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• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90560B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 766 samples; filetype=bam

  Dataset EGAD00001004734

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90689A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 378 samples; filetype=bam

  Dataset EGAD00001004739

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90648B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 620 samples; filetype=bam

  Dataset EGAD00001004736

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90694A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 493 samples; filetype=bam

  Dataset EGAD00001004742

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A95736A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1072 samples

  Dataset EGAD00001004761

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96171A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 492 samples; filetype=bam

  Dataset EGAD00001004768

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A75616A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 230 samples; filetype=bam

  Dataset EGAD00001004724

• SF4297 snRNA-Seq Primary GBM

  Single Nuclei RNA-Seq Primary High-grade Glioma. Gender male age 39. 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 EGAD00001005415

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90554B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 596 samples; filetype=bam

  Dataset EGAD00001004731

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A75616C

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 239 samples; filetype=bam

  Dataset EGAD00001004726

• SF10022 snRNA-Seq Primary High-grade Glioma

  SF10022 single nuclei RNA-Seq Primary High-grade glioma. gender Male Age 65. 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 EGAD00001005409

• Somatic copy-number alterations in plasma circulating tumor DNA from advanced EGFR-mutated lung adenocarcinoma patients

  This is the raw data obtained from shallow whole-genome sequencing of plasma DNA (plasma-seq) for calling of somatic copy number alterations as well as focal amplifications from patients with lung cancer.

  Dataset EGAD00001007505

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90682

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 624 samples; filetype=bam

  Dataset EGAD00001004737

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90689C

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 718 samples; filetype=bam

  Dataset EGAD00001004741

• Whole-exome sequencing of additional thyroid disease cases (2015-08-05)

  Whole-exome sequencing of a cohort of families (probands and affected/unaffected relatives) suffering from one of two rare thyroid disorders: congenital hypothyroidism (CH) and resistance to thyroid hormone (RTH). This dataset contains all the data available for this study on 2015-08-05.

  Dataset EGAD00001001460

• Vγ9Vδ2-T cells in chronic lymphocytic leukemia patients and healthy controls

  RNA sequencing data from Vγ9Vδ2-T cells from chronic lymphocytic leukemia patients and age-mnatched healthy controls. Matched Vγ9Vδ2-T cell samples before and after expansion with autologous monocyte-derived dendritic cells for each donor are included.

  Dataset EGAD00001004325

• RNA-seq normal adjacent colon NKI-AvL TGO series NGS-ProToCol

  The dataset "RNA-seq normal adjacent colon NKI-AvL TGO series NGS-ProToCol" includes 2 x 18 fastq files from paired-end total RNA sequencing on Illumina HiSeq2500 for 18 snap-frozen normal adjacent colon tissues.

  Dataset EGAD00001004057

• Kidney Single Cell Study (2018-08-20)

  We intend to use single cell transcriptome analysis to explore the heterogenity of different cell types within the kidney. . This dataset contains all the data available for this study on 2018-08-20.

  Dataset EGAD00001004304

• Single-cell Transcriptome for glioblastoma intra-tumoral heterogeneity

  Single-Cell RNA Sequencing of 355 cells isolated from 7 tissue fragments of 3 patients corresponding to locally adjacent tumor, multifocal with recurrence and sections segregated by a marker of tumor cellularity (5-ALA).

  Dataset EGAD00001002249

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90689B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 735 samples; filetype=bam

  Dataset EGAD00001004740

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A95664B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 606 samples; filetype=bam

  Dataset EGAD00001004752

• Exome sequencing in bipolar disorder families

  In the present study two large, multiply affected bipolar disorder families from Cuba were investigated using whole exome sequencing (Illumina HiSeq2500 v4). The variant calling files (VCFs) of 15 individuals provided here were generated using the Varbank exome pipeline from the Cologne Center for Genomics (CCG, https://varbank.ccg.uni-koeln.de).

  Dataset EGAD00001004276

• Colorectal organoids and tumoroids - pulldown (2018-08-13)

  Targeted capture of cancer gene panel bait set in single cell derived organoids from colon tissue and colorectal cancer from 1 patient. . This dataset contains all the data available for this study on 2018-08-13.

  Dataset EGAD00001004292

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A95621B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 488 samples; filetype=bam

  Dataset EGAD00001004745

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A95632D

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 635 samples; filetype=bam

  Dataset EGAD00001004749

• Exome sequencing files for "A single mutant clone populates the pancreatic ductal system to generate coexisting neoplastic lesions"

  Files from whole exome sequencing of eight tumors from eight pancreatic cancer patients along with matched PanIN precursor lesion(s) and a matched normal tissue.

  Dataset EGAD00001004044

• Warm_Autopsy_Single_Cell_X10

  Study of cell lineage and embryogenesis using biopsy samples from sites across the whole body (post mortem). Sample donors are recruited sensitively through the Phoenix study and consent to samples being taken after their death for both the Phoenix study and this WTSI study.

  Dataset EGAD00001003240

• Single-cell RNA sequencing on 12346 single T cells from 14 non-small cell lung cancer (NSCLC) patients

  Deep single-cell RNA sequencing data for 12346 T cells from tumour, adjacent normal tissue and peripheral blood of treatment-naïve NSCLC patients

  Dataset EGAD00001003999

• Low-coverage Whole Genome Sequencing, normal adjacent colon NKI-AvL TGO series NGS-ProToCol

  The dataset "Low-coverage Whole Genome Sequencing, normal adjacent colon NKI-AvL TGO series NGS-ProToCol" includes 18 fastq files from single-end low-coverage WGS on Illumina HiSeq2500 for 18 snap-frozen normal adjacent colon tissues.

  Dataset EGAD00001004094

• Tam-seq of germline samples for HGSOC copy-number signatures study

  This dataset contains targeted amplicon sequencing of Germline DNA extracted from 56 blood samples. They were sequenced on Illumina HiSeq 2500 and aligned to human genome assembly GRCh37 (hg19)to produce 127 bam files (2-3 technical replicates per sample).

  Dataset EGAD00001004172

• Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer

  The dataset for Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer includes 17 bam files from next-generation sequencing on the Illumina HiSeq2500. The biospecimens analyzed include matched tumor pre-treatment, post-progression and normal samples.

  Dataset EGAD00001004336

• Sequencing data for CLL patients

  Single-cell RNA-sequencing and other genome-wide approaches were applied to a cohort of CLL patients receiving Venetoclax treatment to study mechanisms of resistance.

  Study EGAS00001005815

• SNP array data for 140 individuals from 5 populations in Pakistan

  We have genotyped 140 individuals from 5 populations in Pakistan, using the OmniExpressExome-8 array, which includes approximately one million autosomal SNP markers.

  Study EGAS00001002965

• Fecal 16S UC sequencing data

  Fecal 16S-V4 rRNA gene sequence data from NCT02749630 ulcerative colitis patients. Stool samples were collected at screening as well as on days 29, 43, 64, 85, and 134 processed for 16SV4 rRNA gene sequencing

  Dataset EGAD00001008818

• Whole Genome Bisulfite sequencing data for Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

  This dataset contains Whole Genome Bisulfite sequencing data from seven samples (six tumor samples and on tumor derived cell line). Sequencing was performed Illumina HiSeq 2000 machine resulting in 14 FASTQ files.

  Dataset EGAD00001008805

• SNF_CyTOFF_20

  Matrix of normal values from 39 marker CyTOF assay performed on baseline BMMC. FCS files from the CyTOF assay were normalized and concatenated using Fluidigm's CyTOF software and then de-multiplexed using Astrolabe Diagnostics, Inc., a commercial, cloud-based platform for single-cell analysis.

  Dataset EGAD00001011146

• Neuroblastoma hybrid capture sequencing panel

  Patient neuroblastoma hybrid capture sequencing panel. 5 samples from 2 donors (BAM files). For each donor, we obtained neuroblastoma tumor samples and neuroblastoma ALKi resistant samples. This dataset was used to study ALKi resistance in neuroblastoma.

  Dataset EGAD00001008343

• Dataset for MCPlus_WGS

  WES/WGS sequencing data of 44 chromothriptic tumor and control runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009277

• Detection of Cancer Mutations by Urine Liquid Biopsy in 12 Bladder Cancer Patients

  Set of FASTQ sequences generated from Urine Liquid Biopsy in 12 Bladder Cancer Patients using the IDT PanCancer Panel, Illumina Nextera Flex for Enrichment libraries (aka DNA Prep libraries) and Illumina NovaSeq 2x150bp sequencing.

  Dataset EGAD00001008429

• Targeted RNA Expression Profiling via scTAMARA-seq

  This dataset comprises targeted single-cell RNA expression profiles derived from the same CD34+ bone marrow sample (patient X.1) used for scTAMARA_DNA. 120 RNA targets were selected using LASSO regression to capture key transcripts predictive of cell state within the hematopoietic compartment.

  Dataset EGAD00001015495

• Enhancer profiling to identify identifies epigenetic markers of endocrine resistance in metastatic castration resistant prostate cancer patients

  ChIP-seq and matched input data of AR, FOXA1 and H3K27ac for mCRPC patient samples taken prior to and after treatment with AR targeted therapy

  Dataset EGAD00001008688

• Dataset for gynecologic_cancer-EXON

  Rare cancer sequencing data of 55 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008877

• Dataset for liposarcoma-EXON

  Rare cancer sequencing data of 29 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008886

• Single-nucleus APP Isoforms in Down Syndrome Brains (long-read)

  16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for APP using custom designed primers.

  Dataset EGAD00001008284

• Single-nucleus SPP1 Isoforms in Down Syndrome Brains (long-read)

  16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for SPP1 using custom designed primers.

  Dataset EGAD00001008285

• Single-nucleus BIN1 Isoforms in Down Syndrome Brains (long-read)

  16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for BIN1 using custom designed primers.

  Dataset EGAD00001008288

• Clinal phenotype dataset

  Clinical data from IMvigor010: Clinical data include race, sex, baseline ecog, tumor stage, node status, prior neoadjuvant, PD-L1 status, number lymph nodes resected, pridis, arm, overall survival and disease free survival for 809 patients across IMvigor010.

  Dataset EGAD00001007576

• Stereotyped subset CLL RNA-seq from 100 patient with CLL

  RNA-sequencing data for 100 stereotypes CLL subset cases. Illumina based short-read sequencing data from a 100 samples from patients with CLL. Oxford Nanopore Technologies long-read sequencing data from 5 samples from patients with CLL.

  Dataset EGAD00001009729

• Bulk RNAseq with monocyte spike-ins

  This dataset contains bulk transcriptomes from the operable cohorts of the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19), used to verify the deconvolution method used for the scRNA-seq dataset.

  Dataset EGAD00001010306

• 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