic renal cell carcinoma (IMmotion150)

  Dataset EGAD00001006960

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0150_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0150_002 for Triple negative breast cancer sample SA609X5XB03231

  Dataset EGAD00001011213

• RNAseq from 13 uveal melanoma patients

  RNAseq from 13 uveal melanoma patients

  Dataset EGAD00001007528

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0169_002

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0169_002 for Diffuse large B-cell lymphoma patient sample TFRIPAIR4_DLBCL

  Dataset EGAD00001010228

• scRNA mCRC PDO

  Chromium 10x scRNA of 6 metastatic colorectal cancer organoids

  Dataset EGAD00001008734

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0167_002

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0167_002 for Diffuse large B-cell lymphoma patient sample TFRIPAIR2_DLBCL

  Dataset EGAD00001010226

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0197_002A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0197_002A for Diffuse large B-cell lymphoma patient sample TFRIPAIR12_DLBCL_rel

  Dataset EGAD00001010235

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0198_002A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0198_002A for Diffuse large B-cell lymphoma patient sample TFRI_Pair_13_DLBCL

  Dataset EGAD00001010236

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0188_002A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0188_002A for Diffuse large B-cell lymphoma patient sample TFRIPAIR11_DLBCL

  Dataset EGAD00001010234

• Illumina_RNA_MET-CELL_Passages

  RNAseq on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample at early/late passages

  Dataset EGAD00001002884

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0079_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0079_001 for Triple negative breast cancer sample SA1035X6XB03216

  Dataset EGAD00001011241

• RNAseq data set of panALL study

  RNAseq data set, panALL study, 16 samples

  Dataset EGAD00001008134

• Analysis of transcriptomic data

  Thirty six samples were sequenced and analysed.

  Dataset EGAD00001008864

• NeurOmics_HD_Biomarker-1_V1

  This data set includes RNAseq data from 136 samples from the TRACK-HD cohort including premanifest, manifest and control subjects. Data can only be used for Huntington's disease related research.

  Dataset EGAD00001002699

• PBMCs of HCC Patients treated with anti-PD1 ICB

  10 samples (one baseline, 9 on-treatment). Fastq files containing 5'GEx data, prepared using 10x Genomics pipeline, sequenced on Illumina HiSeq4000.

  Dataset EGAD00001006645

• Single cell sequencing of newly-diagnosed and recurrent GBM

  Single cell RNA and CITE sequencing of newly-diagnosed and recurrent GBM

  Dataset EGAD00001006778

• The University of Hong Kong Intestinal Metaplasia Organoids Study RNASeq Data

  RNASeq data generated from organoid cultures established from normal gastrointestinal organoids, long-term and paired tumor frozen tissues.

  Dataset EGAD00001015421

• Assessing mitochondrial bioenergetics in coronary artery disease: A translational left ventricular tissue study in humans (The AMBITION study).

  Single nuclei transcriptomic data from the AMBITION study.

  Dataset EGAD00001011078

• Molecular mechanism of Vd2 T cells upon mevalonate metabolism inhibition

  Raw molecular data of Vd2 T cells upon treatment with different stimuli and mevalonate pathway inhibitors.

  Dataset EGAD00001011322

• Effects of busulfan, fludarabine and clofarabine treatment on human small intestinal organoids.

  Instestinal organoids treated with either busulfan, fludarabine or clofarabine for 24h

  Dataset EGAD00001011336

• Single-cell RNA and TCR sequencing of 40 advanced HCC biopsies.

  Single-cell RNA and TCR sequencing of 40 advanced HCC pre-treatment biopsies from 38 patients.

  Dataset EGAD00001011347

• scRNA-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...

  Dataset EGAD00001015545

• Gastric Cancer Organoid Cultures and Tumors RNASeq Data

  RNASeq data generated from organoid cultures established from gastric cancers and normal mucosae, paired tumor frozen tissues, and cultured fibroblast.

  Dataset EGAD00001004302

• Illumina_RNA_T-CELL-XEN

  RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from PDO culture derived from colorectal cancer primary tumor sample

  Dataset EGAD00001002079

• Illumina_RNA_T-XEN-CELL

  RNAseq on Illumina HiSeq2000/2500 of PDO culture derived from Patient-derived xenograft derived from colorectal cancer primary tumor sample

  Dataset EGAD00001002081

• Spatial Maps of Prostate Cancer Transcriptomes

  A total of 14 samples that has been analyzed with the Spatial Transcriptomics method. H&E stain can be sent if requested.

  Dataset EGAD00001004121

• Meso PacBio data

  PacBio data for mesothelioma cell line NCI-H2595.

  Dataset EGAD00001001917

• Rearrangements of Viral and Human Genomes at Human Papillomavirus Integration Events and Their Allele-Specific Impacts on Cancer Genome Regulation

  We discovered genomic and epigenomic dysregulation originating at sites of human papillomavirus (HPV) integration following the Oxford Nanopore long-read analysis of 72 cervical cancer genomes. The integration events had allele-specific effects on the genome, methylome, and transcriptome, which sometimes resulted in the activation of cancer genes. We also examined the 72 samples using Illumina short-read analysis in phs000528.

  Study phs003780

• scMultiome (snRNA + snATAC) data of 26 regionally sampled GBM tissue from 6 patients

  This dataset contains snRNA-seq data of 26 regionally sampled GBM tissue (peritumoral region, tumor edge, and tumor core). Regionally sampled GBM patient tissue was dissociated and nuclei were processed unsorted or by sorting with 7AAD to remove debris and dead cells. Single-nuclei suspension was prepared following the nuclei isolation protocol Single Cell Multiome ATAC + Gene Expression Sequencing protocol using Chromium Nuclei Isolation Kit. Single-nuclei suspension was prepared following the nuclei isolation protocol Single Cell Multiome ATAC + Gene Expression Sequencing protocol using Chromium Nuclei Isolation Kit, nuclei were barcoded and RNA and ATAC libraries were constructed, allowing for simultaneous capture of transcriptome and epigenome from the same cells.

  Dataset EGAD50000001838

• Gene regulation of human stimulated and cultured CD4+ Treg cells

  This dataset maps gene expression regulation in human primary regulatory CD4+ T cells (Tregs) stimulated using PMA and ionomycin or cultured without stimulus for 18 hours. It includes whole genome sequence data for ChM-seq (18 H3K4me3, 20 H3K27ac and 3 inputs), ATAC-seq (42 samples) and whole transcriptome (39 samples). All individuals were genotyped using coreExome Illumina SNP chip array (included in EGAS00001003516).

  Study EGAS00001003515

• WTS data of patients diagnosed with angiosarcoma

  Whole-transcriptome sequencing (WTS) of 6 tumor-normal and 6 tumor-only samples from patients diagnosed with angiosarcoma. Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on HiSeq 2500 and HiSeq 3000 (Illumina) with 2x101 bp and 2x151 bp read length, respectively.

  Dataset EGAD00001005367

• Single-nuclei gene-expression analysis of pheochromocytoma and paraganglioma links tumor subtypes with tumor microenvironment

  This dataset contains raw sequencing reads in FASTQ format from single-nuclei (30 samples) and bulk tissue (40 samples) transcriptome sequencing of pheochromocytoma and paraganglioma tissue specimens. Additionally, data from single-nuclei sequencing of two normal adrenal medulla specimens is included.

  Dataset EGAD00001008403

• Colorectal cancer organoid-stroma biobank cohort

  In colorectal cancers (CRC) the tumor microenvironment plays a key role for prognosis and therapy efficacy. Patient-derived tumor organoids (PDTOs) show enormous potential for preclinical testing, however, purely epithelial cultures features including the ‘consensus molecular subtypes’ (CMS) are largely eradicated. To better reflect the cell type heterogeneity, we established the CRC organoid-stroma biobank of matched PDTOs and cancer-associated fibroblasts (CAFs) from 30 patients. Whole exome sequencing and transcriptome analysis in various in vitro and in vivo contexts was performed to study the influence of the TME on the CRC phenotype.

  Dataset EGAD00001011173

• WTS data of patients diagnosed with NKTL

  Whole-transcriptome sequencing (WTS) of 36 samples from patients diagnosed with NKTL. Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on HiSeq 2500 and HiSeq 3000 (Illumina) with 2x101 bp and 2x151 bp read length, respectively.

  Dataset EGAD00001005230

• Extracellular transcriptome in seminal plasma for non-invasive prostate cancer diagnosis

  A diagnostic non-invasive biomarker test for prostate cancer at an early stage, with high sensitivity and specificity, would improve diagnostic decision making. Extracellular RNAs present in seminal plasma might contain biomarker potential for the accurate detection of clinically significant prostate cancer. So far, the extracellular messenger RNA (mRNA) profile of seminal plasma has not been interrogated for its biomarker potential in the context of prostate cancer. Here, we investigate the mRNA transcriptome in seminal plasma samples obtained from prostate cancer patients (n=25), patients with benign prostate hyperplasia (n=26) and individuals without prostatic disease (n=6). Seminal plasma harbors a complex mRNA repertoire that reflects prostate as its tissue of origin. The endogenous RNA content is higher in the prostate cancer samples compared to the control samples. Prostate cancer antigen 3 (PCA3), a long non-coding RNA with prostate cancer-specific overexpression, and ATP-binding cassette transporter 1 (ABCA1), known to be involved in the prostate cancer pathogenesis, were more abundant in the prostate cancer group. In addition, twelve high confidence fusion transcripts could be detected in prostate cancer samples, including the bona-fide prostate cancer fusion transcript TMPRSS2-ERG. Our findings provide proof-of-principle that the extracellular transcriptome of seminal plasma can reveal information of an underlying prostate cancer.

  Study EGAS00001005277

• Adoptive Cell Therapy of Autologous T cell Receptor-Engineered T Cells Targeting the p53 Neoantigens in Human Solid Tumors

  Adoptive T cell therapy (ACT) using T cell receptor (TCR)-engineered T cells can mediate regression of advanced human cancers. How TCR-transduced T cells change post-ACT in vivo is currently not well understood. We screened 78 patients for TP53 mutations by whole exome sequencing and whole transcriptome sequencing. Of the 78 patient samples, 49 patient samples were previously reported (phs001003) and 2 additional patients were reported in phs002735. In this accession we report the sequencing data of remaining 23 patients and include 6 additional samples from previously published patients. Additionally, we treated a patient with chemo-refractory breast cancer that expressed mutant p53 R175H with autologous T cells transduced with an allogeneic TCR targeting p53 R175H with human leukocyte antigen (HLA) restriction of A*02. The patient had a partial response for 6 months with 55% tumor regression. The T cells from the infusion product and the peripheral blood T cells at 6 weeks post-ACT were analyzed using 10X single cell transcriptome analysis.

  Study phs002928

• Single-Cell Multiomics of the Immune Microenvironment in T-Cell Acute Lymphoblastic Leukemia

  We present single-cell transcriptome and surface protein expression (CITE-seq) data from four healthy donors and fifteen pediatric T cell acute lymphoblastic leukemia (T-ALL) patients at diagnosis and at different treatment timepoints (days 1 – 6 and at time of remission). Mononuclear cells from peripheral blood (PB; longitudinal) or bone marrow (BM; diagnosis only) were isolated and CD45high immune cells and CD45dimCD7+ malignant cells were sorted and subsequently pooled to enrich for immune cells. For comparison,CD45high immune cells from four healthy donors were also sorted. Single-cell sequencing of the transcriptome and surface protein expression (204 antibodies) was performed using the 10x Genomics platform.Multiomics analyses resulted in the identification of a T-ALL subgroup characterized by a remodeled immune microenvironment at initial diagnosis. This immune landscape is dominated by the presence of non-malignant CD4-CD8-TCRab T cells that interact with CXCL16 expressing non-classical monocytes. Leukemia cell intrinsic transcriptional rewiring in these patients is associated with activation of Rap1 signaling.

  Study phs004269

• Non-invasive human skin transcriptome analysis using mRNA in skin surface lipids

  Non-invasive acquisition of mRNA data from the skin can be extremely useful for understanding skin physiology and diseases. Inspired by the holocrine process, in which the sebaceous glands secrete cell contents into the sebum, we focused on the possible presence of mRNAs in skin surface lipids (SSLs). We found that measurable levels of human mRNAs exist in SSLs, where the sebum protects them from degradation by RNases. The AmpliSeq transcriptome analysis was modified to measure SSL-RNA levels, and our results revealed that the SSL-RNAs predominantly comprised mRNAs derived from sebaceous glands, the epidermis, and hair follicles. Analysis of SSL-RNAs non-invasively collected from patients with atopic dermatitis revealed significantly increased expression of inflammation-related genes and decreased expression of terminal-differentiation���related genes, consistent with the results of previous reports. Further, we found that lipid-synthesis���related genes were downregulated in the sebaceous glands of patients with atopic dermatitis. These results indicate that the analysis of SSL-RNAs is a promising strategy to understand the pathophysiology of skin diseases.

  Study JGAS000416

• Non-invasive human skin transcriptome analysis using mRNA in skin surface lipids

  Non-invasive acquisition of mRNA data from the skin can be extremely useful for understanding skin physiology and diseases. Inspired by the holocrine process, in which the sebaceous glands secrete cell contents into the sebum, we focused on the possible presence of mRNAs in skin surface lipids (SSLs). We found that measurable levels of human mRNAs exist in SSLs, where the sebum protects them from degradation by RNases. The AmpliSeq transcriptome analysis was modified to measure SSL-RNA levels, and our results revealed that the SSL-RNAs predominantly comprised mRNAs derived from sebaceous glands, the epidermis, and hair follicles. Analysis of SSL-RNAs non-invasively collected from patients with atopic dermatitis revealed significantly increased expression of inflammation-related genes and decreased expression of terminal-differentiation���related genes, consistent with the results of previous reports. Further, we found that lipid-synthesis���related genes were downregulated in the sebaceous glands of patients with atopic dermatitis. These results indicate that the analysis of SSL-RNAs is a promising strategy to understand the pathophysiology of skin diseases.

  Study JGAS000418

• Non-invasive human skin transcriptome analysis using mRNA in skin surface lipids

  Non-invasive acquisition of mRNA data from the skin can be extremely useful for understanding skin physiology and diseases. Inspired by the holocrine process, in which the sebaceous glands secrete cell contents into the sebum, we focused on the possible presence of mRNAs in skin surface lipids (SSLs). We found that measurable levels of human mRNAs exist in SSLs, where the sebum protects them from degradation by RNases. The AmpliSeq transcriptome analysis was modified to measure SSL-RNA levels, and our results revealed that the SSL-RNAs predominantly comprised mRNAs derived from sebaceous glands, the epidermis, and hair follicles. Analysis of SSL-RNAs non-invasively collected from patients with atopic dermatitis revealed significantly increased expression of inflammation-related genes and decreased expression of terminal-differentiation���related genes, consistent with the results of previous reports. Further, we found that lipid-synthesis���related genes were downregulated in the sebaceous glands of patients with atopic dermatitis. These results indicate that the analysis of SSL-RNAs is a promising strategy to understand the pathophysiology of skin diseases.

  Study JGAS000417

• The T cell receptor repertoire of tumor infiltrating T cells is predictive and prognostic for cancer survival

  Transcriptomic sequencing on pre-immunotherapy melanoma patients.

  Dataset EGAD00001007710

• Long-read mRNA sequencing of retinal organoids

  Long-read (PacBio) sequencing of two retinal organoid samples. One sample was treated with cyclohexamide. Files are ccs BAM format files generated by a Sequel IIe machine.

  Dataset EGAD50000000100

• 16SV4-sequence data

  Raw 16SV4-sequence data from bronchial brushing DNA obtained from healthy volunteers prior to and four weeks after ICS treatment.

  Dataset EGAD50000000527

• COVID-19 progression and convalescence in common variable immunodeficiency patients

  Longitudinal analysis of single-cell RNAseq datasets of PBMCs from COVID-19 CVID patients and controls.

  Study EGAS50000000368

• RNAseq TPM

  RNAseq TPM matrix (transcriptome profiling by high-thoughput sequencing) Matrix (30,727 features by 2,803 samples) of log2-transformed TPM counts from RNAseq data for the four IMvigor trials.

  Dataset EGAD50000001100

• Guardant ctDNA

  This data table represents each patient molecular response based on ctDNA (using Guardant 360) percentage at baseline and cycle 3 day 1

  Dataset EGAD50000001339

• PCNSL single-cell dataset

  This dataset includes 4 samples with scRNA-seq and 3 sample with CITE-seq, scTCR-seq and scBCR-seq.

  Study EGAS50000000474

• Bulk transcriptomics of Human High-Grade-B-Cell-Lymphomas differentiated according to IGH status

  GCB DLBCL MB2 DE and HGBCL-DH-BCL2(-BCL6) cases classified according to IGH status in IGH+ or IGH-undetectable

  Dataset EGAD50000001524

• ST lobular manuscript dataset

  Spatial transcriptomics analysis for 43 breast cancer lobular samples. Note that there are 2 runs per sample Images and read counts will be made availalble on Zenodo upon publication.

  Dataset EGAD50000001467

• NeoPAL study - RNAseq and Targeted DNA sequencing data

  This dataset is composed of 159 RNAseq data (fastq, bam and count tables) and 35 targeted DNAseq data (fastq).

  Dataset EGAD50000001490

• HaJo Cell Line BCRseq Data

  This study includes BCRseq data from the HaJo cell line as well from the corresponding patient and PDX samples.

  Study EGAS50000001434

• RNAseq data of fetal ISCs and iPSCs derived of fetal ISCs

  This dataset includes RNAseq data of the fetal ISCs and iPSCs derived of the fetal ISCs to confirm successful reprogramming

  Dataset EGAD00001008473

• PDX RNA

  RNAseq from PDX tumours under treatment with dpbs or eribulin. Sarcomatous or mixed sarcoma/carcinoma. 6 PDX tumours each with 2 treatments gave 12 pairs of fastq files.

  Dataset EGAD00001009658

• Visium Spatial Transcriptomics

  This dataset contains the Visium Spatial Transcriptomics data from treatment naive melanoma lymph node metastatic samples.

  Dataset EGAD00001010921

• Single-cell RNA and TCR sequencing of PBMC from patients with uveal melanoma

  Single-cell RNA and TCR sequencing of PBMC from patients with uveal melanoma.

  Dataset EGAD00001007913

• Patient TSO500 RNA

  Original patient tumours from which PDX models were derived. TruSight Oncology RNA panel for 2 samples, sequenced over 4 lanes each, gave 8 pairs of fastq files

  Dataset EGAD00001009659

• RNAseq of 25 sarcoma samples

  100 bp paired-end fastq RNAseq files for 25 sarcoma samples. RNAseq data from exon capture library prep.

  Dataset EGAD00001010839

• RNAseq FASTq files from RT4 cells treated with FGFRi Erdafitinib

  RNAseq FASTq files from RT4 cells treated with FGFRi Erdafitinib

  Dataset EGAD00001007999

• in silico drug target prediction for melanoma

  31 samples transcriptomics to simulate the knock-out of all targets of a drug on an objective function such as growth or energy balance.

  Dataset EGAD00001009089

• 10x Genomics Single Cell Gene Expression for SA1096A

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient SA1096

  Dataset EGAD00001009139

• CCMA

  This dataset has the processed WGS data for the cancer models in CCMA.

  Dataset EGAD00001009633

• RNAseq of Degradation of Janus kinases in CRLF2-rearranged acute lymphoblastic leukemia

  RNAseq data set, Degradation of Janus kinases in CRLF2-rearranged acute lymphoblastic leukemia

  Dataset EGAD00001007569

• 5_RNAseq_NOVA1_vs_EGFP_overexpressiong

  3 control iPSC lines differentiated into iPSC-derived motor neurons transduced with either EGFP or NOVA1 lentivirus.

  Dataset EGAD00001008423

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0079_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0079_002 for Triple negative breast cancer patient-derived xenograft SA1035X6XB03211

  Dataset EGAD00001011242

• Single cell sequencing in CNS autoimmune disease

  RNA, T cell receptor and B cell receptor single cell sequencing data generated on T and B cells derived from patients with CNS autoimmune disease

  Dataset EGAD00001006232

• Illumina_RNA_MET-CELL-XEN

  RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from PDO culture derived from colorectal cancer metastasis sample

  Dataset EGAD00001002075

• MGA-NUTM1 fusion in high grade spindle cell sarcoma Data

  There is a total of 4 sample data (2 WGS and 2 RNAseq) belong to 2 patient deposited in this study.

  Dataset EGAD00001004479

• RNAseq of LC2AD with AD80 or DMSO

  RNAseq of LC2AD with AD80 or DMSO Plenker et al., Mechanistic insight into RET kinase inhibitors targeting the DFG-out conformation in RET-rearranged cancer

  Dataset EGAD00001003316

• Discovering the Genetic Basis of Human Neuroblastoma: A Gabriella Miller Kids First Pediatric Research Program (Kids First) Project

  The Gabriella Miller Kids First Pediatric Research Program (Kids First) is a trans-NIH effort initiated in response to the 2014 Gabriella Miller Kids First Research Act and supported by the NIH Common Fund. This program focuses on gene discovery in pediatric cancers and structural birth defects and the development of the Gabriella Miller Kids First Pediatric Data Resource (Kids First Data Resource). All of the WGS and phenotypic data from this study are accessible through dbGaP and kidsfirstdrc.org, where other Kids First datasets can also be accessed. Children with disseminated neuroblastoma have a very high risk of treatment failure and death despite receiving intensified chemotherapy, radiation therapy and immunotherapy. The long-term goal of our research program is to ultimately improve neuroblastoma cure rates by first comprehensively defining the genetic basis of the disease. The central hypothesis to be tested here is that neuroblastoma arises largely due to the epistatic interaction of common and rare heritable DNA variation. Here we will perform a comprehensive whole genome sequencing of 563 quartets of neuroblastoma patient germline and diagnostic tumor DNAs and germline DNAs from both parents. The case series was recently collected through a Children's Oncology Group epidemiology clinical trial and is robustly annotated with complete demographic (age, sex, race, ethnicity), clinical (e.g. age at diagnosis, stage, risk group), epidemiologic (parental dietary and exposure questionnaire) and biological (e.g. tumor MYCN status and multiple other tumor genomic measures) co-variates. Subjects were consented for genetic research and DNA is immediately available for shipment for sequencing. We propose Illumina-based whole genome sequencing in the 593 "trio" germline samples (Aim 1; due to missing parent: 487 full neuroblastoma triads, 106 child-single parent dyads = 1673 whole genome sequences) and matched diagnostic tumor DNA (Aim 2; N=366) at 30x sequencing depth (N=2039 whole genome sequences). Also in Aim 2 we will perform whole exome (100x) and RNA sequencing on the 366 tumor DNA and 228 tumor RNA samples from this cohort. Finally, we propose a pilot study of structural variation using long-range sequencing in 10 non-overlapping tumor samples chosen based on potentially relevant chromosomal alterations discovered with conventional NGS. Thus, a total of 2277 individual samples and 2655 sequences will be generated. We will use our established analytic pipeline that is currently being used to study the germline genomes of all cases sequenced through the NCI supported Therapeutically Applicable Research to Generate Effective Treatments program. We plan a three-stage analytic approach, first focusing on classic de novo and inherited Mendelian damaging alterations. We will next integrate our extensive epigenomic data from human neuroblastoma cell lines and genome-wide association study data (N=5,703 neuroblastoma cases to date) to guide a comprehensive assessment of noncoding variants that influence tumor initiation with a recently established analytic pipeline. Finally, we will utilize the tumor DNA analyses to inform relevance via somatic gain or loss of function effects at the sequence and/or copy number levels. All data generated in this project will be immediately placed into the Genomic Data Commons (GDC) and we will compute within this environment by importing our analytic pipelines into the GDC. These data will be fully integrated into the Kids First Data Resource and freely shared with all academically qualified petitioners. This comprehensive data set derived from a large and richly phenotyped series of neuroblastoma DNA quartets will be integrated with existing germline and/or tumor genomic data from over 6,000 neuroblastoma subjects (but none with matched patient-parent germline sequencing data) to provide an unparalleled opportunity to comprehensively discover the genetic basis of neuroblastoma.

  Study phs001436

• PAK4 inhibition improves PD-1 blockade immunotherapy

  Introduction with rationale and aims for study Immune checkpoint blockade therapies have significantly altered the current landscape of cancer treatment. However, this immunotherapy still fails more often than it succeeds. There are now evidences that the lack of tumour infiltration by immune cells is the main mechanism of primary resistance to PD‐1 blockade therapies for cancer. It has been postulated that cancer cell‐intrinsic mechanisms may actively exclude T cells from tumours, suggesting that the finding of actionable molecules that could be inhibited to increase T cell infiltration may synergize with checkpoint inhibitor immunotherapy. With the idea of finding potential drivers of immune exclusion, we performed RNA sequencing analysis of biopsies from melanoma patients and compared the transcriptomic differences of samples that where infiltrated with those that did not have immune infiltration. Methods RNAseq analysis of gene expressions on biopsies from melanoma patients treated with checkpoint blockade were analysed. We focused on the variable of "infiltration: yes or no,", e.g. tumors that were well infiltrated by immune cells with those that kept immune cells out. Sequencing revealed a list of genes whose expression differed between the infiltrated and noninfiltrated tumors. The kinase PAK4 stood out as a good candidate for inhibition treatment in the future as it was consistently enriched in the samples without immune infiltration. To test whether immunotherapy would work better if we deleted PAK4, we first knocked out PAK4, using CRISPR‐Cas9, in the ‐resistant melanoma cell line, B16. Then they injected the melanoma cells into mice and observed that PAK4 KO tumours now responded to PD‐1 blockade. In order to elucidate whether pharmacological inhibition of PAK4 could recapitulate the results observed in the B16 PAK4 KO tumours, we obtained the PAK4 inhibitor, KPT-9274, from Karyopharm Therapeutics. Indeed, inhibiting PAK4 in combination with anti‐PD‐1 immunotherapy significantly slowed the growth of the B16 melanomas more than either drug alone. Results and Conclusions Transcriptomic analysis of melanoma tumors that were well infiltrated by immune cells with those that kept immune cells out revealed a list of genes whose expression differed between the infiltrated and non-infiltrated tumours. The result suggests that p21 activated kinase 4 (PAK4) is enriched in non-responding tumour biopsies with low T cell and dendritic cell infiltration. In addition, PAK4 decreased WNT activity, a signalling pathway that has previously been involved in immune exclusion. In mouse models, genetic deletion of PAK4 increased T cell infiltration and reversed resistance to PD‐1 blockade in a CD8 T cell-dependent manner. Furthermore, combination of with the PAK4 inhibitor, KPT-9274, improved anti‐tumour responses compared to anti‐PD‐1 alone. Therefore, high PAK4 expression is correlated with low T cell and dendritic cell infiltration and lack of response to PD‐1 blockade, which could be reversed with PAK4 inhibition. The data establish a rationale for targeting this kinase with inhibitors in combination with immune checkpoint inhibitors for patients. Future work and data that we can anticipate for this study Oncogenic signalling pathways and specially the WNT signalling pathway, have been associated with lack of immune infiltration and resistance to PD‐1 blockade therapies. Here, we show that PAK4 overcome resistance to PD‐1 blockade while significantly decreases WNT signalling activity. Therefore, it constitutes the first potential druggable target that is able to reverse oncogenic driven immune cell exclusion. However, the fully mechanism whereby PAK4 sensitizes tumours to immunotherapy remains to be fully elucidated. It is necessary to address whether PAK4 inhibition overcomes resistance through WNT signalling inhibition or if other signalling pathways are involved in the observed phenotype.

  Study phs001919

• Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas

  The mammalian SWI/SNF (mSWI/SNF) family of chromatin remodelers govern cell type-specific chromatin accessibility and gene expression and assemble as three distinct complexes: canonical BAF (cBAF), Polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF). ARID1A and ARID1B are paralog subunits that specifically nucleate the assembly of cBAF complexes and are frequently dual deleted in highly aggressive differentiated endometrial carcinomas (DECs). Here, in cellular models and primary human tumors, we find that ARID1A/B-mediated cBAF loss results in increased ncBAF and PBAF biochemical abundance and function genome-wide to maintain the DEC oncogenic signature. Further, treatment of ARID1A/1B-mutant cell lines and PDX models in vivo with a clinical-grade SMARCA4/2 ATPase inhibitor, FHD-286, markedly attenuates cell proliferation and tumor growth, and synergizes with carboplatin-based chemotherapy. Taken together, these findings reveal the oncogenic contributions of shifted of mSWI/SNF family complex abundance and chromatin-level gene regulatory functions and suggest therapeutic utility of mSWI/SNF complex small molecule inhibitors in dedifferentiated endometrial carcinoma and other cBAF-disrupted cancer types.

  Study EGAS50000001004

• Systematic Growth Factor Profiling Platform for 3D Tumor Models Reveals EstradiolResponsive Cellular Mechanisms of Immunotherapy Resistance

  Epithelial ovarian cancer (EOC) exhibits significant molecular heterogeneity, which is thought to be influenced by the tumor microenvironment (TME). However, the specific factors driving this heterogeneity remain poorly understood. In this study, we integrated growth factoromics and genomic data to identify TME factors contributing to EOC heterogeneity and immunosuppression. Our analysis revealed distinct subgroups of EOC samples with differential responsiveness to specific growth factors, particularly estradiol and R-spondin. Notably, samples with high responsiveness to estradiol and Wnt (C1 cluster) were enriched in the Mesenchymal (MES) molecular subtype, while samples with high responsiveness to R-spondin (C2 cluster) were associated with the Differentiated (DIF) and Immunoreactive (IMR) subtypes. We discovered that the G protein-coupled estrogen receptor (GPER), rather than the classical estrogen receptor alpha (ERα), was the key mediator of estrogen responsiveness and a determinant of molecular subtype classification. Single-cell sequencing analysis identified subsets of estrogen-responsive malignant cell (MAL.PDCD5) and cancer-associated fibroblast (FB.TNFSF10), which were associated with immunosuppressive patterns in the TCGA cohort. Importantly, the interaction between these cell populations significantly increased upon estrogen treatment, suggesting a potential mechanism by which estrogen signaling may contribute to the development of an immunosuppressive TME. Our findings highlight the critical role of estrogen signaling in shaping the molecular heterogeneity and immunosuppressive TME of EOC and provide novel insights into potential therapeutic targets for overcoming immunosuppression in this malignancy.

  Study EGAS50000000422

• BLUEPRINT ChIP-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  ChIP-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  Study EGAS00001000326

• Blina_Tumour_project

  The aim of this study is to reconstruct the embryology of childhood tumours.

  Study EGAS00001006486

• BLUEPRINT Bisulfite-seq (CNAG)

  Bisulfite-Seq

  Study EGAS00001000418

• Transcriptome and Epigenome of TIL Infusion for Cancer Immunotherapy

  Adoptive T cell therapy (ACT) using ex vivo–expanded autologous tumor-infiltrating lymphocytes (TILs) can mediate complete regression of certain human cancers. The impact of TIL phenotypes on clinical success of TIL-ACT is currently unclear. Samples were analyzed from TIL infusion products from metastatic melanoma human patients who responded to TIL-ACT (responders) and patients who did not (non-responders). Single cell transcriptome of TIL infusion products were analyzed for CD8 TIL phenotype and function. In patients with available neoantigen reactive TIL, single cell TCR clonotyping was performed to study anti-tumor TIL states between responders and non-responders. Epigenetic studies on TIL infusion products were performed using ATAC sequencing between paired CD39- C69- and CD39+ CD69+ CD8+ TILs.

  Study phs002436

• Genentech whole genome and transcriptome sequencing of four hepatocellular carcinoma patients

  Hepatitis B virus (HBV) infection is a major risk factor for hepatocellular carcinoma (HCC). In this study we sequenced the whole genome (~80X) and transcriptome of tumor and non-tumor samples from four HCC patients and identified over two hundred HBV integration sites. We found significant clonal expansion of HBV-integrated hepatocytes specifically in the tumor samples. We observed a diverse collection of genomic perturbations near viral integration sites, including gene disruption, viral promoter-driven human transcription, viral-human transcript fusion and DNA copy number alteration. We also sequenced one patient at ultra-high coverage (~240X) to build the most comprehensive HBV-integration landscape yet attempted. Our data suggest that the viral integration significantly expands carcinogenic opportunities in HBV-infected individuals.

  Study phs000384

• Understanding_the_multicellular_dynamics_of_clear_cell_renal_cell_carcinoma___single_cell_RNA_sequencing

  This study will reconstruct the single cellular phylogeny of tumour and immune cells in relation to both genomic, functional, and spatial location. 20 tumours in total will be studied, including non-progressing small renal masses, progressing small renal masses, relatively indolent larger tumours, and high risk tumour with metastatic sampling. We aim to: Generate a focused, comprehensive phylogenetic characterisation of tumour cells Understand the dependencies of the cancer genome, transcriptome, tissue architecture and the single cellular micro-environment Quantify the single cellular composition and functional intra- and inter- tumoural heterogeneity Determine the phylogeny of tumour associated lymphocytes and their relationship to neo-epitopes and the immune microenvironment Investigate the mechanisms by which the tumour-normal interface constrains tumoural growth

  Study EGAS00001003519

• Single-cell transcriptome of T-ALL P1

  In this study, we profiled single-cell transcriptome (10X genomics) of Patient-derived xenografts (PDX) T-ALL replase samples from P1 patient. Primary human T-ALL cells were recovered from cryopreserved bone marrow aspirates of patients enrolled in the ALL-BFM 2009 study. Patient-derived xenografts (PDX) were generated as previously described by intrafemoral injection of 1 Million viable primary ALL cells in NSG mice110 PDX-derived (P1)28 cells were frozen until processing. For scRNA-seq library preparation, cryopreserved cells were thawed rapidly at 37 ℃ and resuspended in 10 ml warm Roswell Park Memorial Institute (RPMI) medium with 100 μg/ml Dnase I. Cells were centrifuged for 5 mins at 300 g, and resuspended in ice-cold phosphate buffered saline (PBS) with 2% foetal bovine serum (FBS) and 5mM EDTA. Cells were stained on ice with anti-murine-CD45-PE (mCD45)(clone 30-F11; BioLegend; 1:20) in the dark for 30 mins. 1:100 DAPI was added and incubated in the dark for 5 mins before sorting. Triple negative cells (DAPI-mCD45-GFP-) were sorted (Fig. S27) using a BD FACSAria™ Fusion Cell Sorter into ice cold 0.03% bovine serum albumin (BSA) in PBS. All isolated cells were immediately used for scRNA-seq libraries, which were generated as per the standard 10x Genomics Chromium 3′ (v.3.1 Chemistry) protocol. Completed libraries were sequenced on a NextSeq5000 sequencer (HIGH-mode, 75 bp paired-end).

  Dataset EGAD00001008325

• Molecular pathways and cellular subsets associated with adverse clinical outcomes in overlapping immune-related myocarditis and myositis

  ScRNA-seq FASTQ files from myocarditis and control cardiac muscle samples; and myositis and control skeletal muscle samples.

  Dataset EGAD50000000488

• T-ALL and Thymus 10x genomics immune profiling

  10x Genomics immune profiling including sequenced libraries of: 5'-end mRNA transcriptomics Beta and alpha chain VDJ transcripts Cell surface expression by 204 DNA barcoded antibodies

  Dataset EGAD50000000533

• scRNA and spatial-seq of human skin wound healing

  Human skin acute wound healing contains 12 samples of scRNA-seq and 16 samples of spatial transcriptomics, Human skin chronic wound data contains 9 samples scRNA-seq.

  Dataset EGAD50000000813

• Tanzania dietary intervention study 2019-2020

  We performed a dietary intervention study comparing western diet, traditional diet and the supplementation of fermented banana beverage in a cohort of 66 individuals (22 in each study arm).

  Dataset EGAD50000000457

• Repertoire sequencies from three different protocols

  This dataset contains sequencing data from Bulk RNAseq, PCR-based RepSeq and SMRT sequencing to compare immunoglobulin repertoire profiling strategies using matched human B-cell samples

  Dataset EGAD50000002217

• Single cell transcriptomes from vascularized human retinal organoids

  Both control and vascularized organoids were processed using the 10x Chromium 3' RNA method. Sequencing reads were aligned with STARsolo.

  Dataset EGAD50000001216

• HCA_Gut_Paediatric_Hirschsprung_s_disease_Teichmann_Spatial_Managed_Access_

  This study involves atlasing the development of the postnatal gut nervous system in order to elucidate the pathogenic mechanisms of Hirschsprung disease.

  Study EGAS00001007152