DAC

DAC: British Columbia Cancer Agency (BCCA), PHSAs Technology Development Office, Data Access Committee

Dac ID Contact Person Email Access Information
EGAC00001000122 Sarah_Jane Lee tdoadmin [at] phsa [dot] ca No additional information is available

This DAC controls 132 datasets:

Dataset ID Description Technology Samples
EGAD00001000692 Files associated with the dataset: HS1626.bam, HS1484.bam, HS1483.bam, HS1482.bam, HS1481.bam, HS1480.bam, HS1479.bam, HS1478.bam, A13805.bam, A13800.bam, A13799.bam, A05253.bam, A05252.bam, A13806.bam Illumina Genome Analyzer,Illumina Genome Analyzer II,Illumina HiSeq 2000 12
EGAD00001000702 Complete set of bam files associated with study EGAS00001000622 190
EGAD00001000794 Small cell carcinoma of the ovary of hypercalcemic type (SCCOHT) is an extremely rare, aggressive cancer affecting children and young women. We identified germline and somatic inactivating mutations in the SWI/SNF chromatin-remodeling gene SMARCA4 in 75% (9/12) of SCCOHT patients in addition to SMARCA4 protein loss in 82% (14/17) of SCCOHT tumors, but in only 0.4% (2/485) of other primary ovarian tumors. These data implicate SMARCA4 in SCCOHT oncogenesis. Illumina HiSeq 2000 11
EGAD00001001417 bam files associated with the study EGAS00001001205 6
EGAD00001001646 Fastq files corresponding to RNA-Seq dataset for PTPN1 project (EGAS00001000554) Illumina Genome Analyzer,Illumina Genome Analyzer II,Illumina HiSeq 2000 10
EGAD00001002896 Amplicon sequencing libraries from the study "Histological Transformation and Progression in Follicular Lymphoma: a Clonal Evolution Study". These are Illumina amplicon deep sequencing libraries (n = 118) to validate somatic predictions made in the whole genome sequencing libraries. Specifically, there are 72 tumor libraries and 46 normal libraries. Some patients may have multiple amplicon libraries sequenced. Illumina HiSeq 2000 118
EGAD00001002897 Whole genome sequencing libraries from the study "Histological Transformation and Progression in Follicular Lymphoma: a Clonal Evolution Study". These are libraries from 41 patients. Specifically: 15 transformed follicular lymphoma (TFL), 6 early progressers (PFL), and 20 non-early progressers (NPFL). For TFL and PFL patients, trios consisting of diagnostic (T1), transformed/progressed (T2) and a matching normal are available (n = 63 libaries in total). For NPFL patients, a tumor-normal pair are available (n = 40 libraries). 103
EGAD00001002898 Oliocapture sequencing libraries from the study "Histological Transformation and Progression in Follicular Lymphoma: a Clonal Evolution Study". These are sequencing libraries from the extension cohort of 277 patients. Specifically, there are 402 tumor libraries and 82 normal libraries. 484
EGAD00001003140 We analyzed the spectrum and clinical significance of MYC and BCL2 mutations in 347 DLBCL cases from population-based cohort of BC, Canada. Illumina MiSeq 347
EGAD00001003148 Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for near-diploid immortalized lymphoblastoid cell line GM18507. NextSeq 500 192
EGAD00001003149 Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for third-passage patient-derived primary triple-negative breast cancer xenograft SA501X3F. Illumina HiSeq 2500 384
EGAD00001003150 Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for fourth-passage patient-derived primary triple-negative breast cancer xenograft SA501X4F. Illumina HiSeq 2500 384
EGAD00001003151 Bulk whole-genome BAM files for 184-hTERT-L2, SA501X3F, and SA501X4F. Illumina HiSeq 2500 3
EGAD00001003152 Microfluidic direct library preparation (DLP) single-cell whole-genome BAM files for near-diploid immortalized breast epithelial cell line 184-hTERT-L2. Illumina HiSeq 2500 192
EGAD00001003265 For CCOC cohorts, OvCaRe cases were reviewed, including frozen material, by at least two expert gynecopathologists prior to inclusion in the sequencing cohort who provided the confirmation on final selected cohort. Frozen H&E from Tokyo were also used for evaluation along with representative H&E photos and review done at the Jikei School of Medicine. All CCOC tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome. Illumina Genome Analyzer II,Illumina HiSeq 2000 70
EGAD00001003266 For ENOC cohorts, OvCaRe cases were reviewed, including frozen material, by at least two expert gynecopathologists prior to inclusion in the sequencing cohort who provided the confirmation on final selected cohort. Frozen H&E from Tokyo were also used for evaluation along with representative H&E photos and review done at the Jikei School of Medicine. For ENOC, DAH985 and DG1288 are recurrent and both were treated with chemotherapy after their first surgery. DAH123 is a untreated sample, metastasis from an primary endometrial tumour. All HGSC, GCT, CCOC and the rest ENOC tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome. Illumina HiSeq 2000 58
EGAD00001003267 For GCT cohorts, OvCaRe cases were reviewed, including frozen material, by at least two expert gynecopathologists prior to inclusion in the sequencing cohort who provided the confirmation on final selected cohort. Frozen H&E from Tokyo were also used for evaluation along with representative H&E photos and review done at the Jikei School of Medicine. All GCT tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome. Illumina HiSeq 2000 20
EGAD00001003268 HGSC cases in the OvCaRe and CRCHUM Tumour Banks were selected according to the following criteria: (i) were administered platinum taxane based therapy; (ii) relapsed within 12 months (365 days) or had at least longer than 4.5 years (1642.5 days) follow-up data; (iii) had at least 50% tumour content by H&E staining and expert pathology review. All cases were re-reviewed by expert pathologists to confirm the diagnosis of HGSC. Germline BRCA1 and BRCA2 was determined for all patients through hereditary cancer screening programs. The design of cases selection as a discovery cohort was engineered to amplify biological differences by selecting cases from the extremes of the outcome distribution. All HGSC tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome. Illumina HiSeq 2000 118
EGAD00001003783 Recent studies using next-generation sequencing strategies have described the landscape of genetic alterations in diffuse large B-cell lymphoma (DLBCL). However, little is known about the clinical relevance of recurrent mutations and copy number alterations and their transcriptional footprints. This study examines the frequency, interaction and clinical impact of recurrent genetic aberrations in DLBCL using high-resolution technologies in a large population-based cohort. Illumina HiSeq 2000,Illumina HiSeq 2500 376
EGAD00001003908 - Six samples from the DEV cell line: 2 controls, 2 transduced with IL4R WT and 2 transduced with IL4R mutant (I242N) - This DEV cell line is not commercially available and was acquired from a colleague in the Netherlands 6
EGAD00001003984 Each tumor sample was cut into three pieces, yielding two end-pieces for cryovials and a middle portion placed in 10% buffered formalin. End pieces were homogenized manually and with a paddle blender (Stomacher). All paraffin-embedded blocks, including formalin-fixed tumor samples and molecular-fixed fallopian tubes, were sectioned and stained with hematoxylin and eosin prior to expert histopathological review to confirm the presence of high grade serous carcinoma. Homogenized end pieces were then flash frozen and later used for WGS. For all tumor and matched normal (peripheral blood) samples, DNA was extracted with the Qiagen AllPrep DNA/RNA kit (tumor samples from patients 25,26,28-32) or the Qiagen Blood and Tissue Extraction Kit (tumor samples from patients 1-4,7,9-17, and all blood samples). For all tumor and normal samples, DNA extraction was followed by library construction and sequencing using Illumina HiSeq2500 whole genome shotgun v4 chemistry with paired-end 125bp reads. Illumina HiSeq 2500 89
EGAD00001003985 Each tumor sample was cut into three pieces, yielding two end-pieces for cryovials and a middle portion placed in 10% buffered formalin. End pieces were homogenized manually and with a paddle blender (Stomacher). All paraffin-embedded blocks, including formalin-fixed tumor samples and molecular-fixed fallopian tubes, were sectioned and stained with hematoxylin and eosin prior to expert histopathological review to confirm the presence of high grade serous carcinoma. Homogenized end pieces were then flash frozen, and RNA was extracted using the miRNeasy Mini kit. Nanodrop was used to assess quality (260/280) and quantity. Total RNA samples were also QC checked using the Caliper HT RNA HiSens assay. Samples ranging from 60-255ng RNA were re-arrayed into a 96-well plate. 5'-RACE PCR was carried out as described in "The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer" (Zhang et al.). Briefly, this involved first round and nested PCR with TRB (TCR beta chain) and IGH (immunoglobulin heavy chain) gene-specific primers. The indexed libraries were sequenced on the Illumina HiSeq platform with paired-end 250bp reads using v2 chemistry reagents. Illumina HiSeq 2500,NextSeq 500 442
EGAD00001003986 A total of 192 positions per patient were deeply sequenced in each corresponding tumor sample (including 4 experimental controls and SNVs predicted to originate at each node of the sample phylogeny, see Zhang et al. for details). Genomic DNA templates were used as starting material to generate PCR products. PCR was set up using Phusion DNA polymerase according to the manufacturer’s specifications. The standard PCR conditions used were an initial denaturation at 98C for 30 seconds, followed by 35 cycles of 98C for 10 seconds, 60C for 15 seconds and 72C for 8 seconds, and a final extension at 72C for 10 minutes. PCR products were cleaned up using PCRClean DX beads. Amplicons were pooled by template for sequencing sample preparation. Sample preparation involved a second round of amplification using Phusion DNA polymerase with 6 PCR cycles, with primers specified in Zhang et al. DNA quality was assessed using the Caliper LabChip GX HighSensitivity Assay and DNA quantity was measured using a Qubit dsDNA HS assay kit on a Qubit fluorometer. The indexed libraries were pooled together and sequenced on the Illumina NextSeq500 platform with paired-end 150bp reads using v2 chemistry reagents. NextSeq 500 180
EGAD00001004142 146 DNA samples obtained from 73 DLBCL patients (matching tumor and normal) were sequenced with PCR free 1.0 genome shotgun sequencing. All files are in bam format. 146
EGAD00001004552 10X genomics chromium single-cell RNA-sequencing of (i) patient derived triple negative breast cancer xenograft (ii) primary tumour and ascites ovarian cancer cell lines at tumour recurrence. NextSeq 550 3
EGAD00001004553 Direct library preparation+ single-cell DNA-sequencing of (i) patient derived triple negative breast cancer xenograft (ii) primary tumour and ascites ovarian cancer cell lines at tumour recurrence. Illumina HiSeq 2500 980
EGAD00001004585 NA Illumina HiSeq 2500,NextSeq 500 40
EGAD00001004719 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1340 samples; filetype=bam Illumina HiSeq 2500 1340
EGAD00001004720 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 2057 samples; filetype=bam Illumina HiSeq 2500 2057
EGAD00001004721 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1970 samples; filetype=bam Illumina HiSeq 2500 1970
EGAD00001004722 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 2091 samples; filetype=bam Illumina HiSeq 2500 2091
EGAD00001004723 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1267 samples; filetype=bam Illumina HiSeq 2500 1267
EGAD00001004724 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 230 samples; filetype=bam Illumina HiSeq 2500 230
EGAD00001004725 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 232 samples; filetype=bam Illumina HiSeq 2500 232
EGAD00001004726 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 239 samples; filetype=bam Illumina HiSeq 2500 239
EGAD00001004727 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 692 samples; filetype=bam Illumina HiSeq 2500 692
EGAD00001004728 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 612 samples; filetype=bam Illumina HiSeq 2500 612
EGAD00001004729 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1700 samples; filetype=bam Illumina HiSeq 2500 1700
EGAD00001004730 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 628 samples; filetype=bam Illumina HiSeq 2500 628
EGAD00001004731 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 596 samples; filetype=bam Illumina HiSeq 2500 596
EGAD00001004732 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1735 samples; filetype=bam Illumina HiSeq 2500 1735
EGAD00001004733 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 585 samples; filetype=bam NextSeq 550 585
EGAD00001004734 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 766 samples; filetype=bam NextSeq 550 766
EGAD00001004735 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 2055 samples; filetype=bam Illumina HiSeq 2500 2055
EGAD00001004736 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 620 samples; filetype=bam Illumina HiSeq 2500 620
EGAD00001004737 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 624 samples; filetype=bam NextSeq 550 624
EGAD00001004738 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 481 samples; filetype=bam NextSeq 550 481
EGAD00001004739 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 378 samples; filetype=bam Illumina HiSeq 2500 378
EGAD00001004740 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 735 samples; filetype=bam Illumina HiSeq 2500 735
EGAD00001004741 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 718 samples; filetype=bam Illumina HiSeq 2500 718
EGAD00001004742 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 493 samples; filetype=bam NextSeq 550 493
EGAD00001004743 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1222 samples; filetype=bam Illumina HiSeq 2500 1222
EGAD00001004744 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 522 samples; filetype=bam Illumina HiSeq 2500 522
EGAD00001004745 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 488 samples; filetype=bam Illumina HiSeq 2500 488
EGAD00001004746 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 509 samples; filetype=bam NextSeq 550 509
EGAD00001004747 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 604 samples; filetype=bam NextSeq 550 604
EGAD00001004748 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 626 samples; filetype=bam NextSeq 550 626
EGAD00001004749 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 635 samples; filetype=bam Illumina HiSeq 2500 635
EGAD00001004750 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1522 samples; filetype=bam HiSeq X Five 1522
EGAD00001004751 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 465 samples; filetype=bam NextSeq 550 465
EGAD00001004752 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 606 samples; filetype=bam Illumina HiSeq 2500 606
EGAD00001004753 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 615 samples; filetype=bam NextSeq 550 615
EGAD00001004754 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 636 samples; filetype=bam NextSeq 550 636
EGAD00001004755 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 968 samples; filetype=bam HiSeq X Five 968
EGAD00001004756 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 480 samples; filetype=bam NextSeq 550 480
EGAD00001004757 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 561 samples; filetype=bam NextSeq 550 561
EGAD00001004758 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 844 samples; filetype=bam HiSeq X Five 844
EGAD00001004759 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 928 samples; filetype=bam HiSeq X Five 928
EGAD00001004760 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 635 samples HiSeq X Five 635
EGAD00001004761 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1072 samples HiSeq X Five 1072
EGAD00001004762 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1436 samples; filetype=bam HiSeq X Five 1436
EGAD00001004763 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 589 samples; filetype=bam HiSeq X Five 589
EGAD00001004764 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 656 samples; filetype=bam HiSeq X Five 656
EGAD00001004765 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 648 samples; filetype=bam HiSeq X Five 648
EGAD00001004766 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 375 samples; filetype=bam HiSeq X Five 375
EGAD00001004767 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 755 samples; filetype=bam HiSeq X Five 755
EGAD00001004768 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 492 samples; filetype=bam HiSeq X Five 492
EGAD00001004769 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 531 samples; filetype=bam HiSeq X Five 531
EGAD00001004770 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1222 samples; filetype=bam HiSeq X Five 1063
EGAD00001004771 Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 522 samples; filetype=bam HiSeq X Five,Illumina HiSeq 2500 742
EGAD00001005141 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005142 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005143 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005144 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005145 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005146 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 24 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005147 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005148 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005149 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005150 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 36 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005151 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 36 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005152 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 24 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005153 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 24 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005154 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005155 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005156 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 24 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005157 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 24 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005158 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005159 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005160 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005161 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005162 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005163 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005164 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005165 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005166 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005167 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005168 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005169 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005170 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005171 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005172 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005173 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005174 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005175 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005176 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005177 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005178 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005179 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005180 Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq Illumina HiSeq 2000 1
EGAD00001005338 Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96146A 1195 samples; filetype=bam HiSeq X Five 3
EGAD00001005340 Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96172B 1694 samples; filetype=bam HiSeq X Five 3
EGAD00001005345 Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96226B 1274 samples; filetype=bam HiSeq X Five 4
EGAD00001005347 Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96193B 2410 samples; filetype=bam HiSeq X Five 3
EGAD00001005348 Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96199A 843 samples; filetype=bam HiSeq X Five 3
EGAD00001005353 Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96199B 1170 samples; filetype=bam HiSeq X Five 3
EGAD00001005354 Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96211C 1397 samples; filetype=bam HiSeq X Five 3
EGAD00001005355 Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96225C 1034 samples; filetype=bam HiSeq X Five 2
EGAD00001005419 Diffuse large B-cell lymphoma (DLBCL) is the most common histologic subtype of non-Hodgkin lymphoma and is notorious for its clinical heterogeneity. Patient outcomes can be predicted by cell-of-origin (COO) classification, demonstrating that the underlying transcriptional signature of malignant B-cells informs biological behavior in the context of standard combination chemotherapy regimens. In the current study, we used mass cytometry (CyTOF) to examine tumor phenotypes at the protein level with single cell resolution in a collection of 27 diagnostic DLBCL biopsy specimens from treatment naïve patients. We found that malignant B-cells from each patient occupied unique regions in 37-dimensional phenotypic space with no apparent clustering of samples into discrete subtypes. Interestingly, variable MHC class II expression was found to be the greatest contributor to phenotypic diversity. Within individual tumors, a subset of cases showed multiple phenotypic subpopulations, and in one case we were able to demonstrate direct correspondence between protein-level phenotypic subsets and DNA mutation-defined subclones. In summary, CyTOF analysis can resolve both inter- and intra-tumoral heterogeneity among primary samples, and reveals that each case of DLBCL is unique and may be comprised of multiple, genetically distinct subclones. 17
EGAD00010000658 DLBCL 148 SNP 6.0 Cohort 1
EGAD00010001515 Nanostring PanCancer immune profiling data for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer Nanostring 120
EGAD00010001542 Expression data for 42 PMBCL patient samples (32 IL4R WT cases and 10 cases with mutations in IL4R) Illumina DASL Assay 42