DAC

St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project Steering Committee

Dac ID Contact Person Email Access Information
EGAC00001000044 PCGP Steering Committee pcgp_data_request [at] stjude [dot] org No additional information is available

This DAC controls 108 datasets:

Dataset ID Description Technology Samples
EGAD00001000085 Somatic Histone H3 mutations Illumina HiSeq 2000 14
EGAD00001000135 Neuroblastoma whole genome sequencing Illumina HiSeq 2000 80
EGAD00001000159 DATA FILES FOR SJOS Illumina HiSeq 2000 37
EGAD00001000160 DATA FILES FOR SJACT Illumina HiSeq 2000 16
EGAD00001000161 DATA FILES FOR SJLGG Illumina HiSeq 2000 33
EGAD00001000162 DATA FILES FOR SJEPD Illumina HiSeq 2000 44
EGAD00001000163 DATA FILES FOR SJPHALL Illumina HiSeq 2000 18
EGAD00001000164 DATA FILES FOR SJRHB Illumina HiSeq 2000 29
EGAD00001000165 DATA FILES FOR SJINF Illumina HiSeq 2000 46
EGAD00001000259 DATA FILES FOR SJAMLM7 Illumina HiSeq 2000 8
EGAD00001000260 Hypodiploid acute lymphoblastic leukemia whole genome sequencing Illumina HiSeq 2000 40
EGAD00001000261 Retinoblastoma whole genome sequencing Illumina HiSeq 2000 8
EGAD00001000268 DATA FILES FOR SJCBF Illumina HiSeq 2000 34
EGAD00001000269 OLD DATA FILES FOR SJMB - Superseded by EGAD00001001864 Illumina HiSeq 2000 68
EGAD00001000352 DATA FILES FOR SJLGG Illumina HiSeq 2000 7
EGAD00001000353 DATA FILES FOR SJLGG Illumina HiSeq 2000 45
EGAD00001000654 DATA FILES FOR BALL-PAX5 Illumina HiSeq 2000 153
EGAD00001000655 DATA FILES FOR Histone-NSD2_RNASeq Illumina HiSeq 2000 8
EGAD00001000657 DATA FILES FOR Histone Capture bams Illumina HiSeq 2000 962
EGAD00001000695 DATA FILES FOR SJLGG Illumina HiSeq 2000 46
EGAD00001000806 Whole Genome Sequencing (WGS) for St. Jude High Grade Glioma (HGG) study Illumina HiSeq 2000 63
EGAD00001000807 Whole Exome Sequencing (WES) for St. Jude High Grade Glioma (HGG) study Illumina HiSeq 2000 148
EGAD00001000853 DATA FILES FOR SJEPD Illumina HiSeq 2000 37
EGAD00001000854 DATA FILES FOR SJEPD Illumina HiSeq 2000 77
EGAD00001000878 DATA FILES FOR SJRHB RNA-Seq Illumina HiSeq 2000 42
EGAD00001000976 WGS DATA FILES FOR SJPhLike Illumina HiSeq 2000 80
EGAD00001001016 DATA FILES FOR SJPhLike-RNASeq Illumina HiSeq 2000 125
EGAD00001001020 DATA FILES FOR SJEWS-WGS Illumina HiSeq 2000 38
EGAD00001001032 DATA FILES FOR SJMEL-WGS Illumina HiSeq 2000 12
EGAD00001001045 DATA FILES FOR SJRB Illumina HiSeq 2000 20
EGAD00001001052 DATA FILES FOR SJTALL Illumina HiSeq 2000 24
EGAD00001001053 DATA FILES FOR SJOS-WGS-2ndBatch Illumina HiSeq 2000 27
EGAD00001001054 DATA FILES FOR Ph-likeALL WES Illumina HiSeq 2000 23
EGAD00001001056 NA Illumina HiSeq 2000 7
EGAD00001001059 DATA FILES FOR SJRHB-WES Illumina HiSeq 2000 56
EGAD00001001065 DATA FILES FOR SJCPC-WGS Illumina HiSeq 2000 8
EGAD00001001098 DATA FILES FOR SJINF RNASeq Illumina HiSeq 2000 63
EGAD00001001245 DATA FILES FOR PCGP SJINF WES Illumina HiSeq 2000 40
EGAD00001001246 DATA FILES FOR PCGP SJMEL WXS Illumina HiSeq 2000 28
EGAD00001001247 DATA FILES FOR PCGP SJMEL RNASEQ Illumina HiSeq 2000 7
EGAD00001001248 DATA FILES FOR PCGP SJETP WXS Illumina HiSeq 2000 13
EGAD00001001352 Data files for CONSERTING (WGS) Illumina HiSeq 2000 38
EGAD00001001415 DATA FILES FOR PCGP Dyer_iPSC WGS Illumina HiSeq 2000 2
EGAD00001001416 DATA FILES FOR PCGP Dyer_iPSC TEBS Illumina HiSeq 2000 18
EGAD00001001418 DATA FILES FOR PCGP Dyer_iPSC 5hmc Illumina HiSeq 2000 8
EGAD00001001432 PCGP Germline Study Whole Genome Sequencing Illumina HiSeq 2000 1337
EGAD00001001433 PCGP Germline Study Whole Exome Sequencing Illumina HiSeq 2000 906
EGAD00001001664 LGG Epilepsy Cohort WGS Illumina HiSeq 2000 18
EGAD00001001665 LGG Epilepsy Cohort WXS Illumina HiSeq 2000 61
EGAD00001001666 LGG Epilepsy Cohort RNA-Seq Illumina HiSeq 2000 34
EGAD00001001864 DATA FILES FOR PCGP MB WGS - Supersedes (EGAD00001000269) Illumina HiSeq 2000 76
EGAD00001001874 NA Illumina HiSeq 2000 16
EGAD00001002530 Additional files for "The Genomic Landscape of Core-Binding Factor Acute Myeloid Leukemias" (EGAS00001000349). This dataset includes the processed RNASeq data referenced in this paper. Illumina HiSeq 2000 36
EGAD00001002654 This dataset contains RNA-seq, ATAC-seq, and ChIP-seq samples from the SJERG cohort. We applied ChIP-Seq for Dux4 on two B-cell ALL cell-lines(REH, Nalm6) along with INPUT. ATAC-Seq on two B-cell ALL cell-lines(REH, Nalm6) and xenograft of a B-cell ALL patient(ERG000016). Illumina HiSeq 2000 13
EGAD00001002667 Additional files for "The Genomic Landscape of Core-Binding Factor Acute Myeloid Leukemias" (EGAS00001000349). This dataset includes the processed Excap data referenced in this paper. Illumina HiSeq 2000 327
EGAD00001002676 DATA FILES FOR PCGP SJERG (WGS) Illumina HiSeq 2000 44
EGAD00001002677 DATA FILES FOR PCGP SJERG (WXS) Illumina HiSeq 2000 42
EGAD00001002679 This dataset contains WES files for the SJACT cohort associated with the paper "Genetic landscape of pediatric Adrenocortical Tumor". In this paper, we analyse 37 adrenocortical tumours (ACTs) by whole-genome, whole-exome and/or transcriptome sequencing. Illumina HiSeq 2000 38
EGAD00001002680 This dataset contains RNA-Seq files for the SJACT cohort associated with the paper "Genetic landscape of pediatric Adrenocortical Tumor". In this paper, we analyse 37 adrenocortical tumours (ACTs) by whole-genome, whole-exome and/or transcriptome sequencing. Illumina HiSeq 2000 26
EGAD00001002681 RNA-seq, ChIP-seq, and ATAC-seq files for PCGP SJERG paper titled "Deregulation of DUX4 and ERG in acute lymphoblastic leukemia" Illumina HiSeq 2000 53
EGAD00001002692 DATA FILES FOR MULLIGHAN MEF2D RNASEQ STRANDED Illumina HiSeq 2000 200
EGAD00001002704 DATA FILES FOR MULLIGHAN MEF2D RNASEQ UNSTRANDED Illumina HiSeq 2000 217
EGAD00001002741 Additional Xenograph files for PCGP SJERG Illumina HiSeq 2000 11
EGAD00001003126 WGS data of medulloblastoma tumor/control pairs. 74
EGAD00001003134 DATA FILES FOR GRUBER SJAMLM7 EXOME Illumina HiSeq 2000 114
EGAD00001003135 DATA FILES FOR GRUBER SJAMLM7 RNASEQ Illumina HiSeq 2000 86
EGAD00001003154 RNA-Seq files for SJOS study Illumina HiSeq 2000 14
EGAD00001003155 WES files for SJMDS paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes' Illumina HiSeq 2000 6
EGAD00001003156 WGS files for SJMDS paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes' Illumina HiSeq 2000 4
EGAD00001003412 NA Illumina HiSeq 2000 152
EGAD00001003413 NA Illumina HiSeq 2000 145
EGAD00001003432 ChIP-Seq data for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors" Illumina HiSeq 2000 20
EGAD00001003433 RNA-Seq data for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors" Illumina HiSeq 2000 95
EGAD00001003434 Whole Exome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors" Illumina HiSeq 2000 149
EGAD00001003435 Whole Genome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors" Illumina HiSeq 2000 150
EGAD00001003781 Paired whole exome sequencing for 32 primary MDS, 14 MDS/MPN, and 8 AML-MRC cases (total = 54). Normal comparator genomic DNA was extracted from lymphocytes purified by flow cytometry. Bulk myeloid cells were used as a source of tumor gDNA. Files uploaded are mapped BAM files. Illumina HiSeq 2000 94
EGAD00001003782 When available (25 primary MDS, 12 MDS/MPN, and 6 AML-MRC cases), high quality RNA (stranded-total) was submitted for RNA-seq. RNA was extracted from bulk myeloid cells which was used as the tumor population. Files uploaded are mapped BAM files. Illumina HiSeq 2000 43
EGAD00001003905 RNA-Seq files accompanying the paper titled "Somatic Histone H3 Mutations in Diffuse Intrinsic Pontine Gliomas and Non-Brainstem Paediatric Glioblastomas". Illumina HiSeq 2000 66
EGAD00001004280 This dataset contains whole genome sequencing BAM files for 78 tumor-normal pairs (a total of 156 samples) used in the St. Jude Clinical Pilot. Mapping was performed using BWA. This dataset accompanies the paper "Clinical Cancer Genomic Profiling by Three-Platform Sequencing of Whole Genome, Whole Exome and Transcriptome" Illumina HiSeq 2000 78
EGAD00001004287 This dataset contains whole exome sequencing BAM files for 78 tumor-normal pairs (a total of 156 samples) used in the St. Jude Clinical Pilot. Mapping was performed using BWA. This dataset accompanies the paper "Clinical Cancer Genomic Profiling by Three-Platform Sequencing of Whole Genome, Whole Exome and Transcriptome" Illumina HiSeq 2000 156
EGAD00001004290 This dataset contains whole genome sequencing BAM files for 78 tumor-normal pairs (a total of 156 samples) used in the St. Jude Clinical Pilot. Mapping was performed using BWA. This dataset accompanies the paper "Clinical Cancer Genomic Profiling by Three-Platform Sequencing of Whole Genome, Whole Exome and Transcriptome" Illumina HiSeq 2000 156
EGAD00001004312 ChIP-Seq files accompanying the paper titled "Identification of Therapeutic Targets in Rhabdomyosarcoma Through Integrated Genomic, Epigenomic, and Proteomic Analyses". Illumina HiSeq 2000 158
EGAD00001004315 WGBS files accompanying the paper titled "Identification of Therapeutic Targets in Rhabdomyosarcoma Through Integrated Genomic, Epigenomic, and Proteomic Analyses". Illumina HiSeq 2000 37
EGAD00001004337 Whole Genome Sequencing files accompanying the paper titled "Structure and evolution of double minutes in diagnosis and relapse brain tumors". Please read the paper for more details. Illumina HiSeq 2000 2
EGAD00001004429 ChIP-Seq files for PCGP ATRX study paper titled "MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma" Illumina HiSeq 2000 121
EGAD00001004446 WGS files for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia" Illumina HiSeq 2000 16
EGAD00001004447 WES files for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia" Illumina HiSeq 2000 128
EGAD00001004461 RNAseq files (dataset 1 of 2) for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia" Illumina HiSeq 2000 1083
EGAD00001004463 RNAseq files (dataset 2 of 2) for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia" Illumina HiSeq 2000 204
EGAD00001004506 WES files for CHEN WTPDX paper titled "Forty-Five patient-derived xenografts capture the clinical and biological heterogeneity of Wilms tumor" Illumina HiSeq 2000 107
EGAD00001004507 RNAseq files for CHEN WTPDX RNASEQ paper titled "Forty-Five patient-derived xenografts capture the clinical and biological heterogeneity of Wilms tumor" Illumina HiSeq 2000 88
EGAD00001004559 WGBS files for PCGP NBL_MYCN_ATRX paper titled "MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma" Illumina HiSeq 2000 24
EGAD00001004566 WES files for Newman MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas" Illumina HiSeq 2000 2
EGAD00001004567 RNASeq files for MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas" Illumina HiSeq 2000 2
EGAD00001004579 WGS files for Newman MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas" Illumina HiSeq 2000 2
EGAD00001004595 VALCAP files for Ma et al. (2019) Genome Biology (accepted) titled “Analysis of error profiles in deep next-generation sequencing data" HiSeq X Ten 47
EGAD00010000462 SJLGG Case samples using Gene Expression Array Affymetrix_U133v2 75
EGAD00010000596 PCGP Ph-likeALL GEA 837
EGAD00010000598 PCGP Ph-likeALL SNP6 1724
EGAD00010000696 PCGP ETP ALL SNP6 0
EGAD00010000698 PCGP INF ALL SNP6 0
EGAD00010001300 Medulloblastoma expression profiling Affymetrix expression array 146
EGAD00010001319 Medulloblastoma methylation profiling Illumina Infinium HumanMethylation450 BeadChip 345
EGAD00010001596 DNA methylation data from patient RMS tumor samples from Illumina 450 K arays Illlimuna EPIC 450 K 32
EGAD00010001635 Over 1.87 million SNP and CNV loci are screened by Affymetrix SNP 6.0 array 415
EGAD00010001636 Over 2.5 million SNP and CNV loci are screened by Illumina Infinium Omni2.5Exome-8 Kit 196
EGAD00010001637 Over 1.87 million SNP and CNV loci are screened by Affymetrix SNP 6.0 array 539
EGAD00010001638 Over 2.5 million SNP and CNV loci are screened by Illumina Infinium Omni2.5Exome-8 Kit 262