3883 results for "RNA AND sequencing OR transcriptome"

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• GLASS-NL Transcriptomic data

  This dataset contains RNA-sequencing data of 169 IDH-mutant astrocytoma samples included in the GLASS-NL cohort

  Dataset EGAD50000000408

• ADARIO Dataset

  RNA editing analyses of BRCA-isogenic cell lines and patient-derived xenografts (PDX)

  Dataset EGAD50000000739

• Genomic Analysis of Mucinous Tumours (GAMuT) - RNA

  RNASeq for Genomic Analysis of Mucinous Tumours (GAMuT)

  Dataset EGAD00001005190

• SF4324 Primary Wildtype GBM Female, 57.

  Single Cell RNA-Seq of Primary GBM. Gender Female, Age, 57.

  Dataset EGAD00001006017

• Dataset for RNA sequencing of Glioblastoma samples

  This dataset contains 10x scRNA sequencing of glioblastoma samples. Sequencing was performed on a Illumina HiSeq 4000. The sequencing was always paired.

  Dataset EGAD50000000081

• Alveolar Rhabdomyosarcoma sequencing data

  This dataset comprises DNA sequencing for tumor and matched normal from an Alveolar Rhabdomyosarcoma patient. It also include RNA sequencing data from the tumor sample.

  Dataset EGAD00001006622

• The study on genomic profiling using clinical specimens (tissue, blood, etc.) form patients with lung and thymic tumors

  The objective is to generate a comprehensive immunogenomic profiling in thymoma using RNA sequencing and TCR repertoire analysis and to evaluate the potential of immunotherapy in thymoma from multiple perspectives.

  Study JGAS000552

• Patient-derived organoids cohort raw FASTQ from SGMedical

  Raw FASTQ files for a glioblastoma multiforme organoid study, including exome sequencing and RNA-seq. 29 runs (paired-end), 58 FASTQ.c4gh files (R1/R2). Short-read Illumina; library strategies include exome capture and stranded total RNA-seq (see Experiment records for kit/instrument details). No processed results are included; access is controlled under the selected Policy.

  Dataset EGAD50000001741

• 16SV4 ribosomal RNA gene sequencing data

  16SV4 ribosomal RNA gene sequencing data of GI samples and associated mixed community cultures collected from pediatric patients at risk for IBD.

  Dataset EGAD50000000485

• Single-cell RNA sequencing of 16 NPM1 mutated AML patients

  This dataset contains paired-end fastq files for single-cell RNA-seq of 16 NPM1 mutated AML patients. 19 fastq pairs are included, with two samples split into two lanes and a second (technical) replicate for one patient. Libraries were constructed using 10x Genomics Chromium Next GEM Single cell 3’ v3.1 and sequencing was performed using Illumina NovaSeq6000.

  Dataset EGAD50000000478

• 5' single cell RNA sequencing

  Pared-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics 5' single cell RNA sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina HiSeq 4000 using recommended cycling parameters.

  Dataset EGAD00001007672

• Single Cell RNA sequencing of Organoids from TSC2+/- patient IPSCs in H- and L-medium

  This dataset contains single cell RNA sequencing data from Organoids grown in high nutrient (H) and low nutrient (L) medium. Organoids were grown for 110 days. Organoids were grown from a patient IPS cell line with a heterozygous mutation in TSC2 (Patient 1 TSC2+/- iPSCs) and an isogenic control cell line (TSC2+/+).

  Dataset EGAD00001006332

• RNA-sequencing data of post-mortem brain tissue taken from individuals with SCA3 and controls

  Spinocerebellar ataxia type 3 (SCA3) is the most common autosomal dominant inherited ataxia worldwide, caused by a CAG repeat expansion in the Ataxin-3 gene resulting in a polyglutamine (polyQ)-expansion in the corresponding protein. Here we have RNA-sequencing data from the cerebellum of individuals with SCA3 and matched controls.

  Dataset EGAD00001009317

• RNAseq and T cell receptor (TCR) profiling of PBMC cells 3 months post Omicron exposure

  This dataset contains RNA-seq and T cell receptor (TCR) sequencing files from a cohort (n=20) 3 months post positive PCR for SARS-CoV-2. A total of 10 hospitalised (samples H1-10) and 10 non-hospitalised (samples NH1-10) are contained within this dataset. 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.

  Dataset EGAD50000001356

• Dataset for WGS and RNA samples of acute myeloid leukemia with MNX1 expression

  This dataset contains 10 samples of WGS, ATAC, 4C and RNAseq samples of patients with acute myeloid leukemia. The sequencing was performed on Illumina HiSeq 4000, 2000 and HiSeq X using Illumina TruSeq Nano DNA and Agilent Strand Specific RNA Kits. The sequencing was always paired.

  Dataset EGAD50000001098

• RNA sequencing data of pediatric hyperdiploid acute lymphoblastic leukemia (set 5)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of five hyperdiploid ALL patients (ALLT-502, ALLK-130, ALLK-134, ALLK-137, ALLK-139). Novogene's internal method was used in directional library preparation including rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002592

• RNA-sequencing on thyroid samples from fetuses with Down syndrome and fetuses with no genetic/developmental abnormality

  The current data pertains RNA-sequencing reads obtained from thyroid samples acquired from fetuses with Down syndrome and fetuses with no genetic/developmental abnormality. Total RNA was isolated from left lobe from thyroid samples using a hand-held homogenizer and the Promega ReliaPrep RNA Miniprep System (Thermo Fisher Scientific). RNA yield was determined with the NanoDrop Microvolume Spectrophotometer (Thermo Fisher Scientific). Fragmentation and mRNA library preparation was performed using the Kapa mRNA Hyperprep Kit (Roche, Basel, Switzerland). Libraries were equimolar pooled and quality was checked on a TapeStation system using the DNA1000 ScreenTape (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced with poly(A) selection to sequence all messenger RNA for gene expression analysis on the NovaSeq6000 PE150 (Illumina, San Diego, CA, USA), producing at least 40M 150-bp paired-end reads per library.

  Dataset EGAD50000000387

• Paired RNA-Seq of 32 samples of chemo-naïve and post-chemotherapy PDAC tumors

  Paired RNA-Seq of 32 samples of chemo-naïve and post-chemotherapy PDAC tumors (HIPO_015) to define the molecular and cellular impact of neoadjuvant chemotherapy. Transcriptome analysis combined with high resolution mapping of whole tissue sections identified GATA6 (Classical), KRT17 (Basal-like) and Cytochrome P450 3A (CYP3A) co-expressing cells that were preferentially enriched in post-CTX resected samples. The sequencing was done on HiSeq2000/HiSeq2500 using the Takara_SMARTer_Ultra_Low_Input_RNA_and_NEBNext_ChIP-Seq Kit.

  Dataset EGAD00001010884

• RNAseq of human fetal pancreas development

  The dataset comprises RNA-seq information of 4 subpopulations sorted from human fetal pancreas of 3 different donors. Low input libraries were generated using the Smart-seq2 protocol after Ampure XP cleanup of the total RNA extracted from the sorted cells. Libraries were multiplexed and sequenced paired-end over 2 lanes of HiSeq4000 each. Raw data was aligned to the human genome refernence GRCh37 using STAR v2.5.1b with GENCODE v19 as transcriptome reference, and unaligned reads were folded into the final uploaded bams.

  Dataset EGAD00001004210

• Study of biomarkers implicated in radio-immunotherapy response in metastatic cancer

  RNA sequencing data of tumors from 53 patients with advanced or metastatic cancer

  Dataset EGAD50000001644

• Single cell RNA sequencing of PBMC samples from CRC patients

  This data contains scRNA-seq on 14 PBMC samples from colorectal cancer patients.

  Dataset EGAD50000000841

• Single-nucleus RNA-sequencing of normal adrenal cortex and adrenocortical tumors

  BAM generated using Cell Ranger v3.1.0 and Space Ranger v1.3.1 and anonymized using BAMBoozle

  Dataset EGAD50000000835

• Repeated Sampling experiment

  Repeated Sampling Experiment containing 135 fastq files of RNA sequencing. These represent time series of different organ areas sampled during autopsies.

  Dataset EGAD50000000330

• CLL RNA-seq

  This dataset contains Illumina stranded RNA-seq from of 19 chronic lymphocytic leukemia (CLL) patients with or without mutation in SF3B1, as well as 6 B cell samples from healthy individuals. RNA was extracted from CLL cells.

  Dataset EGAD50000000078

• snRNA splicing signature RNA-Seq

  This dataset has RNA-Seq fastq files which were generated as part of the snRNA splicing signature study. Analysis can be performed to regenerate splicing signatures found for RNU4-2, RNU5B-1 and RNU5A-1 by comparing cases versus controls.

  Dataset EGAD50000001299

• RNA-Seq of acute lymphoblastic leukemia in LLAG-0707 study

  This dataset contains RNA-Seq data of acute lymphoblastic leukemia in LLAG-0707 study. Diagnostic samples of 188 patients were sequenced. Reads were aligned to hg19 genome reference using STAR. Aligned bam files are provided in this dataset.

  Dataset EGAD50000001181

• RNA-seq data for genomic determinants of response and resistance to inotuzumab in B-ALL

  RNA-seq data for 101 samples with B-cell acute lymphoblastic leukemia

  Dataset EGAD50000000095

• RNA-seq dataset for gamma delta (γδ) T-ALL patients

  RNA-seq data for 85 patients with acute lymphoblastic leukemia expressing the gamma delta T cell receptor (γδ T-ALL)

  Dataset EGAD50000000027

• BLUEPRINT release January 2015, RNA-Seq for monocyte

  RNA-Seq data for 8 monocyte sample(s). 8 run(s), 8 experiment(s), 8 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 EGAD00001001191

• RNA-seq

  RNA-seq of primary and metastatic sites from highly clinically annotated HGSC samples. Samples were obtained pre-treatment based on a laparoscopic triage algorithm from patients who underwent R0 tumor debulking, or received neoadjuvant chemotherapy (NACT) with excellent (ER) or poor response(PR).

  Dataset EGAD00001005238

• SF11956 scRNA-Seq GBM IDHR132H Wildtype Male

  SF11956 IDHR132H WT GBM. Male, 63. Single Cell RNA seq from high grade glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005392

• SF11644 scRNA-Seq primary GBM

  SF11644 Primary GBM Gender Male age 57. Single Cell RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005393

• SF11949 scRNA-Seq primary oligodendroglioma G3 IDH1 Mutant Male

  SF11949 Primary oligodendroglioma G3 IDH1 Mutant. Male, 40 Single Cell RNA seq from primary astrocytoma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005397

• SF11979 snRNA-Seq Primary GBM IDHR132H Wildtype Female

  Single Nuclei Primary GBM IDHR132H Wildtype. Female 76. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005430

• Human tumour and matched-normal single-cell RNAseq

  We profiled 16 high-grade gliomas patient tumour samples by single-cell and single-nuclei RNA-seq and 3 normal-matched single-cell RNA-seq using 10X Chromium 3'. The fastq files are provided.

  Dataset EGAD00001006097

• RNA-seq of HCC patients undergoing sorafenib treatment.

  RNA-seq dataset (BAM files) of 28 HCCs and 19 non-tumor livers derived from 8 patients undergoing sorafenib treatment.

  Dataset EGAD00001008204

• Pediatric high grade glioma RNA-Seq

  We performed RNA-Seq in DIPG and hemispheric HGG.

  Dataset EGAD00001008278

• RNA-Seq data on multiple myeloma CD138positive bone marrow plasma cells

  RNA-Seq data on multiple myeloma CD138positive bone marrow plasma cells, 11 samples, sequenced on HiSeq 4000 and HiSeq X-Ten, using mostly the TruSeq stranded mRNA Kit.

  Dataset EGAD00001008619

• RNA-seq for identification of neotranscripts

  This dataset contains RNA-seq data (Fastq files of paired-end data) of 18 patient tumors used for identification of neotranscripts in 18 different types of fusion-driven sarcomas and other cancers as described in Vibert et al., Mol Cell 2022 (PMID: 35550257)

  Dataset EGAD00001008832

• Bulk RNA-Seq Digital Gene Expression Matrix

  Raw read counts and normalized read counts for each gene

  Dataset EGAD50000002489

• README-for-EGAS00001004349-linking-HIPO-K09R-RNA-files

  Dataset EGAD00001006785

• SF10432 Wildtype Primary GBM Female, 50

  Single Cell-RNA Seq of Wildtype Primary GBM for Female, Age 50.

  Dataset EGAD00001006019

• RNAseq data for EGAS00001004572

  Bulk RNA-seq data of tumours in EGAS00001004572.

  Dataset EGAD00001006876

• Impact of Mobile Element Insertions on Human Transcriptome Variation

  Mobile DNA elements are ubiquitous in nearly all species and mobile element insertions can affect nearby gene expression through many mechanisms, from disrupting coding regions to initiating DNA methylation to altering RNA splicing patterns. Thousands of mobile element insertions are still polymorphic in human populations, and these polymorphic mobile element insertions (pMEIs) can contribute to transcriptome and phenotypic variation in humans. We identified and genotyped pMEIs using the whole genome sequencing (WGS) data from the Genotype-Tissue Expression (GTEx) project. We then used the extensive multi-tissue transcriptome data from the GTEx project to systematically assess the effects of pMEIs on human transcriptome variation.

  Study phs002030

• Case-control study with RNA-seq transcriptome between ASD patients and non ASD controls.

  Aim: To elucidate gene expression differences in the cerebellar tissues between ASD and normal control segmented by age. Object: The cerebellar tissues used in our study are from 16 autistic patients and 17 control patients. Method: We investigated the mRNA expression differences using RNA-seq between ASD and controls by age. We further investigated mRNA isoform expressions segmented by age.

  Study JGAS000668

• RNA sequencing data of pediatric T-cell acute lymphoblastic leukemia (set 2)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample and from a relapse sample from tonsil of one T-ALL patient (ALLT-317). Data from the relapse sample from bone marrow of this patient is in set 1 of this submission. TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic and relapse tumor samples were sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002585

• RNA sequencing data of pediatric B-other acute lymphoblastic leukemia (set 1)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of four B-other ALL patients (ALLT-314, ALLT-319, ALLT-327, ALLT-334), and from relapse sample of one B-other ALL patient (ALLT-316) . NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Globin-Zero Gold rRNA Removal Kit (Illumina) was utilized for rRNA removal. The diagnostic and relapse tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002598

• Sequencing data for filanesib-treated hepatoblastoma samples

  This dataset contains RNA sequencing data of two hepatoblastoma PDX cell models. Cells were either treated with KSP inhibitor filanesib or with DMSO (controls).

  Dataset EGAD50000001314

• RNAseq data of brain metastasis samples

  Paired-end RNA sequencing data from 95 brain metastasis samples with different primary origins. Sequencing was performed on the Illumina HiSeq 3000.

  Dataset EGAD50000000799

• Dataset of RNA-sequencing of childhood acute myeloid leukemia

  This dataset includes 139 bam files of mRNA sequencing. All subjects are tumor samples of pediatric acute myeloid leukemia.

  Dataset EGAD00001005078

• RNA sequencing of intestinal metaplasia

  We perform bulk RNA-seq of 10 and single cell RNAseq of 2 intestinal metaplasia samples. We also perform stereoseq spatial transcriptomic analysis of 4 gastric cancer samples. The dataset contain cram files from 10 bulk RNAseq samples, and raw fastq files from 2 single cell RNAseq and 4 stereo-seq samples.

  Dataset EGAD50000002010

• APP p.V742L and control fibroblasts RNA-seq

  This dataset consists of 16 FASTQ file pairs containing 3` RNA-sequencing data of patient-derived fibroblasts and three age- and sex-matched control fibroblast lines (CTR1, CTR2, and CTR3). The patient and CTR1 fibroblast lines have three biological replicates, while CTR2 and CTR3 lines both have one sample. Each sample has two lanes.

  Dataset EGAD50000001825

• MS meninges single nuclei RNA sequencing

  10X 3' (RNA) samples of isolated single nuclei from highly inflamed leptomeninges and adjacent grey matter from 3 MS patients used in the paper.

  Dataset EGAD50000001235

• T-ALL RNA-Seq raw data files

  The data set consists of unprocessed RNA-Seq data from 225 patients diagnosed with T cell acute lymphoblastic leukemia in fastq file format. Samples from bone marrow or peripheral blood were subjected to mRNA library prep using Poly-A selection and sequencing on a NovaSeq 6000 system yielding approximately 30 million reads per sample.

  Dataset EGAD50000000308

• DESIGN II HNSCC RNA-Seq

  RNA-Seq data of 28 HPV-negative HNSCC specimens from patients treated at the Netherlands Cancer Institute (Amsterdam), VU Medical Centre (Amsterdam) or MAASTRO Clinic (Maastricht) in The Netherlands. HNSCC biopsy samples were obtained prior to treatment (chemo-radiotherapy) for the prospective study within the DESIGN project and used for polyA mRNA sequencing.

  Dataset EGAD00001005722

• RNA-seq samples

  Raw FASTQ files obtained by RNA sequencing of tumor samples from patients (age 12-29) with newly diagnosed, recurrent intermediate or high-grade sarcoma.

  Dataset EGAD00001008393

• Single-cell RNA-seq of AML blasts pre and post culture

  This dataset contains 6 Fastq files from 3 samples (pre-culture (n=1), post culture in standard (n=1) or niche-llike (n=1) conditions) from 1 AML patient. They correspond to single-cell RNA sequencing on Illumina plateform of 3 libraries prepared with 10X Genomics gene expression V3.1 chemistry.

  Dataset EGAD00001008772

• scRNA Seq of MCSP+ melanoma DCC and bulkRNA Seq of MelDCC lines

  Single cell RNA Seq of: 193 MCSP+ DCC isolated from SLNs of melanoma patients, 9 MCSP+ cells isolated from LNs of non-melanoma patients, 14 melanocytes from a healthy donor. Bulk RNA Seq of 10 samples from 4 DCC-PDX-derived cell lines. Sequencing on NovaSeq6000. Fastq files.

  Dataset EGAD00001009662

• Sequencing data from the study "Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer"

  This dataset consists of 71 whole-genome samples and 47 RNA-seq samples. All WGS samples are provided in .bam format and RNA-seq samples are provided as .fq.gz (paired-end). Next-generation sequencing data on whole genomes were processed by aligning sequencing reads to a reference genome (NCBI build 37/hg19) using bwa-mem (0.7.13-r1126).

  Dataset EGAD50000001978

• Natural variation of circulating RNAs in human serum

  The Janus Serum Bank (JSB) is a population-based cancer research biobank. This dataset contains small RNA sequencing (RNA-seq) data of 520 JSB samples from cancer-free individuals. Sequencing libraries were indexed and 12 samples were sequenced per lane on a HiSeq 2500 (Illumina) to an average depth of 18 million reads per sample. The dataset files are raw FASTQ files from the sequencing machine (50bp, single-end sequencing)

  Dataset EGAD00001003968

• RNA-sequencing and targeted DNA-sequecing of human thyroid tumors and normal samples

  RNA-sequencing data: 5 normal thyroid tissues, 14 papillary thyroid carcinomas, 2 lymph node metastases, 19 poorly differentiated thyroid carcinomas and 17 anaplastic thyroid carcinomas; Targeted DNA-sequencing of the 165 genes included in the “Solid and Haematological tumors” panel (BRIGHTCore, Brussels, Belgium): 2 normal thyroid tissues, 2 poorly differentiated thyroid carcinomas and 7 anaplastic thyroid carcinomas; 2 FASTQ files for each sample (paired).

  Dataset EGAD00001011678

• MPNST study - scRNA

  10X single nucleus RNA data of one MPNST patient, including one primary and five recurrence regions

  Dataset EGAD50000002565

• PACA-CA RNASeq bam files

  Bam files for PACA-CA RNA Seq analysis, for DCC release 27

  Dataset EGAD00001003945

• Whole exome RNA sequencing of FFPE material from 49 pediatric BCP-LBL patients.

  This study contain the results of whole exome-targeted transcriptome analyses of FFPE material from 49 pediatric B-cell precursor lymphoblastic lymphoma patients. Data are provided as Fastq files.

  Study EGAS50000000289

• FFPE tumor RNA exome capture sequencing

  This dataset includes raw, untrimmed FASTQ files generated from bulk RNA exome capture sequencing of FFPE tumor samples from 268 stage III colorectal cancer patients, prior to receiving adjuvant chemotherapy treatment. RNA libraries were prepared with the Illumina TruSeq RNA Exome kit and sequenced (PE51bp) using an Illumina NovaSeq 6000 with an S4 flow cell. The metadata file "RNAseq_metadata.tsv" contains columns with relevant quality metrics "DV200" and "cDNA_ng_ul" per sample, and a column indicating whether the sample was part of one or more published analyses: Franken et al., Eur. J. Cancer, 2026. PMID: 41650786. DOI: https://doi.org/10.1016/j.ejca.2026.116262 Crnovrsanin et al., XXX, 2026. PMID: XXX. DOI: XXX

  Dataset EGAD50000002440

• RNA sequencing in primary inflammatory (TPP) macrophages following deletion of a disease-associated gene desert at chr21q22, disruption of ETS2, or treatment of ETS2-edited macrophages with a HIF1α stabiliser.

  This dataset comprises raw RNA sequencing data (FASTQs) from primary inflammatory (TPP) macrophages that were unedited (non-targeting control, NTC), edited to delete the disease-associated chr21q22 enhancer region (n=5), or edited to disrupt ETS2 with 1 of 2 independent gRNAs (n=9). We also performed RNA-sequencing in NTC or ETS2-edited TPP macrophages that were treated for 12 hours with vehicle (DMSO) or roxadustat (30 uM, n=3). Macrophages were detached using Accutase and lysed. RNA was extracted from cell lysates using an AllPrep DNA/RNA Mini Kit (Qiagen). Sequencing libraries were prepared from 10ng RNA using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) following the manufacturer’s instructions. The quality and molarity of all libraries was assessed using a BioAnalyzer 2100 and the libraries were sequenced on a NextSeq500. Raw data are provided as 50 bp paired-end Illumina reads.

  Dataset EGAD00001011338

• RNA Editing in breast cancer

  High-throughput sequencing screens suggest that RNA editing, which consists in the substitution of adenosine with inosine by the RNA-specific adenosine deaminase (ADAR) enzyme, occurs at several thousand positions across the human genome. Recent evidences have shown that RNA-editing could promote proliferation and carcinogenesis; however, the general principles of ADAR activity on the transcriptome and how ADAR is controlled in cancers remain to be established. The main aim of this project was to investigate the phenomenon of RNA editing in breast and other cancers. The frequency of A-to-I editing was evaluated in 58 breast cancers equally distributed among the different molecular subtypes and 10 normal breast tissues. The analysis was focused on defining: the relationship between the global amount of editing and ADAR expression; the ability to predict the level of editability of specific sites; the distribution of editing in normal and tumour samples and among different breast cancer subtypes; and the clinical, pathological and genomic factors affecting editing.

  Study EGAS00001000495

• scRNA-seq Next GEM-X Flex

  Single-cell RNA sequencing (scRNA-seq) was generated using the 10x Genomics GEM-X Flex Gene Expression Multiplexed platform

  Dataset EGAD50000001186

• scRNA-seq Next GEM Single Cell 3ʹ

  Single-cell RNA sequencing (scRNA-seq) was generated using the 10x Genomics Chromium Next GEM Single Cell 3ʹ platform

  Dataset EGAD50000001185

• Transcriptomic characterization of the histopathological growth patterns in breast cancer liver metastases

  20 fastq files of RNA-sequencing of the 2 main histopathological grow patterns observed in liver metastases.

  Dataset EGAD50000000331

• Pharmacogenomics of T-ALL

  Whole exome seq (N=21) and RNA-seq (N=36) data of additional T-ALL

  Dataset EGAD00001006434

• Single Nuclei RNA sequencing batch 2

  This dataset includes the 2 extra normal samples adjacent to PTC tumors that were multiplexed and profiled using kits from different batches.

  Dataset EGAD00001011364

• Single nucleus and spatial transcriptomic characterization of prostate cancer versus normal controls

  10x Genomics Visium and Chromium platforms were used for spatial and single-nuclei RNA-sequencing, respectively. Cohort consisted of 8 prostate cancer patients (8 prostate cancer + 8 paired non-malignant control samples, fresh-frozen)

  Study EGAS50000001143

• Morphological and gene expression changes in SCA1 cerebral organoids suggest neurodevelopmental disease characteristics

  Cerebral organoids were generated from controls, individuals with SCA1 and gene-edited SCA1 hiPS cells. At day 31 and day 60, RNA sequencing was performed showing differential of several genes involved in neural development.

  Study EGAS50000001720

• Comparison of the single-cell and single-nucleus hepatic myeloid landscape within decompensated cirrhosis patients

  In-patient comparison of single-cell RNA-sequencing (scRNA-seq) and single-nucleus (snRNA-seq) technologies and accompanying tissue processing protocols on transjugular liver biopsy from decompensated cirrhosis patients (n = 3).

  Study EGAS50000000073

• RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project

  RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project

  Dataset EGAD00001001944

• Single-cell RNA sequencing generated from 11 glioma patient samples

  This dataset includes paired-end fastq files from 6 IDH-mutant, 5 IDH-wild-type glioma patient samples of unmatched initial and recurrent timepoints profiled using single-cell RNA sequencing.

  Dataset EGAD00001007772

• Validated Single-cell RNA sequencing in early breast cancer

  Single-cell RNA and VDJ sequencing of early breast cancer

  Dataset EGAD00001006608

• Transcript read counts derived from RNA sequencing data collected for NABUCCO cohort 1 (NCT03387761)

  Data from NABUCCO cohort 1 (NCT03387761). This dataset includes the Transcript read counts derived from the RNA sequencing data. The samples are pre-treatment (n=18) and post-treatment (n=18), and not all samples are paired. The data processing pipeline can be found on the Methods section from the Nature Medicine paper (https://doi.org/10.1038/s41591-020-1085-z)

  Dataset EGAD00001006854

• Illumina RNA-Seq paired of 10 different tumor samples from the Master program (H021)

  Fastq files of paired RNA-Seq of 10 different tumor samples, for which Nanopore and Illumina sequencing was compared. Illumina sequencing was carried out with HiSeq4000 or HiSeq X-Ten using the Illumina TruSeq stranded mRNA Kit.

  Dataset EGAD00001008971

• 10X single-cell Multiome (RNA+ATAC) and single-cell RNAseq of xenograft-derived HSPC, progenitors and myeloid progeny

  10X genomics chromium single-cell ATAC+RNA (Multiome) was use to prepare single-nucleus RNA- and ATAC-seq libraries for human HSPC sorted from xenografts recovered from inflammatory challenge. 10X genomics 3' kits were used to prepare single-cell RNA-seq libraries for committed progenitors and myeloid cells from the same xenografts. These were sequenced on an Illumina NovaSea 6000 platform; BAM files are provided. Samples from 3 conditions were sequenced for each cell type; 3 chromatin accessibility runs and 9 gene expression runs are provided.

  Dataset EGAD50000002328

• RNA sequencing of Notch inhibitor treated HCC PDX models across timepoints

  To study the effect of Notch inhibition on the transcriptional profiles our PDX models, we generated bulk RNA-seq data for two Notch inhibition sensitive and three Notch inhibition insensitive models across multiple timepoints (8h, 24h, 48h, 7d, 17d) using anti-JAG1, anti-Notch2, anti-Notch1 or anti-gD antibodies. 3-5 samples were collected for each treatment condition, resulting in a total of 96 samples. Isolated RNA was used as input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and sequenced on Illumina HiSeq 2500 (Illumina) to produce FASTQ files.

  Dataset EGAD50000000737

• Study of wound response like states in glioblastoma

  In order to investigate wound reponse-like states in glioblastoma, we carried out experiments on primary tissue as well as organoids. Single cell RNA sequencing was performed on core and periphery of three human glioblastoma. Bulk RNA sequencing was performed on glioblastoma-derived organoids subject to treatment for 72h with plasma, hypoxia, or both, and analyzed at 0, 24, 72, and 144h.

  Study EGAS50000001442

• RNAseq of human intestinal epithelial cell layers cultured in OGM, ENR, and ENRRT

  This dataset contains RNA sequencing data in fastq and bam format from 24 samples of human jejunum organoids grown in 3D configuration or as 2D monolayers on anodisc imaging chambers (AICs) in medium formulations OGM, ENR, and ENRRT. The RNA sequencing samples were sequenced using paired-end sequencing (2x150 bp) on an Illumina NovaSeq 6000 instrument at the SciLifeLab National Genomics Infrastructure (NGI) in Uppsala.

  Dataset EGAD50000001766

• Dataset for WGS and RNA samples of acute myeloid leukemia with MNX1 expression (non-hipo)

  This dataset contains 115 samples of WGS, ATAC, 4C and RNAseq samples of patients with acute myeloid leukemia. The sequencing was performed on Illumina HiSeq 4000, 2000 and HiSeq X using Illumina TruSeq Nano DNA and Agilent Strand Specific RNA Kits. The sequencing was always paired.

  Dataset EGAD50000001097

• Exome and RNA-sequencing data from a relapsed t(1;19) acute lymphoblastic leukemia

  Sequence data is from 4 samples from an adult patient with TCF3-PBX1 t(1;19)-positive acute lymphoblastic leukemia. Exome sequencing was performed on a skin biopsy (normal tissue control) and leukemic bone marrow biopsies taken at diagnosis and at two relapse time points. RNA-sequence data is from leukemic bone marrow from two relapse biopsies.

  Dataset EGAD00001002203

• Time course acetalax bisacodyl treatment

  RNA-Seq raw data of PDX treated with acetalaxor bisacodyl for 4h00 to 24h00.

  Dataset EGAD50000000875

• RNA-sequençing of 21 inflammatory hepatocellular adenomas and 1 non-tumoral sample

  Dataset EGAD00001005284

• RNA-SEQ data from 47 CAF (Cancer Associated Fibroblast) samples sorted from fresh breast cancer

  Dataset EGAD00001003808

• Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas: RNAseq variants

  Variants called from RNA-seq data of meningioma tumors.

  Dataset EGAD00001002649

• Follicular T cell lymphoma

  Paired-end RNA-seq of follicular T cell lymphoma for the discovery of fusion transcripts

  Dataset EGAD00001006379

• Single cell targeted RNA sequencing

  Single cell hybrid-capture targeted sequencing of CD19 CAR T-cell infusion products used for standard of care treatment for relapsed/refractory large B-cell lymphoma.

  Dataset EGAD00001006327

• Single cell sequencing of newly-diagnosed and recurrent GBM

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

  Dataset EGAD00001006778

• Whole transcriptome RNA sequencing on bone marrow and peripheral blood samples from patients with acute myeloid leukemia at diagnosis or relapse.

  One hundred cryopreserved bone marrow and peripheral blood samples from patients with acute myeloid leukemia (AML) with 10-90% blasts were selected from the biobank of the Department of Hematology of Leiden University Medical Center (LUMC). The AML cases cover all subtypes, and specifically include known subtype-defining balanced chromosomal translocations according to the WHO classification. The samples were obtained from 96 patients and include three pairs of de novo and relapsed AML and one pair of de novo and presumed therapy-related AML (tAML). Total RNA was isolated from mononuclear cells without prior enrichment for leukemic blasts. The quality and integrity of total RNA was checked and RNA libraries were prepared using the TruSeq RNA library preparation kit v2 (Illumina, San Diego, CA) in an ISO/IEC 17025-accredited protocol. This workflow started with enrichment of messenger RNA by oligo dT magnetic beads. After fragmentation, cDNA synthesis was performed, followed by adaptor ligation and PCR amplification. Paired-end sequencing with a read length of 126 bp was performed on an Illumina HiSeq 2500 v4 sequencer to at least 12.5 Gbp per sample. Image analysis, base calling, and quality check was performed with Illumina data analysis pipeline RTA v1.18.64 and Bcl2fastq v1.8.4. RNAseq reads are provided in compressed Sanger FASTQ format.

  Dataset EGAD00001004187

• Analysis of lymphocytes specific gene expression pattern by RNA-Seq in patients with IgG4-related disease: Comparison between submandibular glands and peripheral blood

  We compared the gene expression of PanT and CD19+B cells by RNA-Seq between SMGs versus PBMCs in IgG4-RD, or IgG4-RD versus pSS versus HCs in PBMCs.

  Study JGAS000630

• Targeted RNA-Seq

  This dataset contains targeted RNA-Seq generated with the Illumina RNA Pan-Cancer panel. It comprises 2200 cancers from children and adults. The cancers represent a wide range of CNS, solid and haematopoietic tumours. Samples are from pathology specimens including FFPE, fresh frozen, bone marrow aspirate and peripheral blood. Samples were tested in a clinical diagnostic lab to identify relevant SNVs, indels and gene fusions.

  Dataset EGAD50000000980

• RNA-seq dataset

  RNA-seq data from CD20+ sorted cells obtained from peripheral blood and lymph node Follicular Lymphoma patients. These samples were unstimulated after thawing and additionally, peripheral blood samples were stimulated during 7 days in culture as described in Dobaño-López C et al. Stranded RNA-seq libraries were performed using the TruSeq library kit (Illumina, San Diego, CA, USA). Libraries were sequenced on a NextSeq 2000 (Illumina) in a 2x50bp length.

  Dataset EGAD50000000347

• RNA-seq of atypical 3q26 samples

  RNA was isolated using phenol-chloroform extraction followed by DNase digestion or using the Qiagen Allprep DNA/RNA kit and protocol (Qiagen, #80204). cDNA synthesis was done using the SuperScript II Reverse Transcriptase kit (Invitrogen). Quantitative real-time PCR was performed by using primers as described previously13,21 on the 7500 Fast Real-time PCR System (Applied Biosystems). Relative levels of gene expression were calculated using the ΔΔCt method

  Dataset EGAD00001006106

• RNA-Seq of response to Tozinameran vaccination in individuals with KTx/dialysis or healthy controls.

  Low-input RNA-Seq (~200 cells per sample) of CD4+ T cells in patients with kidney transplants, dialysis, or healthy controls after the second dose of Tozinameran COVID-19 vaccine. RNA-Seq was performed using the Smart-Seq v4 ultra-low input protocol. The dataset includes 4 healthy control samples, 3 kidney transplant recipients, and 4 patients undergoing dialysis.

  Dataset EGAD00001007689

• RNA-Seq of Myeloid Cells in Dendritic Cell Therapy Response

  RNA libraries were prepared from 100 ng of total RNA using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, then sequenced (2×150 bp) on the Illumina NextSeq550. Transcript-level quantification was done with kallisto, followed by gene-level summarization (tximport) and differential expression analysis (DESeq2). Quality control included PCA, hierarchical clustering, and deconvolution with CIBERSORTx to exclude non-myeloid genes. Final analyses identified transcriptomic differences among healthy donors and three patient subgroups based on response to dendritic cell therapy.

  Dataset EGAD50000001681