Cancer Team Data Access Committee

Contact Information

Dr Charles C Mullighan
charles.mullighan@stjude.org

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This DAC controls 21 datasets

Dataset ID	Description	Technology	Samples
EGAD00001008416	WGS (tumor and germline samples) was performed to identify structural variants in the UBTF/CDX2 subgroup. RNA-seq was performed to detect gene fusion in the UBTF/CDX2 subgroup. HiChIP was performed to investigate 3D chromatin architecture and enhancer landscapes of representative patient samples and cell lines harboring Type I and II FLT3-PAN3 deletions and amplifications.	Illumina HiSeq 3000 Illumina NovaSeq 6000	15
EGAD50000000022	7 Isoform sequencing or Long-read RNAseq mapped bam files. Reads were aligned to HG38 reference using Minimap2.	PacBio RS II	7
EGAD50000000023	19 H3K27ac HICHIP from T-ALL patient samples and one healthy normal control sample. Reads were aligned to HG38 reference.	Illumina NovaSeq 6000	20
EGAD50000000024	19 ATAC-seq from T-ALL patient samples and one healthy normal control sample. Reads were aligned to HG38 reference	Illumina NovaSeq 6000	20
EGAD50000000027	RNA-seq data for 85 patients with acute lymphoblastic leukemia expressing the gamma delta T cell receptor (γδ T-ALL)	Illumina HiSeq 3000	85
EGAD50000000028	Whole genome sequencing data for 61 samples with acute lymphoblastic leukemia expressing the gamma delta T cell receptor (γδ T-ALL) and 29 germline samples	Illumina HiSeq 3000	90
EGAD50000000095	RNA-seq data for 101 samples with B-cell acute lymphoblastic leukemia	Illumina HiSeq 2500	101
EGAD50000000096	Whole genome sequencing data for 45 samples with B-cell acute lymphoblastic leukemia	Illumina HiSeq 2500	45
EGAD50000000097	Whole exome sequencing data for 69 samples with B-cell acute lymphoblastic leukemia	Illumina HiSeq 2500	69
EGAD50000000102	Whole genome sequencing data for 423 samples, including diagnosis and germline, across multiple cancer types for cfDNA cohort	Illumina HiSeq 2500	423
EGAD50000000103	Whole exome sequencing data for 457 samples, including diagnosis and germline sample, across multiple cancer types for cfDNA cohort	Illumina HiSeq 2500	457
EGAD50000000104	Cell free DNA sequencing data for 233 samples across multiple cancer types for cfDNA cohort	Illumina NovaSeq 6000	273
EGAD50000000150	Whole exome sequencing data for 425 samples with B-cell acute lymphoblastic leukemia	Illumina HiSeq 2500	425
EGAD50000000151	RNA-seq data for 14 samples with B-cell acute lymphoblastic leukemia	Illumina HiSeq 2500	14
EGAD50000000666	Cell free DNA sequencing data for 13samples with whole genome sequencing across multiple cancer types for cfDNA cohort	Illumina NovaSeq 6000	13
EGAD50000000667	Cell free DNA sequencing data for 9 samples with expanded panel across multiple cancer types for cfDNA cohort	Illumina NovaSeq 6000	9
EGAD50000001346	This dataset includes single cell (sc)RNA-seq of N=13 AML patients. The dataset includes bam files that have been purged of reads mapping to cells where a majority of the reads from that cell mapped to the human genome. All scRNA-seq data were generated using the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) from 10X Genomics.	Illumina NovaSeq 6000	13
EGAD50000001424	This dataset includes single cell (sc)RNA-seq of N=3 patient-derived xenograft (PDX) samples profiled at baseline (no drug treatment) and N=12 samples from one PDX profiled during the course of treatment (N=1 sample each for 4 treatment arms x 3 timepoints). The dataset includes bam files that have been purged of reads mapping to cells where a majority of the reads from that cell mapped to the mouse genome. All scRNA-seq data were generated using the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) from 10X Genomics.	Illumina NovaSeq 6000	15
EGAD50000001425	This dataset includes whole exome sequencing (WES) data from PDX samples post-drug treatment (N=1 vehicle, N=1 gilteritinib, N=1 venetoclax and N=1 VenGilt). Bam files are provided for each sample. The VenGilt-treated sample underwent whole genome amplification using the Qiagen REPLI-g kit (#150345) prior to sequencing due to the very low cell number.	Illumina HiSeq 2500	4
EGAD50000001563	This dataset includes whole genome sequencing of two patient-derived xenograft (PDX) samples with NUP98-Rearranged Acute Myeloid Leukemia. Bam files are provided for each sample.	Illumina NovaSeq X	2
EGAD50000001564	This dataset includes RNA-seq of two patient-derived xenograft (PDX) samples with NUP98-Rearranged Acute Myeloid Leukemia. Bam files are provided for each sample.	Illumina NovaSeq X	2