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• Transcriptome data of periadrenal and subcutaneous fat in patients with hyperaldosteronism in comparison to patients with non-functional adenomas

  We analyzed subcutaneous adipose tissue (scAT) and periadrenal adipose tissue (paAT) from patients with Aldosterone-Producing Adenomas (APA) and, as controls, non-functional adrenal adenomas (NFA). RNA sequencing and immunohistochemistry of AT was performed (IHC, only on scAT). IHC markers included adipokines (leptin, adiponectin) and transcription factors (eg, c-jun, CaMKII)

  Dataset EGAD50000001590

• Proteogenomic Landscape of Squamous Cell Lung Cancer

  To provide a detailed analysis on how genomic and transcriptomic alterations related to proteome level changes in squamous cell lung cancer (SCC), we performed an integrated analysis incorporating DNA copy number, somatic mutations, expression RNA-sequencing, and expression proteomics in 108 SCC nested within clinical outcome, tumor pathology, and other clinically relevant data.

  Study phs001781

• SCLC MeDIP

  Mimicry of neuronal features are emerging as malignant regulators of cancer growth and metastasis. Neuroendocrine (NE) cancers and small cell lung cancers (SCLC) in particular have been shown to share expression profiles marking various stages of neuronal differentiation. Here, methylation profile from SCLC patients' tumour and normal tissue has been investigated genome wise.

  Study EGAS50000000506

• WGS of CTCs enriched using high-throughout microfluidic device from entire cancer patient leukopak

  Single-cell low-pass WGS analysis (illumina platform, PE150, 1-2x coverage) was performed on CTCs enriched using high-throughout microfluidic device from entire leukopak from patients with metastatic prostate cancer (GU-1 and GU-2) and metastatic hepatocellular carcinoma (HCC-1 and HCC-2).

  Study EGAS50000000723

• Cachexia - Non-Cachexia Metagenome Analysis

  Cancer cachexia has been linked to gut bacterial alterations, but alterations of gut viruses, mostly bacteriophages, have not yet been explored. We performed shotgun metagenomic sequencing of DNA from stool samples of 78 cachectic and 42 non-cachectic cancer patients. K-mer-based matching to reference databases revealed abundance variations of bacteria and viruses. Beyond bacterial alterations, cachectic patients exhibited significantly lower bacteriophage abundance, predominantly affecting Caudovirales and Siphoviridae species (double-stranded DNA) but also Inoviridae and Microviridae families (single-stranded DNA).

  Study EGAS00001007156

• Genomic Predictors of Response to Immune Checkpoint Therapy

  Immune checkpoint therapies, including monoclonal antibodies to programmed cell death-1 (PD-1) and cytotoxic % lymphocyte associated protein-4 (CTLA-4), yield durable clinical responses across many tumor types, including metastatic melanoma, non-small cell lung cancer (NSCLC), and renal cell carcinoma (RCC). However, predictors of response to these therapies in RCC are still unknown. Genomic characterization of large clinical cohorts of patients treated with anti-CTLA-4 and anti-PD-1 agents in melanoma and NSCLC have suggested that high mutational burden, high neoantigen burden, and high expression of certain genes in pre-treatment tumors may be associated with patient response to these therapies. In this study, we sought to investigate genomic predictors of response to anti-PD1 therapy in metastatic RCC in two independent clinical cohorts using whole exome and whole transcriptome sequencing.

  Study phs001493

• Elucidation of disease state by multi-layered omics analysis

  We performed a comprehensive metagenome-wide association study by utilizing whole-genome shotgun sequencing. We elucidated a gut microbiome???s role in human biology of the Japanese population.

  Study JGAS000205

• BCAC TIIC Data

  Data on spatially-resolved tissue infiltrating immune cells (TIICs) from 17,265 breast cancer patients of European descent, from studies participating in the Breast Cancer Association Consortium, together with linked clinical data.

  Study EGAS50000001477

• Cabozantinib Response in ETV6-NTRK3 G623R Positive Carcinoma HIPO-021

  We report a case of marked response to cabozantinib in a secondary entrectinib-resistant tumor harboring the ETV6-NTRK3 fusion with a G623R solvent-front mutation.

  Study EGAS00001004494

• Mutations of whole genome sequencing in single cells in normal esophageal epithelium

  In order to obtain insight into the mutations in normal esophageal epithelium, we performed whole genome sequencing of 13 single cell-derived colonies isolated from 7 cases.

  Study EGAS00001003281

• TB-DAR Whole Genome Sequencing Study

  116 Whole Genome Sequencing (WGS) samples from the TB-DAR study, which consists of a cohort of adult pulmonary tuberculosis patients recruited in Dar es Salaam, Tanzania.

  Study EGAS00001005850

• BCG-Flu Challenge Study Human RNA-seq

  Whole blood RNA sequencing data generated from human samples collected as part of the BCG-Flu Challenge study. The dataset includes 746 samples. Paired-end sequencing was performed on an Illumina NovaSeq 6000 platform with a 150 bp paired-end configuration. Raw FASTQ files are provided.

  Dataset EGAD50000002407

• 10x single-nucleus RNA-seq of postoperative human FCD II brain tissues

  This dataset contains 10x Genomics single-nucleus RNA sequencing data from postoperative brain tissues of patients with focal cortical dysplasia type II (FCD II). The samples were processed using the Chromium platform.

  Dataset EGAD50000001403

• WES data from primary CRC

  Whole exome sequencing from ffpe samples DNA was extracted from FFPE tissue samples from colorectal cancer biopsies. Exome libraries where prepared using the KAPA Hyper Plus Kit (Roche Diagnostics) followed by target enrichment by hybridisation capture using the Roche Hyper Exome Kit. Sequenced on NovaSeq6000 to generated 2x 151 paired-end reads.

  Dataset EGAD50000000924

• IBS-D RNA-seq raw data

  The data set consists of fastq raw files from RNA-seq of seven mucosal biopsies of the colon from seven patients, among them three patients with irritable bowel syndrome with diarrhea-predominant symptoms. Paired end sequencing on Illumina NovaSeq 6000 was used.

  Dataset EGAD50000000063

• Breast Cancer Sequential Sampling Targeted Capture

  This study aims to target capture sequence regions of interest from DNA derived from breast cancer patients who received neo-adjuvant chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved.

  Dataset EGAD00001000784

• 200PG : WGS Raw Sequence (fastq)

  200PG : WGS Raw Sequence (fastq) : Raw WG sequence data (fastq) in this dataset are from the 124 CPCGene Tumour/Normal Pairs used in the 200PG Study. https://www.ncbi.nlm.nih.gov/pubmed/28068672

  Dataset EGAD00001001094

• AML-PMP miRNA-Seq

  miRNA libraries of the AML-PMP project were sequenced on the Illumina HiSeq 2000 instrument, approximately 16 samples per HiSeq lane, to a median depth of 5.7 million reads per library.

  Dataset EGAD00001009772

• 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

• scATAC-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 EGAD00001015546

• 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

• Transcriptomic subgroups in soft tissue tumors correlate with morphologic subtype, genomic features, and outcome

  We assessed gene expression (GGE) profiles and gene fusions as detected by transcriptome sequencing (RNA-seq) of 704 soft tissue tumors (STT) representing 56 different tumor types. Comparison with follow-up data identified transcriptional subclusters among sarcomas with complex genomes and among adipocytic tumors that correlated with metastasis-free survival and local recurrences, respectively. Thus, RNA-seq analysis of STT provides clinically important information.

  Study EGAS50000001472

• miRNA Profiling of Maternal and Non-Maternal Healthy Adult Blood Plasma Using Small RNA-Sequencing

  We compared several performance characteristics of four miRNA profiling methods: small RNA-sequencing, HTG EdgeSeq, Abcam FirePlex, and NanoString nCounter. We used pools of synthetic miRNAs and extracellular RNA from healthy individuals to assess these characteristics.

  Study phs001892

• Whole exome sequencing and RNA sequencing of patient-derived pancreas neoplasm organoids

  Pancreatic cancers arise from two different precursors; intraductal papillary mucinous neoplasms (IPMN) and pancreatic intraepithelial neoplasm (PanIN), while biological differences in cancers originated from them remain obscure. Here, we analyzed their genomic and transcriptomic landscapes using patient-derived organoids.

  Study JGAS000263

• Whole genome bisulfite sequencing of hepatitis B virus-associated hepatocellular carcinoma tumor and non-cancerous samples

  To understand comprehensive epigenetic alterations in hepatitis B virus-associated HCC, we have conducted a whole genome bisulfite sequencing of 5 tumor samples and 3 non-cancerous samples (3 pairs and 2 tumors).

  Study EGAS00001002230

• Loss of functional mutation in RPL27 and RPS27 identified by whole-exome sequencing in Diamond-Blackfan Anemia

  We performed whole-exome sequencing analysis of 48 patients with no documented mutations/deletions involving known Diamond-Blackfan anemia genes and identified 10 mutations in previous known causative genes and 2 mutations in novel ribosomal genes.

  Study EGAS00001000875

• Whole exome sequencing of Ewing and CIC-DUX4 sarcoma tumoroid models

  Tumoroid models from Ewing sarcoma and CIC-DUX4 sarcoma models were generated from patient tumor biopsies. Tumoroids were established in 3D matrigel domes and then propagated on a matrige layer. Whole exome sequencing was performed with established tumoroid models.

  Study EGAS50000000379

• RNA sequencing of Ewing and CIC-DUX4 sarcoma tumoroid models

  Tumoroid models from Ewing sarcoma and CIC-DUX4 sarcoma models were generated from patient tumor biopsies. Tumoroids were established in 3D matrigel domes and then propagated on a matrige layer. RNA sequencing was performed with established tumoroid models.

  Study EGAS50000000380

• Analyses of transcriptome and epigenome in cardiac fibroblasts

  We report genome-wide bulk RNA- and ATAC-seq analysis of cardiac fibroblasts isolated from two patients. Cells were pre-treated with either KAT5 inhibitor or vehicle, and their fibrotic responses after TGF-β stimulation was measured.

  Study EGAS50000000835

• Clonal evolution and clinical implications of genetic abnormalities in blastic transformation of chronic myeloid leukaemia

  Blast crisis (BC) predicts dismal outcomes in patients with chronic myeloid leukaemia (CML). We comprehensively investigated genetic abnormalities in 136 BC and 148 chronic phase (CP) samples obtained from 216 CML patients using exome and targeted sequencing.

  Study EGAS00001005075

• Single-cell transcriptome of human fetal pancreas and in vitro pancreatic spheroids

  This dataset combines single cell transcriptome data from fetal pancreas at 7-10 wpc, embryonic stem cell-derived pancreas progenitors and spheroids generated from both fetal pancreas and human pluripotent stem cell-derived pancreas progenitors.

  Study EGAS00001005151

• iPSC and iPSC derived pericytes

  Bulk RNA sequencing of iPSCs and iPSC derived pericytes from three cell lines MNZTASi019-A, MNZTASi021-A and MNZTASi022-A. Data includes one iPSC data set per cell line and iPSC derived pericyte differentiations per cell line (3 differentiations from MNZTASi019-A and MNZTASi021-A, 2 from MNZTASi022-A). RNA-seq data was generated using an Illumina Stranded mRNA 150bp paired-end library preparation.

  Dataset EGAD50000000255

• RNA-sequencing data from human FSHD and control skeletal muscle biopsies

  This project includes RNA-sequencing data from human FSHD and control skeletal muscle biopsies. This project includes data from 28 FSHD patients (total 37 samples, including vastus lateralis and tibialis anterior muscles) and 12 control individuals (total 24 samples, including vastus lateralis and tibialis anterior muscles).

  Dataset EGAD00001008337

• Characterization of Leukemic Stem Cells in DNMT3Amut and NPM1mut AMLs

  Using a novel sorting strategy, we performed ultra low input RNAseq from FACS-sorted populations from diagnostic DNMT3Amut and NPM1mut AML patients. Primary samples were retrospectively collected based on their mutational profile. Samples were thawed, stained and FACS sorted using combination of lineage markers, CD34, GPR56 and NKG2DLigands. RNA was extracted and library prepared from 13 samples.

  Dataset EGAD00001009293

• Single-cell RNA-seq of murine splenocytes from Bcl6tg/+ and Cd70-/-; Bcl6tg/+ diffuse large B-cell lymphoma mouse models and Cd70-/- and wild-type controls.

  Study EGAS00001007570

• RNA sequencing of skin tissue and peripheral blood mononuclear cells from patients with atopic dermatitis and healthy controls.

  We performed RNA-sequencing of skin tissue obtained from patients with atopic dermatitis, psoriasis and controls in Japanese population.

  Study JGAS000780

• Metagenomic analysis of vaginal and breast milk microbiomes to study maternal-to-infant microbial transmission and early-life microbiome development.

  Metagenomic Characterization of Vaginal and Breast Milk Microbiomes in Lifelines NEXT to Investigate Maternal-to-Infant Microbial Transmission.

  Study EGAS50000001716

• MPN_TGS2_Follow_up___PT1_Vori_other

  Targetted capture and resequencing of 94 known myeloid genes across MPN trials (PT1 and Voriconazole study) as well as remaining MPN samples. New bait design Jan 2014.

  Study EGAS00001000765

• AT2 COPD Transcriptomics

  We generated transcriptomes of primary human lung AT2 cells isolated from distal parenchyma of ex-smoker controls and COPD patients, with both mild and severe disease.

  Study EGAS00001007387

• ICGC PedBrain DNA methylation sequencing

  DNA methylation profiling of 107 medulloblastoma and 8 control samples by high-coverage whole-genome bisulfite (WBGS) sequencing and Illumina Infinium HumanMethylation450k array.

  Study EGAS00001000561

• Phylogenetic evolution of metastatic melanoma.

  To explore molecular factors associated with evolution and resistance in melanoma evolution, we multi-lesion sequenced primary and metastatic sites collected from autopsy in seven patients.

  Study EGAS00001003582

• UIC HNSCC RNA-Seq and miRNA-Seq Data

  This dataset contains matched RNA-Seq and miRNA-Seq fastq files from 109 match samples of 34 human Papillomavirus-negative Head and Neck cancer patients, including 72 lymph nodes, 29 tumor and 8 normal samples.

  Dataset EGAD00001004489

• ChIP-sequencing

  Raw reads from ChIP- [Anti-Histone H3 (acetyl K27) (Abcam, ab4729)] and input sequencing of EBV transformed lymphoblastoid cells from three carriers of TET2 mutation (Ly9, Ly11 and Ly14) and two wild-type (Ly8 and Ly10) family members using Illumina HiSeq Rapid paired-end 60 bp sequencing.

  Dataset EGAD00001004781

• Synchronous Colorectal Cancer genome sequencing

  Here, we performed a characterisation of 12 tumours and matched normal samples from 3 syCRC patients by whole genome sequencing: Patient A (tumours A1 and A2), Patient B (tumours B1-B5), and Patient C (tumours C1-C5). Somatic SNVs, indels and stuructural variants were called.

  Dataset EGAD00001006131

• scATAC-seq of first and second trimester human gonads - HUGODECA dataset

  Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging. ArrayExpress Accession: E-MTAB-10570

  Dataset EGAD00001009387

• sc-RNA and sc-BCR sequencing of multiple myeloma and precursors

  bam files of sc-RNA and sc-BCR sequencing of multiple myeloma and precursors from 65 samples

  Dataset EGAD00001009648

• bfast CohortD OSPL

  ctDNA sample data (one sample per line) for BFAST Cohort D including sample-level summaries like tumor fraction (cTF).

  Dataset EGAD50000000147

• BLUEPRINT September 2016, RNA-Seq Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38

  RNA-Seq data for 1 sample(s) Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001002954

• BLUEPRINT September 2016, RNA-Seq Acute Myeloid Leukemia from venous blood, on Genome GRCh38

  RNA-Seq data for 1 sample(s) Acute Myeloid Leukemia from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001002958

• BLUEPRINT September 2016, ChIPmentation T-cell Acute Lymphocytic Leukemia from capillary blood, on Genome GRCh38

  ChIPmentation data for 2 sample(s) T-cell Acute Lymphocytic Leukemia from capillary blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002938

• WGS data for medulloblastoma samples (ICGC)

  WGS data of medulloblastoma tumor/control pairs.

  Dataset EGAD00001003127

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0837_SA501X2

  40 samples; filetype=bam

  Dataset EGAD00001004812

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0443_SA501X7A

  48 samples; filetype=bam

  Dataset EGAD00001004813

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0472_SA501X7A

  50 samples; filetype=bam

  Dataset EGAD00001004814

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0582_SA501X10A

  45 samples; filetype=bam

  Dataset EGAD00001004815

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0680_SA501X10A

  61 samples; filetype=bam

  Dataset EGAD00001004816

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0544_SA532X6

  68 samples; filetype=bam

  Dataset EGAD00001004817

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0650_SA532X6

  71 samples; filetype=bam

  Dataset EGAD00001004818

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0738_SA609X6

  48 samples; filetype=bam

  Dataset EGAD00001004819

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0739_SA609X6

  52 samples; filetype=bam

  Dataset EGAD00001004820

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0740_SA609X6

  60 samples; filetype=bam

  Dataset EGAD00001004821

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0741_SA609X6

  55 samples; filetype=bam

  Dataset EGAD00001004822

• McGill EMC Community projects Release 7 for cell line "lung epithelial"

  Complete reference epigenome (as defined by IHEC) of a lung epithelial cell line with non-small Cell Lung Adenocarcinoma

  Dataset EGAD00001007679

• 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

• Bulk RNA-Seq

  Human data for transcriptome (bulk RNA-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells

  Dataset EGAD00001010906

• Bulk ATAC-Seq Illumina NextSeq 500 (10M reads)

  Human data for chromatin accessibility (ATAC-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells

  Dataset EGAD00001010908

• 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

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0145_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0145_001 for Triple negative breast cancer patient-derived xenograft SA1035X7XB03338

  Dataset EGAD00001011244

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0145_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0145_002 for Triple negative breast cancer patient-derived xenograft SA1035X7XB03340

  Dataset EGAD00001011245

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0151_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0151_001 for Triple negative breast cancer patient-derived xenograft SA1035X8XB03425

  Dataset EGAD00001011247

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0175_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0175_002 for Triple negative breast cancer patient-derived xenograft SA1035X8XB03631

  Dataset EGAD00001011249

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0014_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0014_001 for Triple negative breast cancer patient-derived xenograft SA604X6XB01979

  Dataset EGAD00001011251

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0015_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0015_001 for Triple negative breast cancer patient-derived xenograft SA604X6XB01979

  Dataset EGAD00001011252

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0019_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0019_001 for Triple negative breast cancer patient-derived xenograft SA604X7XB02089

  Dataset EGAD00001011253

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0020_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0020_002 for Triple negative breast cancer patient-derived xenograft SA604X8XB02164

  Dataset EGAD00001011254

• 10x Single Cell Gene Expression Library TENX063

  10x Single Cell Gene Expression library TENX063 for Triple negative breast cancer patient-derived xenograft SA609X3XB01584

  Dataset EGAD00001011268

• A108879A

  Whole genome sequencing for single cells for library A108879A 1567 cells; filetype=bam

  Dataset EGAD00001007093

• A95732B

  Whole genome sequencing for single cells for library A95732B 655 samples; filetype=bam

  Dataset EGAD00001008231

• A96228B

  Whole genome sequencing for single cells for library A96228B 1125 samples; filetype=bam

  Dataset EGAD00001008218

• A95707A

  Whole genome sequencing for single cells for library A95707A 1359 samples; filetype=bam

  Dataset EGAD00001008228

• A96145A

  Whole genome sequencing for single cells for library A96145A 642 samples; filetype=bam

  Dataset EGAD00001008232

• A96149A

  Whole genome sequencing for single cells for library A96149A 751 samples; filetype=bam

  Dataset EGAD00001008234

• A96155B

  Whole genome sequencing for single cells for library A96155B 1028 samples; filetype=bam

  Dataset EGAD00001008236

• A96157C

  Whole genome sequencing for single cells for library A96157C 938 samples; filetype=bam

  Dataset EGAD00001008237

• A96165A

  Whole genome sequencing for single cells for library A96165A 779 samples; filetype=bam

  Dataset EGAD00001008239

• A96174B

  Whole genome sequencing for single cells for library A96174B 1447 samples; filetype=bam

  Dataset EGAD00001008242

• A96177B

  Whole genome sequencing for single cells for library A96177B 683 samples; filetype=bam

  Dataset EGAD00001008244

• Genomics of Prostate Cancer

  This dataset includes genomic data from patients with prostate cancer. Specimens include archival active surveillance biopsies, radical prostatectomy specimens selected based on evidence of PD-L1 expression and/or T lymphocyte infiltrates, and rapid autopsy material from patients deceased of prostate cancer. These data include low pass whole genome sequencing and targeted sequencing with matched normal.

  Study phs002398

• EHMT2 alterations cause a Kleefstra-like syndrome

  We report clinical and molecular correlates associated with six de novo EHMT2 variants identified in patients presenting with a Kleefstra syndrome–like phenotype. Transcriptomic profiling of patient-derived fibroblasts and induced pluripotent stem cells (iPSCs) reveals shared gene expression signatures between EHMT2 variant carriers and Kleefstra syndrome, compared with cell lines derived from healthy donors.

  Study EGAS50000001637

• IL1R1+ cancer-associated fibroblasts drive tumor development and immunosuppression in colorectal cancer

  180502: RNA-Sequencing data of cocultured matched CRC patient (P4) derived normal fibroblasts (NFs), cancer associated fibroblasts (CAFs) and tumor spheroids. 200503_coculture: RNA-Sequencing data of cocultured CRC patient derived normal fibroblasts (NFs) or cancer associated fibroblasts (CAFs) (P16, P19, P22, P32, P41, P42) and tumor spheroids (HT29). 200503_il1b: RNA-Sequencing data of IL-1β stimulated fibroblasts (NFs and CAFs) Cole: scRNA-sequencing of matched CRC tumour samples and normal tissue counterparts derived from 3 patients. 220501: RNA-Sequencing of FACS sorted IL1R1 high and IL1R1 low CT5.3 CAFs

  Dataset EGAD00001010322

• Whole genome and transcriptome analysis of anaplastic thyroid carcinoma

  Whole genome and transcriptome analysis of anaplastic thyroid carcinoma

  Study EGAS00001001214

• The ACS study

  Dac EGAC00001002140

• Whole-exome sequencing of MDS and related myeloid neoplasms

  Myelodysplastic syndromes(MDS) and related myeloid neoplasms (myelodysplasia) are heterogenous group of myeloid neoplasms characterized by deregulated blood cell production with evidence of myeloid dysplasia. Previously, frequent mutations in genes on RNA splicing machinery and DNA methylation pathway have been identified. However, comprehensive analysis of genetic alterations have not performed on a large cohort of these diseases. Therefore, in this study, we performed whole-exome sequencing of MDS and related myeloid neoplasms.

  Study JGAS000023

• Identification of mutations and structural rearrangements in plasma DNA form metastatic prostate cancer patients

  In this study we analysed patients with metastatic prostate cancer to scan their tumor genomes noninvasively in plasma DNA. We enriched 1.3 Mbp of seven plasma DNAs (4 CRPC cases: CRPC1-3 and CRPC5; 3 CSPC cases: CSPC1-2 and CSPC4) including exonic sequences of 55 cancer genes and 38 introns of 18 genes, where fusion breakpoints have been described using Sure Select Custom DNA Kit.

  Study EGAS00001000453

• Dataset for hepatopancreaticobiliary_malignancy-RNA

  Rare cancer sequencing data of 119 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008863

• INVADE cohort

  Cohort of bulk RNAseq data from DCIS, invasive and microinvasive breast cancer at diagnosis. This dataset covers 18 DCIS cases, 17 microinvasive and 20 primary invasive breast cancer.

  Study EGAS50000000219

• WES analysis of tumor samples

  Whole exome sequencing was performed on paired tumor (N=8) from ER+ advanced breast cancer, obtained prior to combined CDK4/6i and endocrine therapy and at disease progression.

  Study EGAS50000000430

• snRNA-seq/snATAC-seq multiome of first and second trimester human gonads - HUGODECA dataset

  Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging. ArrayExpress Accession: E-MTAB-11708

  Dataset EGAD00001009388

• CTD-ILD BALF and blood scRNA-seq dataset

  CTD-ILD BALF and blood scRNA-seq dataset consists of single-cell transcriptome data of bronchoalveolar lavage fluid (BALF) and blood derived from 30 connective tissue disease-associated interstitial lung disease (CTD-ILD) and 12 idiopathic interstitial pneumonia (IIP) patients.

  Dataset EGAD00001011334

• GCAT| WGS FASTQ V1

  This dataset include FASTQ files of 808 samples from GCAT cohort. Technology used HiSeq 4000, read length 150 bp, inner mate distance 300 bp. For each sample the paired -ends are generated in separated files. Each FASTQ is splitted in multiple LANEs and grouped by the Multiplex index.

  Dataset EGAD00001008201