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• WGS samples for multiple myeloma (hipo-067 and hipo-K08K)

  Four PAIRED WGS samples, tumor and control, were sequenced on a HiSeq X Ten and the library preparation kit used was Illumina TruSeq Nano DNA. The tumor was multiple myeloma from bone marrow.

  Dataset EGAD00001008150

• 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

• 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

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90694B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1222 samples; filetype=bam

  Dataset EGAD00001004743

• 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

• RNAseq of SCCOHT patient tumors

  This data set contains BAM files of the RNAseq analysis for three SCCOHT patient tumors. Total mRNA was isolated from fresh frozen tumor samples. RNA sequencing was performed using Illumina HiSeq 4000, paired end 150 bp.

  Dataset EGAD00001007829

• Merged single-cell RNA-seq data for 22 Hodgkin lymphomas and 5 reactive lymph nodes

  This dataset contains merged data from the 22 Hodgkin lymphoma and 5 reactive lymph node samples, including count data and cell cluster assignments.

  Dataset EGAD00001006221

• Whole-exome sequencing and microRNA profiling predicted relapse risk of stage I lung adenocarcinomas

  This dataset contains BAM files for whole exome-sequencing of stage I lung adenocarcinomas from Asian patients. In total, there are 113 patients and 262 samples, including 113 tumor samples, 113 adjacent normal samples and 36 buffy coat samples.

  Dataset EGAD00001006188

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90554A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 628 samples; filetype=bam

  Dataset EGAD00001004730

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90600C

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 2055 samples; filetype=bam

  Dataset EGAD00001004735

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90706

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 522 samples; filetype=bam

  Dataset EGAD00001004744

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A95732A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 928 samples; filetype=bam

  Dataset EGAD00001004759

• Sequencing data for oesophageal and related samples - Rogerson et al (RNA)

  Data supporting: "Repurposing of KLF5 activates a cell cycle signature during the progression from Barrett’s Oesophagus to Oesophageal Adenocarcinoma." Rogerson et al. RNA-seq data 2 samples

  Dataset EGAD00001005915

• Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation

  As part of the study "Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation" we wanted to identiffy the SNVs that are located in STRC and which ones in STRCP1. For this we applied targeted long-read sequencing.

  Dataset EGAD00001011305

• 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

• FACS-based purification and paired-end RNA sequencing

  We performed a prospective investigation in Sézary syndrome by the application of a standardized multiparameter flow cytometry, FACS-cell sorting, and RNA-sequencing for an in-depth immunophenotypic and transcriptional profiling of Sézary cells.

  Dataset EGAD00001007687

• 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

• 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

• 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

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90685

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 481 samples; filetype=bam

  Dataset EGAD00001004738

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96156B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 375 samples; filetype=bam

  Dataset EGAD00001004766

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96165A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 755 samples; filetype=bam

  Dataset EGAD00001004767

• 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

• sQTL summary statistics

  This dataset contains the sQTL summary statistics (nominal pass, significant sQTLs). sQTL mapping was performed with QTLtools. This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity.

  Dataset EGAD00001005042

• Exome sequencing of control DNA samples from patients with Waldenstrom macroglobulinemia

  DNA extracted from sorted CD3+ cells (16 patients) was used for exome capture with the SureSelect All Exon Kit following the standard protocols. Paired-end sequencing (2 x 100 bp) was performed using HiSeq2000 sequencing instruments.The files are in FASTQ format.

  Dataset EGAD00001005323

• 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

• 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

• CBD-RAW-SC-VDJ-T: 10X Single-Cell VDJ TCR

  Raw Illumina sequencing data. For further information regarding this dataset, please contact Benjamin Fairfax and Rachael Bashford-Rogers at contact@combat.ox.ac.uk.

  Dataset EGAD00001007965

• 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

• CYPTAM - PacBio SMRT sequencing

  Dataset contains CYP2D6 sequencing data of 566 individuals who used tamoxifen as adjuvant breast cancer therapy. Phenotype data consists of the ratio between the metabolites endoxifen and desmethyltamoxifen (Metabolic ratio (MR)) as a proxy for CYP2D6 enzyme activity. Each sample is linked to one bam-file containing the CYP2D6 sequence.

  Dataset EGAD00001005972

• 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

• 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

• 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

• 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

• 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

• 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 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