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• The Transcriptomic Landscape of Oncogenic PI3K Reveals Key Functions in Splicing and Gene Expression Regulation

  This study includes RNA-seq of paired tumor biopsies from PIK3CA-mutated breast cancer patients that underwent treatment with PI3Kα inhibitors.

  Study phs002840

• Targeted sequencing data on sequential liquid biopsy samples from mCRPC patients receiving cabazitaxel

  Sequencing data from mCRPC patients receiving cabazitaxel. Targeted sequencing data of prostate cancer relevant genes using the PCF-SELECT capture panel. cfDNA from baseline, on-treatment and progression samples taken on cabazitaxel were sequenced as well as patient match WBC DNA

  Dataset EGAD50000001840

• LongVar low-coverage data

  This dataset includes sequencing data from participants of the LongVar study. Specifically, it comprises low-coverage whole genome sequencing (WGS) data which was derived from cell-free DNA from blood samples. These data were generated to compare imputation accuracy. 133 individuals agreed to share their data, and are healthy volunteers.

  Dataset EGAD50000001607

• Human embryonic stem cells dopaminergic neurons scRNA-seq

  The dataset includes 2 samples of Single cell RNA-seq (10X Genomics) from Human Embryonic stem cells. 2 samples with 2 replicates of timepoints 17 and 28 of dopaminergic neuron differentiation.

  Dataset EGAD50000001592

• Melanoma transcriptomic data from patients undergoing immunotherapy

  This dataset contains raw RNA sequencing data from melanoma patient tumor samples collected before and during immunotherapy. The data support investigation of treatment-related changes in tumor cell populations. Samples were analyzed as part of a study exploring cellular responses to immune-based therapies.

  Dataset EGAD50000001569

• Single-cell TCR sequencing data of patients with T follicular helper cell lymphomas

  This dataset contains single-cell TCR sequencing data generated by the Cellranger pipeline (v3.1.0, 10X Genomics) from 9 LN and 16 PB samples of 14 patients with T follicular helper cell lymphomas (TFHLs) as well as 7 homeostatic LN (HLN) samples.

  Dataset EGAD50000000403

• Single-cell RNA sequencing data of patients with T follicular helper cell lymphomas

  This dataset contains single-cell count data generated by the Cellranger pipeline (v3.1.0, 10X Genomics) from 9 LN and 16 PB samples of 14 patients with T follicular helper cell lymphomas (TFHLs) as well as 7 homeostatic LN (HLN) samples.

  Dataset EGAD50000000402

• Single-cell BCR sequencing data of patients with T follicular helper cell lymphomas

  This dataset contains single-cell BCR sequencing data generated by the Cellranger pipeline (v3.1.0, 10X Genomics) from 5 LN and 1 PB samples of 5 patients with T follicular helper cell lymphomas (TFHLs) as well as 7 homeostatic LN (HLN) samples.

  Dataset EGAD50000000400

• Illumina Infinium MethylationEPIC Array IDAT files generated from 11 glioma patient samples

  This dataset includes IDAT files from 6 IDH-mutant, 5 IDH-wild-type glioma patient samples of unmatched initial and recurrent timepoints profiled using the Illumina Infinium MethylationEPIC Array.

  Dataset EGAD00010002157

• Non-invasive bladder cancer cfDNA dataset

  The dataset contains 30 primary bladder cancer patients, 28 recurrent bladder cancer patients and 31 hematuria controls. Shallow WGS of cell-free DNA enzymatic methyl sequencing libraries was performed on an Illumina Novaseq S4 PE150bp. Samples are provided as raw reads without any prior processing.

  Dataset EGAD50000001935

• Whole genome sequence data from Illumina HiSeqX instruments

  This dataset includes bam files from 120 samples. These samples were sequenced using 2x150bp reads on an Illumina HiSeqX sequencer and aligned using the Isaac aligner. All samples were processed with TruSeq DNA PCR-free sample preparation.

  Dataset EGAD00001003562

• Genome-wide data of Erasmus Rucphen Family (ERF) Study

  The data consists of 678189 genome-wide polymorphic variants of 3658 individuals from ERF/GRIP region in a variant call format (vcf) file. ERF has been genotyped with different genotyping platform: Illumina 318 k, 350 k, 610 k and Affymetrics 200 k.

  Dataset EGAD00001003571

• Whole Exome Sequencing of a Melanoma Patient with Acquired Resistance to MEK plus CDK4/6 Inhibition

  Longitudinal biopsies from a melanoma patient who initially responded to MEK plus CDK4/6 inhibitor therapy were whole exome sequenced to identify potential resistance mutations. The biopsies included normal tissue, pre-treatment, on-treatment, and several post-resistance timepoints.

  Dataset EGAD00001003989

• ChIPseq of neuroblastoma

  This dataset contains 4 samples (2x input and 2x H3K27ac ChIPseq) in the IC-pPDXC-63 cell line.

  Dataset EGAD00001006557

• BASIS BC WGS Dataset

  We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Dataset EGAD00001001337

• Somatic genetic basis of Wilms’ tumour

  We investigated the somatic genetic basis of Wilms’ tumour and found complex phylogenetic relations between tumours.

  Dataset EGAD00001004774

• 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

• SmartSeq2 index cultures

  SmartSeq2 read out of index cultured cell sorted with the classification and erythroid-myeloid panel developed in main Figure 6.

  Dataset EGAD00001008187

• RNA-Seq of chronic lymphocytic leukemia

  398 runs and 184 samples of CLL paired RNA-Seq. Sequences were prepared with the Illumina TruSeq RNA Kit. Paired sequencing was done on Hiseq2000 or Hiseq2500.

  Dataset EGAD00001009637

• sWGS data of Pap test smears and tumor tissues

  Shallow whole-genome sequencing data divided into three groups: - sWGS data from Pap smears of patients with confirmed high grade serous ovarian cancer - sWGS data from matched tumor tissue (at diagnosis) from the same patients - sWGS data from Pap tests smears of healthy women

  Dataset EGAD00001010141

• WGS

  Purified DNA from PDX samples were subjected to WGS. Libraries were performed using the TruSeq DNA PCR-Free kit (Illumina) starting with 1μg of input DNA and performed following manufacturer's instructions. Libraries were sequenced on a NovaSeq 6000 (2x151 bp) instrument (Illumina). A mean coverage of 30.4x was obtained.

  Dataset EGAD00001010309

• Discovering novel mechanisms of taxane resistance in human breast cancer by whole-exome sequencing

  Taxanes are key drugs in the treatment of breast cancer, but some breast cancers are resistant to taxanes. Obtaining extensive genomic information in a short time has recently become possible. We used whole exome-sequencing (WES) to investigate mechanisms of taxane resistance in human breast cancer. We selected six patients with breast cancer whose tumors responded well to anthracycline treatment but grew rapidly during neoadjuvant taxane-based chemotherapy. We then performed WES of these samples and identified somatic mutations of candidate genes that are thought to affect taxane resistance.

  Study JGAS000370

• WGS minibam files for SJLIFE

  WGS minibam files for SJLIFE

  Dataset EGAD00001003396

• dataset for BGI bladder cancer project

  dataset for BGI bladder cancer project

  Dataset EGAD00001000758

• BLUEPRINT September 2016, ATAC-seq for osteoclast from venous blood, on Genome GRCh38

  ATAC-seq data for 2 sample(s) for osteoclast from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002907

• BLUEPRINT September 2016, ATAC-seq Multiple Myeloma for plasma cell from bone marrow, on Genome GRCh38

  ATAC-seq data for 4 sample(s) Multiple Myeloma for plasma cell from bone marrow, on Genome GRCh38. 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002920

• BLUEPRINT September 2016, ATAC-seq for plasma cell from tonsil, on Genome GRCh38

  ATAC-seq data for 2 sample(s) for plasma cell from tonsil, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002912

• BLUEPRINT September 2016, ATAC-seq for naive B cell from tonsil, on Genome GRCh38

  ATAC-seq data for 3 sample(s) for naive B cell from tonsil, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002903

• DAC for pediatric AML genomic sequences

  DAC for dataset containing matched tumor-healthy genomic sequences from patients with pediatric AML

  Dac EGAC50000000666

• Metastatic_Prostate_Follow_Up_2

  Validation/deeper sequencing for metastatic prostate cancer samples

  Study EGAS00001000756

• Metastatic_Prostate_Follow_Up

  Validation/deeper sequencing for metastatic prostate cancer samples

  Study EGAS00001000730

• Targeted Gene Panel for 171 PTCLs

  Targeted Gene Panel for 171 PTCLs

  Dataset EGAD00001003967

• Screening for human epigenetic variation at CpG islands

  Screening for human epigenetic variation at CpG islands

  Dataset EGAD00001000059

• SNP data for Ovarian cancer PRS

  SNP data for Ovarian cancer PRS (cases)

  Dataset EGAD00001008143

• KiCS WGS data for academic and for-profit use

  Data from samples that are marked for both academic and for-profit use.

  Dataset EGAD00001009699

• BLUEPRINT September 2016, ATAC-seq for monocyte RPMI_LPS_T=4hrs from venous blood, on Genome GRCh38

  ATAC-seq data for 1 sample(s) for monocyte RPMI_LPS_T=4hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002922

• BLUEPRINT September 2016, ATAC-seq for monocyte RPMI_T=24hrs from venous blood, on Genome GRCh38

  ATAC-seq data for 1 sample(s) for monocyte RPMI_T=24hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002921

• BLUEPRINT September 2016, ATAC-seq for monocyte RPMI_T=1hr from venous blood, on Genome GRCh38

  ATAC-seq data for 1 sample(s) for monocyte RPMI_T=1hr from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002919

• BLUEPRINT September 2016, ATAC-seq for germinal center B cell from tonsil, on Genome GRCh38

  ATAC-seq data for 2 sample(s) for germinal center B cell from tonsil, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002917

• BLUEPRINT September 2016, ATAC-seq for monocyte RPMI_T=6days from venous blood, on Genome GRCh38

  ATAC-seq data for 1 sample(s) for monocyte RPMI_T=6days from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002914

• BLUEPRINT September 2016, ATAC-seq for monocyte RPMI_LPS_T=1hr from venous blood, on Genome GRCh38

  ATAC-seq data for 1 sample(s) for monocyte RPMI_LPS_T=1hr from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002913

• BLUEPRINT September 2016, ATAC-seq for germinal center B cell from venous blood, on Genome GRCh38

  ATAC-seq data for 1 sample(s) for germinal center B cell from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002911

• BLUEPRINT September 2016, ATAC-seq for monocyte RPMI_BG_T=4hrs from venous blood, on Genome GRCh38

  ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=4hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002910

• BLUEPRINT September 2016, ATAC-seq for monocyte RPMI_BG_T=24hrs from venous blood, on Genome GRCh38

  ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=24hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002909

• BLUEPRINT September 2016, ATAC-seq for monocyte RPMI_BG_T=1hr from venous blood, on Genome GRCh38

  ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=1hr from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002906

• BLUEPRINT September 2016, ATAC-seq for unswitched memory B cell from venous blood, on Genome GRCh38

  ATAC-seq data for 3 sample(s) for unswitched memory B cell from venous blood, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002905

• BLUEPRINT September 2016, ATAC-seq for monocyte RPMI_BG_T=24hrs_RPMI_T=5days from venous blood, on Genome GRCh38

  ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=24hrs_RPMI_T=5days from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002904

• BLUEPRINT September 2016, ATAC-seq for naive B cell from venous blood, on Genome GRCh38

  ATAC-seq data for 3 sample(s) for naive B cell from venous blood, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002902

• BLUEPRINT September 2016, ATAC-seq for monocyte RPMI_LPS_T=24hrs_RPMI_T=5days from venous blood, on Genome GRCh38

  ATAC-seq data for 2 sample(s) for monocyte RPMI_LPS_T=24hrs_RPMI_T=5days from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002901

• BLUEPRINT September 2016, ATAC-seq for monocyte RPMI_LPS_T=24hrs from venous blood, on Genome GRCh38

  ATAC-seq data for 1 sample(s) for monocyte RPMI_LPS_T=24hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002900