title: KP-MRT-NS-DMSO, 0, 6, Replicate3

description:
ATTCACAG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005425_G2]

status: Public on Mar 09 2022

type: genomic

city: Memphis

first: Zhaoming

last: Wang

state: TN

address: 262 Danny Thomas Place

department: Epidemiology & Cancer Control

country: USA

institute: St. Jude Children's Research Hospital

description: blood from survivor of childhood cancer

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChips using standard Illumina protocal

scan_protocol: Arrays were stained and scanned using the Illumina HiScan system with standard recommended Illumina scanner setting

data_processing:
GenomeStudio V2011.1
Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

label_protocol: Standard Illumina Protocal

extract_protocol: DNA extracted from periperihal blood mononuclear cells using the QIAamp DNA Blood Mini Kit (Qiagen cat#51106)

tag: gender

value: Female

tag: age

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043916_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003413_G2]

description: blood from survivor of childhood cancer

value: Male


title: KP-MRT-NS-DMSO, 0, 6, Replicate2

type: SRA

city: New York

first: Prabhjot

middle: Singh

last: Mundi

state: NY

address: 1130 St. Nicholas Avenue

department: Medicine; Systems Biology

institute: COLUMBIA UNIVERSITY HEALTH SCIENCES

description:
GACGTACC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

library_source: transcriptomic

data_processing:
Alignment with STARv2.5.3 to GRCh38
Gene-level raw counts summarization with STARv2.5.3 quant-mode.
Variance stabilization (normalization) with DESeq2 (R bioconductor package)
Gene expression signature and metaviper analysis as described in manuscript.
Genome_build: GRCh38.v90
Supplementary_files_format_and_content: Tab delimited text output of raw counts from STAR alignment and gene count quantification. Tab delimited text output for gene expression signatures and VIPER analysis of differential protein activity for perturbation samples.
RNAseq: Raw Counts (aligned to GRCh38v90 with STAR)
PLATEseq: MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt: Raw Counts (aligned to GRCh38v90 with STAR)
PLATEseq: MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt: PLATESeq sample map cell lines samples treated with selinexor and vehicle control (from A204, G401,KPMRT-RY,KPMRT-NS)
PLATEseq: MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt: Differential gene expression signature selinexor vs. DMSO control in MRT cell lines; signatures are computed against reference samples from the same matched cell line only.
PLATEseq: MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt: VIPER assessed differential protein activity selinexor vs. DMSO control in MRT cell lines; signatures are computed against reference samples from the same matched cell line only; the analysis was integrated across networks using metaVIPER

molecule: total RNA

source_name: KP-MRT-NS Malignant Rhabdoid Tumor Cell Line

growth_protocol: The cells were grown in logarithomic phase till treatment

extract_protocol:
mRNAs were extracted using polyA selection kits, TruSeq
For PLATEseq multiplexed platform protocol details, see reference PMID: 28740083.
RNA Sequencing was performed on an Illumina NextSeq 500

treatment_protocol: Drug perturbations profiles in cell lines were done at 6 and/or 24 hours after introducing drug, as indicated by appropriate column names in the sample plate maps and processed data files

tag: cell line

value: KP-MRT-NS

tag: cell type

value: Malignant Rhabdoid Tumor Cell

tag: treatment

value: DMSO at 6 hours


title: KP-MRT-NS-DMSO, 0, 24, Replicate3

description:
GCTTACCA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: DMSO at 24 hours


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS044169_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-NS-DMSO, 0, 24, Replicate2

description:
AGAGCGCA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB043898_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043941_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-NS-MOCK, 0, 6, Replicate3

description:
TTTTGCGA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: Untreated at 6 hours


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004094_G2]

description: blood from survivor of childhood cancer


title: KP-MRT-NS-MOCK, 0, 6, Replicate1

description:
AAGCACCA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043959_G1]

description: blood from survivor of childhood cancer


title: G401-Selinexor, 0.030, 24, Replicate2

description:
GCAGGATC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

source_name: G401 Malignant Rhabdoid Tumor Cell Line

value: Selinexor 0.030 uM at 24 hours


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043900_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM043919_G1]

description: blood from survivor of childhood cancer


title: G401-Selinexor, 0.030, 24, Replicate1

description:
TAGATGTG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: G401-Selinexor, 0.030, 24, Replicate3

description:
GCGTAGGA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004227_G3]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMEL043946_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-NS-Selinexor, 0.030, 6, Replicate1

description:
CCTAACAA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: Selinexor 0.030 uM at 6 hours


title: G401-Selinexor, 0.003, 24, Replicate3

description:
TGTGGTAT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: Selinexor 0.003 uM at 24 hours


title: KP-MRT-NS-Selinexor, 0.003, 6, Replicate1

description:
TTTCGACA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: Selinexor 0.003 uM at 6 hours


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043901_G1]

description: blood from survivor of childhood cancer


title: G401-Selinexor, 0.003, 24, Replicate1

description:
CGAATCTT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: G401-DMSO, 0, 24, Replicate3

description:
CTGTGAGT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: KP-MRT-NS-DMSO, 0, 6, Replicate1

description:
CCTATGCC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: G401-Selinexor, 0.003, 24, Replicate2

description:
AAATAGCG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: KP-MRT-NS-MOCK, 0, 24, Replicate2

description:
TGCTAGTA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

value: Untreated at 24 hours


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL043897_G1]

description: blood from survivor of childhood cancer


title: KP-MRT-NS-MOCK, 0, 6, Replicate2

description:
ACACACAC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: G401-MOCK, 0, 24, Replicate3

description:
CGACCCTA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB044167_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043933_G1]

description: blood from survivor of childhood cancer


title: G401-DMSO, 0, 24, Replicate2

description:
CATATGAG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: G401-DMSO, 0, 24, Replicate1

description:
TCGTGCTT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043912_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004779_G3]

description: blood from survivor of childhood cancer


title: G401-MOCK, 0, 24, Replicate1

description:
GGGCAGAT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: G401-Selinexor, 0.030, 6, Replicate1

description:
GGTACCTC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: G401-Selinexor, 0.003, 6, Replicate2

description:
CACTCAGA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: G401-DMSO, 0, 6, Replicate3

description:
TCCAGCAA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: G401-Selinexor, 0.030, 6, Replicate2

description:
CTGATTCA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: G401-MOCK, 0, 24, Replicate2

description:
GCTGCGTA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043905_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004707_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB043934_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043937_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004247_G3]

description: blood from survivor of childhood cancer


title: G401-Selinexor, 0.003, 6, Replicate3

description:
TCCAATGA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043924_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML007031_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043948_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST011277_G2]

description: blood from survivor of childhood cancer


title: G401-Selinexor, 0.003, 6, Replicate1

description:
GAAGGAGA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB044165_G1]

description: blood from survivor of childhood cancer


title: G401-DMSO, 0, 6, Replicate2

description:
TGTAGCCC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS043137_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL043126_G1]

description: blood from survivor of childhood cancer


title: G401-DMSO, 0, 6, Replicate1

description:
GATCGTGC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: G401-MOCK, 0, 6, Replicate3

description:
AGCAAGTT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: A204-Selinexor, 0.030, 24, Replicate2

description:
CGTGTCCA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt

source_name: A204 Malignant Rhabdoid Tumor Cell Line


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB043960_G1]

description: blood from survivor of childhood cancer


title: G401-MOCK, 0, 6, Replicate2

description:
AGCAGCGT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: A204-Selinexor, 0.030, 24, Replicate1

description:
GGGAATGT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004086_G2]

description: blood from survivor of childhood cancer


title: A204-Selinexor, 0.030, 24, Replicate3

description:
ATCACTGG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041431_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043942_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL043945_G1]

description: blood from survivor of childhood cancer


title: A204-Selinexor, 0.003, 24, Replicate1

description:
TGGATTGA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: A204-Selinexor, 0.003, 24, Replicate3

description:
CAGCGATT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT043136_G1]

description: blood from survivor of childhood cancer


title: A204-Selinexor, 0.003, 24, Replicate2

description:
TTAATGGC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: A204-DMSO, 0, 24, Replicate3

description:
ATCAAACG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: A204-DMSO, 0, 24, Replicate2

description:
ATTGCGTT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL043926_G1]

description: blood from survivor of childhood cancer


title: A204-DMSO, 0, 24, Replicate1

description:
ACCCAGGT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: A204-MOCK, 0, 24, Replicate3

description:
CACGGACT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042890_G1]

description: blood from survivor of childhood cancer


title: A204-MOCK, 0, 24, Replicate2

description:
CTAATCCC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: A204-MOCK, 0, 24, Replicate1

description:
AAACCCTC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005377_G2]

description: blood from survivor of childhood cancer


title: G401-MOCK, 0, 6, Replicate1

description:
AAGTCGGG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJST043961_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS042865_G1]

description: blood from survivor of childhood cancer


title: A204-Selinexor, 0.030, 6, Replicate2

description:
GTGACACC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS043935_G1]

description: blood from survivor of childhood cancer


title: A204-Selinexor, 0.003, 6, Replicate2

description:
ATCCCGAG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005072_G3]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL043134_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB043124_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043453_G1]

description: blood from survivor of childhood cancer


title: A204-Selinexor, 0.003, 6, Replicate1

description:
CTGAATAC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS003205_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043922_G1]

description: blood from survivor of childhood cancer


title: A204-DMSO, 0, 6, Replicate1

description:
AGCCGGAT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: A204-Selinexor, 0.030, 6, Replicate3

description:
CATCGACC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL043461_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM043455_G1]

description: blood from survivor of childhood cancer


title: A204-MOCK, 0, 6, Replicate1

description:
CAAAGTCG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS042888_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL043133_G1]

description: blood from survivor of childhood cancer


title: A204-DMSO, 0, 6, Replicate3

description:
AAAGGCCC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: G401-Selinexor, 0.030, 6, Replicate3

description:
CTGTCCGA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: KPMRT-YM

description: Malignant Rhabdoid Tumor Cell line, CUIMC sequenced, RNASeq

source_name: Malignant Rhabdoid Tumor Cell line

value: KPMRT-YM


title: KPMRT-RY

value: KPMRT-RY


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB043947_G1]

description: blood from survivor of childhood cancer


title: A204-MOCK, 0, 6, Replicate3

description:
ACTGGGAT
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: A204-MOCK, 0, 6, Replicate2

description:
GGAGGGAA
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJLM043956_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB043454_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042864_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041369_G2]

description: blood from survivor of childhood cancer


title: A204-Selinexor, 0.030, 6, Replicate1

description:
GACGATCG
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: A204-Selinexor, 0.003, 6, Replicate3

description:
CGATTTAC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: ATRT-BT16


title: KPMRT-AN

value: KPMRT-AN


title: A204-DMSO, 0, 6, Replicate2

description:
GAATGGGC
MRT_cell_lines_selinexor_treated_PDX_Plateseq_counts.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_samples_barcordes.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_geneexpressionsignature.txt
MRT_cell_lines_selinexor_treated_PDX_Plateseq_viperanalyzeddifferentialproteinactivity.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJST043460_G1]

description: blood from survivor of childhood cancer


title: G401


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003856_G2]

description: blood from survivor of childhood cancer


title: CHLA266


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT042887_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042889_G1]

description: blood from survivor of childhood cancer


title: ATRT-BT12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL043459_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS043451_G1]

description: blood from survivor of childhood cancer


title: A204


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMEL042863_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB003902_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043932_G1]

description: blood from survivor of childhood cancer


title: MENI-TB107: WHO Grade-1 histology

institute: Columbia University Irving Medical Center

data_processing:
Alignment with STARv2.5.3 to GRCh38 or with bowtie2 to Hg19 and mm10 for PDX samples, as indicated below
Gene-level raw counts summarization with STARv2.5.3 quant-mode. In the case of PDX samples, xenomapper tool was to generate counts from reads selectively mapping to human transcriptome and not mouse.
Variance stabilization (normalization) with DESeq2 (R bioconductor package)
Gene expression signature and viper analysis as described in manuscript.
Genome_build: GRCh38.v90 or as indicated below.
Supplementary_files_format_and_content: Tab delimited text output of raw counts from STAR alignment and gene count quantification. Tab delimited text output for VIPER analysis of differential protein activity for perturbation or pharmacodynamic samples.

source_name: CUIMC Meningioma Patient Tumor Sequencing Project

extract_protocol:
RNAs were extracted using polyA selection kits, TruSeq
For PLATEseq multiplexed platform protocol details, see reference PMID: 28740083.
RNA Sequencing was performed on an Illumina NextSeq 500 or NovaSeq 6000 sequencer, as indicated below for each file.

tag: sample type

value: meningioma


title: KPMRT-NS

value: KPMRT-NS


title: MENI-TB106: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042862_G1]

description: blood from survivor of childhood cancer

value: Female


title: MENI-TB105: WHO Grade-1 histology


title: MENI-TB103: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042686_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS043122_G1]

description: blood from survivor of childhood cancer

value: Male


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS043132_G1]

description: blood from survivor of childhood cancer


title: MENI-TB101: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL043965_G1]

description: blood from survivor of childhood cancer


title: MENI-TB100: WHO Grade-2 histology


title: MENI-TB104: WHO Grade-2 histology


title: MENI-TB102: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041411_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM043918_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043450_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM042886_G1]

description: blood from survivor of childhood cancer


title: MENI-TB099: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB043458_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML003318_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041383_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043120_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS042871_G1]

description: blood from survivor of childhood cancer


title: MENI-TB090: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL043928_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL043944_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM043955_G1]

description: blood from survivor of childhood cancer


title: MENI-TB093: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042859_G1]

description: blood from survivor of childhood cancer


title: MENI-TB085: WHO Grade-2 histology


title: MENI-TB096: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043129_G1]

description: blood from survivor of childhood cancer


title: MENI-TB084: WHO Grade-2 histology


title: MENI-TB089: WHO Grade-1 histology


title: MENI-TB098: WHO Grade-2 histology


title: MENI-TB095: WHO Grade-1 histology


title: MENI-TB082: WHO Grade-2 histology


title: MENI-TB097: WHO Grade-1 histology


title: MENI-TB094: WHO Grade-2 histology


title: MENI-TB088: WHO Grade-1 histology


title: MENI-TB091: WHO Grade-1 histology


title: MENI-TB092: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043958_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS043448_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043449_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT043957_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042837_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM043128_G1]

description: blood from survivor of childhood cancer


title: MENI-TB083: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL043118_G1]

description: blood from survivor of childhood cancer


title: MENI-TB081: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS042870_G1]

description: blood from survivor of childhood cancer


title: MENI-TB087: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042858_G1]

description: blood from survivor of childhood cancer


title: MENI-TB080: WHO Grade-2 histology


title: MENI-TB079: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL043447_G1]

description: blood from survivor of childhood cancer


title: MENI-TB086: WHO Grade-2 histology


title: MENI-TB071: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS003208_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042857_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML043975_G1]

description: blood from survivor of childhood cancer


title: MENI-TB075: WHO Grade-1 histology


title: MENI-TB076: WHO Grade-1 histology


title: MENI-TB073: WHO Grade-1 histology


title: MENI-TB077: WHO Grade-1 histology


title: MENI-TB068: WHO Grade-1 histology


title: MENI-TB072: WHO Grade-1 histology


title: MENI-TB070: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042869_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML042701_G1]

description: blood from survivor of childhood cancer


title: MENI-TB078: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042726_G1]

description: blood from survivor of childhood cancer


title: MENI-TB069: WHO Grade-1 histology


title: MENI-TB067: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT042847_G1]

description: blood from survivor of childhood cancer


title: MENI-TB066: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS043117_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB043127_G1]

description: blood from survivor of childhood cancer


title: MENI-TB065: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042747_G1]

description: blood from survivor of childhood cancer


title: MENI-TB074: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042762_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042724_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML042702_G1]

description: blood from survivor of childhood cancer


title: MENI-TB062: WHO Grade-1 histology


title: MENI-TB060: WHO Grade-1 histology


title: MENI-TB058: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042764_G1]

description: blood from survivor of childhood cancer


title: MENI-TB064: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042680_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042707_G1]

description: blood from survivor of childhood cancer


title: MENI-TB057: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042855_G1]

description: blood from survivor of childhood cancer


title: MENI-TB063: WHO Grade-1 histology


title: MENI-TB055: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML042703_G1]

description: blood from survivor of childhood cancer


title: MENI-TB052: WHO Grade-2 histology


title: MENI-TB053: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042757_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042671_G1]

description: blood from survivor of childhood cancer


title: MENI-TB059: WHO Grade-1 histology


title: MENI-TB061: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042723_G1]

description: blood from survivor of childhood cancer


title: MENI-TB049: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042697_G1]

description: blood from survivor of childhood cancer


title: MENI-TB048: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042854_G1]

description: blood from survivor of childhood cancer


title: MENI-TB056: WHO Grade-1 histology


title: MENI-TB045: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042751_G1]

description: blood from survivor of childhood cancer


title: MENI-TB043: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042705_G1]

description: blood from survivor of childhood cancer


title: MENI-TB051: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042685_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042706_G1]

description: blood from survivor of childhood cancer


title: MENI-TB041: WHO Grade-2 histology


title: MENI-TB047: WHO Grade-2 histology


title: MENI-TB054: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042843_G1]

description: blood from survivor of childhood cancer


title: MENI-TB040: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042672_G1]

description: blood from survivor of childhood cancer


title: MENI-TB038: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML042700_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042756_G1]

description: blood from survivor of childhood cancer


title: MENI-TB037: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042661_G1]

description: blood from survivor of childhood cancer


title: MENI-TB050: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML007134_G1]

description: blood from survivor of childhood cancer


title: MENI-TB035: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042738_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042678_G1]

description: blood from survivor of childhood cancer


title: MENI-TB044: WHO Grade-2 histology


title: MENI-TB046: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042711_G1]

description: blood from survivor of childhood cancer


title: MENI-TB042: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042754_G1]

description: blood from survivor of childhood cancer


title: MENI-TB033: WHO Grade-1 histology


title: MENI-TB032: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042731_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042655_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042752_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042733_G1]

description: blood from survivor of childhood cancer


title: MENI-TB031: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042664_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005016_G3]

description: blood from survivor of childhood cancer


title: MENI-TB030: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042742_G1]

description: blood from survivor of childhood cancer


title: MENI-TB039: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042720_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042763_G1]

description: blood from survivor of childhood cancer


title: MENI-TB034: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042852_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042660_G1]

description: blood from survivor of childhood cancer


title: MENI-TB036: WHO Grade-2 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042709_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042673_G1]

description: blood from survivor of childhood cancer


title: MENI-TB029: WHO Grade-1 histology


title: MENI-TB026: WHO Grade-1 histology


title: MENI-TB027: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042741_G1]

description: blood from survivor of childhood cancer


title: MENI-TB028: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042759_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042682_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042654_G1]

description: blood from survivor of childhood cancer


title: MENI-TB023: WHO Grade-1 histology


title: MENI-TB021: WHO Grade-1 histology


title: MENI-TB024: WHO Grade-1 histology


title: MENI-TB019: WHO Grade-1 histology


title: MENI-TB025: WHO Grade-1 histology


title: MENI-TB018: WHO Grade-3 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042745_G1]

description: blood from survivor of childhood cancer


title: MENI-TB022: WHO Grade-1 histology


title: MENI-TB020: WHO Grade-1 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS003713_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042739_G1]

description: blood from survivor of childhood cancer


title: MENI-TB017: WHO Grade-3 histology


title: MENI-TB016: WHO Grade-3 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042681_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML007029_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042710_G1]

description: blood from survivor of childhood cancer


title: MENI-TB015: WHO Grade-3 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042674_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042679_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT042849_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL042730_G1]

description: blood from survivor of childhood cancer


title: MENI-TB011: Benign arachnoid tissue


title: MENI-TB010: Benign arachnoid tissue


title: MENI-TB014: WHO Grade-3 histology


title: MENI-TB004: Benign arachnoid tissue


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042753_G1]

description: blood from survivor of childhood cancer


title: MENI-TB013: WHO Grade-3 histology


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM042768_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042746_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042667_G1]

description: blood from survivor of childhood cancer


title: MENI-TB012: Benign arachnoid tissue


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL042851_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042748_G1]

description: blood from survivor of childhood cancer


title: CUAC1498_human (CNS.16474)

source_name: PDX tumor sample, RNASeq

value: PDX of meningioma

tag: ID


title: MENI-TB008: Benign arachnoid tissue


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042675_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042740_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042663_G1]

description: blood from survivor of childhood cancer


title: MENI-TB007: Benign arachnoid tissue


title: PDX_Pharmacodynamic_BC_GIST_Plate2

source_name: PDX tumor samples treated and vehicle control (from BC.32398), Multiplexed RNASeq (PLATESeq)


title: PDX_Pharmacodynamic_Plateseq

source_name: PDX tumor samples treated and vehicle control (from GIST.81050, CAR.23659, CNS.16474, PAC.05647), Multiplexed RNASeq (PLATESeq)


title: CUAC1431 (GIST.81050)

value: PDX of GIST sarcoma


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCRC042713_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041973_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042037_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042750_G1]

description: blood from survivor of childhood cancer


title: CUAC1427_human (CAR.23659)

source_name: Patient tumor sample, RNASeq

value: colon cancer

tag: condition

value: liver metastasis


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042721_G1]

description: blood from survivor of childhood cancer


title: PDX_Pharmacodynamic_BC_GIST_Plate1

source_name: PDX tumor samples treated and vehicle control (from GIST.81050, BC.32398), Multiplexed RNASeq (PLATESeq)


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL042729_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML007008_G1]

description: blood from survivor of childhood cancer


title: PDX_Pharmacodynamic_GIST_TruSeq

source_name: PDX tumor samples treated and vehicle control (from GIST.81050), RNASeq (TruSeq)


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL042060_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS041989_G1]

description: blood from survivor of childhood cancer


title: TB006_human (CNS.16474)

value: meningeal recurrence


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042743_G1]

description: blood from survivor of childhood cancer


title: CUAC1497_human (CAR.23659)

value: PDX of colon cancer


title: CUAC1618-stranded_human (PAC.05647)

value: PDX of pancreatic cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS041501_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS003216_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003817_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCRC042712_G1]

description: blood from survivor of childhood cancer


title: MENI-TB009: Benign arachnoid tissue


title: CUAC1499_human (BC.97359)

value: PDX of breast cancer


title: CUAC1430 (BC.32398)


title: CUAC1420 (GIST.81050)

source_name: Patient tumor sample 3, peritoneal metastasis * PDX developed from this, RNASeq

value: GIST sarcoma

value: peritoneal metastasis


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042683_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042052_G1]

description: blood from survivor of childhood cancer


title: CUAC1419 (GIST.81050)

source_name: Patient tumor sample 2, peritoneal metastasis, RNASeq


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041861_G1]

description: blood from survivor of childhood cancer


title: CUAC1437_human (BC.97359)

value: breast cancer

value: chest wall metastasis


title: CUAC1407_human (BC.32398)

source_name: Patient tumor sample, brain metastasis, RNASeq

value: brain metastasis


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041886_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042692_G1]

description: blood from survivor of childhood cancer


title: B211-p6-TR2

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

description:
Technical replicate 2
R1 fastq file: cDNA; R2 fastq file: barcode/UMI

data_processing:
Dropseq (v1.0) – see Macosko et al., PMID: 26000488.
DESeq2 (v1.28.1): rlog transformation.
Genome_build: Human GRCh38
Supplementary_files_format_and_content: PDAC_PDO_B211_B188_LogTransform.tsv: Tab-delimited text file containing rlog transformed read counts for each technical replicate.

source_name: PDAC PDOs

extract_protocol:
Qiagen AllPrep® DNA/RNA micro kit.
RT and template switch with primers containing Barcode, UMI and adapter. Full length amplification of the cDNA. Fragmentation and Adapter ligation with NEB Ultra II FS kit and final amplification of the 3’-end with Illumina overhangs. Sequencing of cDNA in Read1 and sequencing of Barcode and UMI in Read2.

value: FOLFIRINOX

tag: tissue

value: PDAC patient-derived organoids

tag: passage


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGICT042114_G1]

description: blood from survivor of childhood cancer

tag: gender

value: Female

tag: age


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS042129_G1]

description: blood from survivor of childhood cancer

value: Male

tag: anthracyclines

tag: alkylating agent,classic


title: CUAC1418 (GIST.81050)

source_name: Patient tumor sample 1, peritoneal metastasis, RNASeq


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042122_G1]

description: blood from survivor of childhood cancer

source_name: peripheral blood mononuclear cells

tag: corticosteroids

tag: epipodophyllotoxins


title: B188-p7-TR1

description:
Technical replicate 1
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: B188-p7-TR2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041975_G1]

description: blood from survivor of childhood cancer

tag: vincristine

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042044_G1]

description: blood from survivor of childhood cancer

tag: brainrt

tag: chestrt


title: Subject12 at-diagnosis CD4+ T cells

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Libraries were sequenced on the Illumina NextSeq 500 platform to produce 75bp paired end reads. The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the human genome by Rsubread version 1.32.2.
Fragment (read-pair) counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function.
Genes were identified using Gencode annotation v35.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text; columns represent Ensembl Gene ID, total gene length (total base count of all exons) and the number of read-pairs mapping to that gene. The supplementary file T1D_RNA_seq_counts.txt.gz collates the counts for all samples in one file.

source_name: Peripheral blood

extract_protocol:
RNA was isolated using the miRNeasy Micro Kit (QIAGEN, cat. no. 217084) following manufacturer's protocol.
Libraries were prepared with an Illumina TruSeq Total Stranded RNA kit according to the manufacturer's protocol.

tag: subject

tag: Sex

value: Insulin

tag: time point

value: At-diagnosis (for progressor)

tag: progressed to t1d

value: No

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type

value: CD4+ T

tag: data set

value: A batch 2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042097_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: age

tag: anthracyclines

tag: alkylating agent,classic


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041897_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042043_G1]

description: blood from survivor of childhood cancer

tag: brainrt

tag: chestrt


title: Subject12 at-diagnosis NK cells

tag: subject

tag: Sex

tag: treatment

tag: time point

tag: progressed to t1d

value: NK

value: B


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042758_G1]

description: blood from survivor of childhood cancer


title: Subject12 at-diagnosis B cells

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type


title: Subject12 at-diagnosis CD8+ T cells

tag: age

value: CD8+ T

tag: data set


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM042140_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042725_G1]

description: blood from survivor of childhood cancer

tag: vincristine

tag: platinum

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041949_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042089_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM042139_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM041713_G2]

description: blood from survivor of childhood cancer


title: Subject12 pre-clinical CD4+ T cells

tag: subject

tag: Sex

tag: treatment

tag: time point

value: Pre-clinical

tag: progressed to t1d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041862_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041845_G1]

description: blood from survivor of childhood cancer


title: Subject11 at-diagnosis NK cells

value: Yes

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type


title: Subject11 at-diagnosis CD8+ T cells

tag: age

tag: data set


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005068_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins


title: Subject11 at-diagnosis CD4+ T cells

tag: subject

value: A batch 1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004271_G1]

description: blood from survivor of childhood cancer

tag: vincristine

tag: platinum

tag: brainrt

tag: chestrt


title: Subject11 at-diagnosis B cells

tag: Sex

tag: treatment

tag: time point

tag: progressed to t1d

tag: iaa (mu/l)


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041876_G1]

description: blood from survivor of childhood cancer

tag: age


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042049_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB019565_G1]

description: blood from survivor of childhood cancer


title: B211-p6-TR1

tag: tissue

tag: passage


title: Subject11 pre-clinical CD8+ T cells

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type

tag: data set


title: Subject11 pre-clinical B cells

tag: subject


title: Subject12 pre-clinical NK cells


title: Subject12 pre-clinical B cells


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041888_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML007095_G1]

description: blood from survivor of childhood cancer

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042690_G1]

description: blood from survivor of childhood cancer

tag: age


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM042770_G1]

description: blood from survivor of childhood cancer


title: Subject12 pre-clinical CD8+ T cells

tag: Sex

tag: treatment

tag: time point

tag: progressed to t1d

tag: iaa (mu/l)


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042735_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042008_G1]

description: blood from survivor of childhood cancer


title: Subject9 at-diagnosis NK cells

value: Placebo

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type

tag: data set


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGICT042113_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids


title: Subject9 at-diagnosis CD8+ T cells

tag: subject


title: Subject9 pre-clinical CD4+ T cells


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042039_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins

tag: vincristine

tag: platinum

tag: brainrt

tag: chestrt


title: Subject9 pre-clinical B cells

tag: Sex

tag: treatment

tag: time point

tag: age

tag: progressed to t1d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042027_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042110_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042659_G1]

description: blood from survivor of childhood cancer


title: Subject8 at-diagnosis CD8+ T cells

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS041991_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids


title: Subject9 at-diagnosis CD4+ T cells

tag: subject

tag: data set


title: Subject8 at-diagnosis CD4+ T cells


title: Subject9 at-diagnosis B cells


title: Subject11 pre-clinical CD4+ T cells


title: Subject8 at-diagnosis B cells


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041404_G2]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins

tag: vincristine

tag: platinum

tag: brainrt

tag: chestrt


title: Subject9 pre-clinical CD8+ T cells

tag: Sex

tag: treatment

tag: time point

tag: age

tag: progressed to t1d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041863_G1]

description: blood from survivor of childhood cancer


title: Subject11 pre-clinical NK cells

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS042132_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041955_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins

tag: vincristine

tag: platinum


title: Subject7 at-diagnosis NK cells

tag: subject

tag: Sex

tag: data set


title: Subject8 pre-clinical B cells

tag: treatment

tag: time point

tag: age


title: Subject8 at-diagnosis NK cells

tag: progressed to t1d

tag: iaa (mu/l)

tag: gadab (u/ml)


title: Subject9 pre-clinical NK cells

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type


title: Subject8 pre-clinical NK cells


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042658_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: anthracyclines

tag: alkylating agent,classic

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041954_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042030_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041410_G2]

description: blood from survivor of childhood cancer


title: Subject8 pre-clinical CD4+ T cells

tag: subject

tag: Sex

tag: treatment

tag: time point

tag: data set


title: Subject7 at-diagnosis CD4+ T cells

tag: age

tag: progressed to t1d

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)


title: Subject7 at-diagnosis CD8+ T cells

tag: znt8a (u/ml)

tag: cell type


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042104_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: anthracyclines

tag: alkylating agent,classic

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042024_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042106_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042749_G1]

description: blood from survivor of childhood cancer


title: Subject7 at-diagnosis B cells

tag: subject

tag: Sex

tag: treatment

tag: time point

tag: data set


title: Subject7 pre-clinical CD8+ T cells

tag: age

tag: progressed to t1d

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)


title: Subject8 pre-clinical CD8+ T cells

tag: znt8a (u/ml)

tag: cell type


title: Subject7 pre-clinical B cells


title: Subject7 pre-clinical NK cells


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042040_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: anthracyclines

tag: alkylating agent,classic

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041393_G2]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003606_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042011_G1]

description: blood from survivor of childhood cancer


title: Subject6 at-diagnosis CD8+ T cells

tag: subject

tag: Sex

tag: treatment

tag: time point

tag: data set


title: Subject6 at-diagnosis CD4+ T cells

tag: age

tag: progressed to t1d

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)


title: Subject6 at-diagnosis NK cells

tag: znt8a (u/ml)

tag: cell type


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041977_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: anthracyclines

tag: alkylating agent,classic

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042018_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042007_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042047_G1]

description: blood from survivor of childhood cancer


title: Subject7 pre-clinical CD4+ T cells

tag: subject

tag: Sex

tag: treatment

tag: time point

tag: data set


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042669_G1]

description: blood from survivor of childhood cancer

tag: age


title: Subject6 at-diagnosis B cells

tag: progressed to t1d

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)


title: Subject6 pre-clinical NK cells

tag: cell type


title: Subject5 at-diagnosis NK cells


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042657_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: anthracyclines

tag: alkylating agent,classic

tag: brainrt

tag: chestrt


title: Subject6 pre-clinical B cells

tag: subject


title: Subject5 at-diagnosis CD8+ T cells

tag: Sex


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041960_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041926_G1]

description: blood from survivor of childhood cancer

tag: age


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041401_G2]

description: blood from survivor of childhood cancer


title: Subject5 pre-clinical CD8+ T cells

tag: treatment

tag: time point

tag: progressed to t1d

tag: iaa (mu/l)

tag: data set


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042095_G1]

description: blood from survivor of childhood cancer

tag: gender


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML007006_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines


title: Subject6 pre-clinical CD8+ T cells

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML041900_G1]

description: blood from survivor of childhood cancer

tag: alkylating agent,classic

tag: brainrt

tag: chestrt


title: Subject5 pre-clinical CD4+ T cells

tag: subject

tag: Sex


title: Subject5 pre-clinical NK cells

tag: age


title: Subject6 pre-clinical CD4+ T cells

tag: treatment


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041847_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041867_G1]

description: blood from survivor of childhood cancer

tag: gender


title: Subject5 at-diagnosis B cells

tag: time point

tag: progressed to t1d

tag: iaa (mu/l)

tag: data set


title: Subject4 at-diagnosis CD8+ T cells

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041938_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042111_G1]

description: blood from survivor of childhood cancer

tag: age

tag: corticosteroids


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041952_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins

tag: vincristine


title: Subject4 at-diagnosis CD4+ T cells

tag: subject

tag: Sex

tag: treatment


title: Subject4 at-diagnosis NK cells

tag: time point

tag: progressed to t1d

tag: iaa (mu/l)


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML007013_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041934_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041932_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041892_G1]

description: blood from survivor of childhood cancer


title: Subject4 pre-clinical NK cells

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type

tag: data set


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042041_G1]

description: blood from survivor of childhood cancer

tag: age

tag: anthracyclines

tag: alkylating agent,classic

tag: brainrt

tag: chestrt


title: Subject4 at-diagnosis B cells

tag: subject

tag: Sex


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042125_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine


title: Subject5 at-diagnosis CD4+ T cells

tag: treatment

tag: time point

tag: progressed to t1d

tag: iaa (mu/l)


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041911_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: platinum


title: Subject4 pre-clinical CD8+ T cells

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type

tag: data set


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMEL042055_G1]

description: blood from survivor of childhood cancer

tag: age

tag: anthracyclines

tag: alkylating agent,classic

tag: brainrt

tag: chestrt


title: Subject3 at-diagnosis NK cells

tag: subject

tag: Sex


title: Subject3 at-diagnosis CD8+ T cells

tag: treatment

tag: time point


title: Subject3 at-diagnosis CD4+ T cells

tag: progressed to t1d

tag: iaa (mu/l)


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041967_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum


title: Subject5 pre-clinical B cells

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type

tag: data set


title: Subject3 pre-clinical CD8+ T cells

tag: age


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003604_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: brainrt

tag: chestrt


title: Subject4 pre-clinical CD4+ T cells

tag: subject

tag: Sex

tag: treatment

tag: time point

tag: progressed to t1d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041921_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine


title: Subject4 pre-clinical B cells

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)


title: Subject3 pre-clinical NK cells

tag: age

tag: cell type

tag: data set


title: Subject3 at-diagnosis B cells


title: Subject3 pre-clinical CD4+ T cells


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042029_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: platinum

tag: brainrt

tag: chestrt


title: Subject3 pre-clinical B cells

tag: subject

tag: Sex

tag: treatment

tag: time point

tag: progressed to t1d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML041902_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS003265_G1]

description: blood from survivor of childhood cancer

tag: age


title: Subject1 at-diagnosis NK cells

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042010_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: platinum

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041965_G1]

description: blood from survivor of childhood cancer

tag: chestrt


title: Subject1 at-diagnosis CD4+ T cells

tag: subject

tag: Sex

tag: treatment

tag: time point

tag: data set


title: Subject1 at-diagnosis CD8+ T cells

tag: progressed to t1d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042074_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: age

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS041993_G1]

description: blood from survivor of childhood cancer


title: Subject1 pre-clinical NK cells

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: cell type


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041858_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: platinum

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003802_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041868_G1]

description: blood from survivor of childhood cancer


title: Subject1 pre-clinical CD8+ T cells

tag: subject

tag: Sex

tag: treatment

tag: time point

tag: data set


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS003213_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: age

tag: corticosteroids

tag: epipodophyllotoxins


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042084_G1]

description: blood from survivor of childhood cancer

tag: vincristine


title: Subject1 at-diagnosis B cells

tag: progressed to t1d

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004190_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: platinum

tag: brainrt


title: Subject1 pre-clinical CD4+ T cells

tag: subject

tag: Sex

tag: treatment

tag: cell type


title: Subject1 pre-clinical B cells

tag: time point

tag: age

tag: data set


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042045_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: chestrt


title: Subject 11 pre-clinical ATACseq

library_source: genomic

data_processing:
An Illumina NextSeq500 was used to generate 75bp paired-end reads using standard Illumina protocols and software.
Sequence reads were aligned to the human genome using Bowtie2 v2.2.5.
For each sample, mitochondrial reads are removed from the aligned BAM file using the removeChrom python script developed by Harvard Informatics (https://github.com/harvardinformatics/ATAC-seq). Properly paired reads were used for downstream analysis.
Filtered ATAC-seq reads from all the samples were merged using samtools function “merge” in a single file.
PCR duplicates were marked using Picard MarkDuplicates
Peak calling was carried out on the merged file using MACS2 and ATAC-seq reads overlapping the peaks were summarized for each sample using featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files; rows correspond to peaks; columns provide genomic location of the peak and the number of read pairs mapping to that peak. The supplementary file T1D_ATACseq_counts.txt.gz consolidates the counts for all samples in one file.

source_name: Peripheral blood CD4+ T cells

extract_protocol: Omni-ATAC-seq protocol as described by Corces et al https://doi.org/10.1038/protex.2017.096

value: Peripheral blood CD4+ T cells

tag: age (years)

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)

tag: progressed to t1d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS041992_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: platinum

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042032_G1]

description: blood from survivor of childhood cancer

tag: age


title: Subject 6 pre-clinical ATACseq

tag: cell type

tag: subject

tag: Sex


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041907_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: corticosteroids

tag: epipodophyllotoxins


title: Subject 9 pre-clinical ATACseq

tag: age (years)


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004746_G1]

description: blood from survivor of childhood cancer

tag: vincristine

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL006063_G2]

description: blood from survivor of childhood cancer


title: Subject 5 pre-clinical ATACseq

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)


title: Subject 3 pre-clinical ATACseq

tag: znt8a (u/ml)

tag: progressed to t1d


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042038_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: platinum


title: NB in mouse GS media #1

city: LYON

first: Olivier

last: IMBAUD

state: Rhône-Alpes

address: Faculty of Medicine and Pharmacy - 3rd floor 8 Rockefeller Avenue

department: NeuroMyoGene Institut (INMG)

country: France

institute: UCBL | CNRS UMR 5310 | INSERM U1217

description:
07_E15-5_GS_S7_R1_001
rawcounts_expression_matrix.txt

data_processing:
Demultiplexing was performed using Bcl2fastq v2.17.1.14.
Trimming and quality check was performed using CutAdapt v1.9.1.
Mapping was performed with TopHat v.2.1.0.
Quantification was done using HTSeq-count v.0.11.3.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: rawcounts_expression_matrix.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: IGR-N91 neuroblastoma cells

growth_protocol: IGR-N91 cells were cultured in hanging drops.

extract_protocol:
Total RNA was extracted with RNeasy PLUS mini kit (Qiagen) and the quality was checked with a Bioanalyzer 2100 (Agilent, RIN >8.0).
RNAseq libraries were prepared with 50 ng of total RNA with SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara, Clontech).
Samples were sequenced in whole RNAseq using the NextSeq500 Illumina Platform (75 bp single read).

treatment_protocol: IGR-N91 cell aggregates were cultured with control, E8-cSGCM, E8-cDRGCM or E15.5-mSGCM. Aggregates of about 2.7x10^6 cells were then retrieved 20 hours later before storing to -80°C.

tag: cell line

tag: cell type

value: Neuroblastoma cells

tag: culture condition


title: Subject 12 pre-clinical ATACseq

tag: subject

tag: Sex


title: NB in chick GS media #2

description:
04_E8_GS_S4_R1_001
rawcounts_expression_matrix.txt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041846_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: age

tag: corticosteroids

tag: epipodophyllotoxins

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042013_G1]

description: blood from survivor of childhood cancer

tag: vincristine

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041843_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS003714_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042046_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041924_G1]

description: blood from survivor of childhood cancer


title: NB in chick DRG media #2

description:
06_E8_DRG_S6_R1_001
rawcounts_expression_matrix.txt


title: NB in chick GS media #1

description:
03_E8_GS_S3_R1_001
rawcounts_expression_matrix.txt


title: NB in chick DRG media #1

description:
05_E8_DRG_S5_R1_001
rawcounts_expression_matrix.txt


title: NB in mouse GS media #2

description:
08_E15-5_GS_S8_R1_001
rawcounts_expression_matrix.txt


title: NB in control media #2

description:
02_E8_CTRL_S2_R1_001
rawcounts_expression_matrix.txt

value: Control


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041923_G1]

description: blood from survivor of childhood cancer

value: Female


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041928_G1]

description: blood from survivor of childhood cancer

value: Male


title: NB in control media #1

description:
01_E8_CTRL_S1_R1_001
rawcounts_expression_matrix.txt


title: Subject 7 pre-clinical ATACseq

tag: age (years)

tag: iaa (mu/l)

tag: gadab (u/ml)

tag: ia2ab (u/ml)

tag: znt8a (u/ml)


title: Subject 8 pre-clinical ATACseq

tag: progressed to t1d


title: Subject 1 pre-clinical ATACseq

tag: cell type


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042082_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: platinum


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041859_G1]

description: blood from survivor of childhood cancer

tag: gender


title: ATAC_preE60

city: buenos aires

first: Patricia

last: Saragüeta

state: CABA

address: Vuelta de Obligado 2490

country: Argentina

institute: IByME

data_processing:
Sequencing reads were trimmed to remove Illumina adaptors and low-quality ends using Trimmomatic v0.33 in paired-end mode.
Trimmed reads were quality checked with FastQC and aligned to reference human genome hg38 (UCSC) using BWA v0.7.12 with default parameters, keeping alignements that mapped uniquely to the reference (Samtools v1.2).
Genome_build: hg38

source_name: endometrial adenocarcinoma

growth_protocol: Ishikawa cells were routinely cultured in DMEM/F12 (1:1) supplemeted with 10% FCS and gentamycin

extract_protocol:
Cells were lyzed with 50ul cold lysis buffer (Tris-Cl pH 7.4 10mM; NaCl 10mM; MgCl2 3mM; NP-40 0.1% v/v) and centrifuged at 500xg for 10min at 4ºC. Nuclei were resuspended in TD Buffer with 1.5ul Tn5 Transposase (Nextera, Illumina) and incubated 15 minutes at 37ºC. DNA was isolated using Qiagen MinElute column.
Purified DNA was submitted to 10 cycles of PCR amplification using NEBNext High-Fidelity 2X PCR Master Mix (Univ. primer: AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG ; Indexed primers: CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGT). Library were size selected using AMPure XP beads and sequenced on a NextSeq 500 instrument (2x75 nt).

treatment_protocol: 50,000 cells were seeded in culture plates using DMEM/F12 (1:1) without phenol red and supplemented with 5% dextran-coated charcoal stripped FCS and gentamycin for 48h, followed by overnight incubation in DMEM/F12 (1:1) without phenol red and without FCS. After overnight incubation, cells were treated or not with R5020 10nM and E2 10nM for 60min.

tag: disease state

value: endometrial adenocarcinoma

tag: cell line

value: Ishikawa

tag: passages

value: epithelial-like

tag: growth mode

value: adherent

tag: treatment

value: 60min E2-treated 12h E2-pretreated Ishikawa cells


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042088_G1]

description: blood from survivor of childhood cancer

tag: age

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041947_G1]

description: blood from survivor of childhood cancer


title: ATAC_preR60

value: 60min R5020-treated 12h E2-pretreated Ishikawa cells


title: ATAC_E60

value: 60min E2-treated Ishikawa cells


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042006_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042020_G1]

description: blood from survivor of childhood cancer


title: ATAC_T0

value: untreated Ishikawa cells


title: ATAC_R60

value: 60min R5020-treated Ishikawa cells


title: ATAC_preT0

value: 12h E2-pretreated Ishikawa cells


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041909_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042048_G1]

description: blood from survivor of childhood cancer