title: RNA-seq #1 of QSER1/TET1 DKO PP1 cells Batch3

city: Beijing

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

institute: Peking University Third Hospital

description:
16_S25
QSER1/TET1 DKO_PP1_1_Batch3

data_processing:
RNA-seq data was aligned to the hg19 reference genome using STAR 2.3.0e.
Read counts were derived from featureCounts 1.4.6-p5.
Genome_build: hg19
Supplementary_files_format_and_content: reads counts in .txt format

source_name: Pancreatic Progenitors (PP1) differentiated from hESCs

growth_protocol: H1 hESCs were maintained in the chemically defined feeder-free, serum-free E8 condition (Thermo Fisher Scientific, A1517001) on polystyrene plates coated with human recombinant vitronectin (Thermo Fisher Scientific, A14700) at 37°C with 5% CO2. hESCs were dissociated with 0.5 mM EDTA and split every 3–4 days at a 1:10–1:15 ratio. 10 µM Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Selleck Chemicals, S1049) was added into the culture medium when passaging or thawing cells. Cells were routinely confirmed to be mycoplasma-free by the MSKCC Antibody and Bioresource Core Facility. All experiments were approved by the Tri-SCI Embryonic Stem Cell Research Oversight Committee (ESCRO). For spontaneous differentiation to embryoid bodies (EBs), hESCs were dissociated into single cells with TryplE Select (Thermo Fisher Scientific, 12563029). 5x106 cells in 5 ml Essential 6 medium (E6) (Thermo Fisher Scientific, A1516401) were added into one well of a ultra low attachment 6-well plate (Thermo Fisher Scientific, 3471) and placed on an orbital shaker (within an incubator at 37°C with 5% CO2) at 100rpm to induce sphere formation. The E6 medium was changed every day until day 10 when cells were harvested for downstream applications. For differentiation to pancreatic progenitors (PP), 2 days prior to differentiation, hESCs were treated with TrypLE Select (Invitrogen, 12563-029) for dissociation into single cells and seeded onto vitronectin-coated plates at ~0.3 million cells per well of a 12-well plate. hESCs were maintained in E8 medium for 2 days to reach ~80% confluence. Cells were washed with PBS once and differentiated to definitive endoderm (DE), foregut (FG), pancreatic progenitor (PP1), and late stage pancreatic progenitor (PP2) by the following protocol. The medium was changed every day during differentiation. S1/2 media: MCDB 131 medium (Life Technologies, 10372-019) further supplemented with 1.5 g/l sodium bicarbonate (Fisher Scientific, s22060), 1× Glutamax (Thermo Fisher Scientific, 35050061), 10 mM Glucose (Sigma-Aldrich, G8769), 0.5% BSA (LAMPIRE Biological Products, 7500804). S3/4 media: MCDB 131 medium further supplemented with 2.5 g/l sodium bicarbonate, 1× Glutamax, 10 mM Glucose, 2% BSA. DE, S1 (3 days): Cells were differentiated toward DE using S1/2 media supplemented with 100 ng/ml Activin A (PeproTech, 120-14E) for 3 days. 5 μM and 0.5 μM CHIR99021 (Stemgent, 04-0004-10) were added at the first and second day of DE differentiation, respectively. FG, S2 (2 days): S1 cells were rinsed with 1X DPBS (without Mg2+ and Ca2+) and then exposed to S1/2 media supplemented with 50 ng/ml of KGF (FGF7) (PeproTech, 100-19) and vitamin C (Sigma-Aldrich, A4544) for 2 days. PP1, S3 (Yang condition) (2 days): Cultures were switched to S3/4 media supplemented with 50 ng/ml of FGF7, 0.25 mM vitamin C, and 1uM retinoic acid (RA) (Sigma-Aldrich, R2625) for 2 days. PP2, S4 (4 days): Cultures were continued to S3/4 media supplemented with 2 ng/ml of FGF7, 0.25 mM vitamin C, 0.1 uM RA, 200 nM LDN (Stemgent, 04-0019), 0.25 uM SANT-1 (Sigma, S4572), 100 nM TPB (EMD Millipore, 565740), and 1:200 ITS-X for 4 days.

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (Qiagen, 74136). DNA was removed from RNA samples using genomic DNA eliminator spin columns. Samples were submitted to MSKCC Integrated Genomics Operation core for quality control and sequencing.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000, with additional reads generated on a HiSeq 2500 in Rapid mode in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit or HiSeq Rapid SBS Kit v2, respectively (Illumina). An average of 54 million paired reads was generated per sample. At the most the ribosomal reads represented 1.9% of the total reads generated and the percent of mRNA bases averaged 69%.

treatment_protocol: No treatments were applied prior to RNA extraction

tag: cell line

value: Differentiated from H1 hESCs

tag: genotype

value: Inactivating mutations in QSER1 and TET1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019717_G1]

status: Public on Mar 19 2021

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
Unmethylated and methylated signal intensities provided in the SJLIFE_IlluminaEPIC_2052samples_GEO_03162021_signal.txt
Average Beta provided in the SJLIFE_IlluminaEPIC_2052samples_GEO_03162021_processed.txt

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: vinca alkaloids

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019718_G1]

description: blood from survivor of childhood cancer

value: Male


title: RNA-seq #1 of TET1 KO PP1 cells Batch3

type: SRA

country: China

description:
13_S22
TET1KO_PP1_1_Batch3

library_source: transcriptomic

molecule: total RNA

value: Inactivating mutation in TET1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019742_G1]

description: blood from survivor of childhood cancer


title: RSD 34

city: Rome

first: Luisa

last: Lo Iacono

address: via del fosso di Fiorano 64

department: behavioral neuroscience

country: Italy

institute: Fondazione Santa Lucia IRCCS

data_processing:
Illumina novaSeq base call (BCL) files were converted in fastq file through bcl2fastq(version v2.20.0.422)
Sequence reads were trimmed using bbduk software[2] (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6)
Alignment was performed with STAR 2.6.0a on rn6 assembly downloaded from UCSC Genome Browser website
The expression levels of genes were determined with htseq-count 0.9.1 by using Ensembl genes annotations (Version 6.0).
Individual sample counts were normalized via Relative Log Expression (RLE) using DESeq2 R library
Genome_build: rn6 genome from UCSC genome browser
Supplementary_files_format_and_content: excl file including raw gene counts values for each sample in a matrix. We remove all genes having Perc MM reads > 20% and the genes having < 1 cpm in less than n_min1 samples.  All the genes not passing either of the filters are indicated in the column “Removed gene” with TRUE.

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
Hearts were excised, flash frozen on dry ice, and punches form left ventricles were dissected. RNA was extracted using Norgen minicolumn ( Total RNA purification Kit) and quality checked via Agilent  2100 bioanalyzer assay
Libraries were prepared from 100ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH). Libraries were sequenced on a NovaSeq 6000 sequencing system using an S1, 100 cycles flow cell (Illumina Inc.)
RNA-Seq (mRNA 3' Digital Gene Expression)

treatment_protocol: Social defeat stress was based on a classical “resident–intruder” paradigm (Miczeck, 1979), The defeat sessions were repeated for 8 consecutive days.

tag: strain

value: wild-type Groningen rats

tag: tissue

value: Heart - left ventricle

tag: Sex

value: male

value: adult

tag: treatment

value: Repeated Social Defeated (RSD)


title: RSD 33


title: CTR 26

value: Unhandled control


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS018864_G1]

description: blood from survivor of childhood cancer

tag: gender


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB019817_G1]

description: blood from survivor of childhood cancer

tag: age


title: RNA-seq #1 of QSER1 KO PP1 cells Batch3

description:
10_S19
QSER1KO_PP1_1_Batch3

tag: cell line

tag: genotype

value: Inactivating mutation in QSER1


title: CTR 23


title: RNA-seq #1 of WT PP1 cells Batch3

description:
7_S16
WT_PP1_1_Batch3

value: Wild type sequence


title: RNA-seq #3 of QSER1/TET1 DKO PP1 cells Batch3

description:
18_S27
QSER1/TET1 DKO_PP1_3_Batch3


title: RNA-seq #3 of QSER1 KO PP1 cells Batch3

description:
12_S21
QSER1KO_PP1_3_Batch3


title: CTR 22


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB019824_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids


title: RNA-seq #2 of QSER1/TET1 DKO PP1 cells Batch3

description:
17_S26
QSER1/TET1 DKO_PP1_2_Batch3


title: RNA-seq #3 of TET1 KO PP1 cells Batch3

description:
15_S24
TET1KO_PP1_3_Batch3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019732_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins

tag: vinca alkaloids

tag: asparaginase enzymes


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019727_G1]

description: blood from survivor of childhood cancer

tag: antimetabolites

tag: brainrt

tag: chestrt


title: RNA-seq #3 of WT PP1 cells Batch3

description:
9_S18
WT_PP1_3_Batch3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019778_G1]

description: blood from survivor of childhood cancer

tag: abdominalrt

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019842_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #2 of TET1 KO PP1 cells Batch3

description:
14_S23
TET1KO_PP1_2_Batch3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS018871_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB019823_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #2 of QSER1 KO PP1 cells Batch3

description:
11_S20
QSER1KO_PP1_2_Batch3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019737_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #3 of QSER1 KO Day10 EBs Batch3

description:
29_S38
QSER1KO_EB_3_Batch3

source_name: Day 10 Embryoid Bodies (EBs) differentiated from hESCs


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB019828_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018887_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #2 of QSER1 KO Day10 EBs Batch3

description:
25_S34
QSER1KO_EB_2_Batch3


title: RNA-seq #1 of TET1 KO Day10 EBs Batch3

description:
22_S31
TET1KO_EB_1_Batch3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018484_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019840_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #3 of WT Day10 EBs Batch3

description:
28_S37
WT_EB_3_Batch3


title: RNA-seq #2 of WT PP1 cells Batch3

description:
8_S17
WT_PP1_2_Batch3


title: RNA-seq #2 of WT Day10  EBs Batch3

description:
24_S33
WT_EB_2_Batch3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019716_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #2 of QSER1/TET1 DKO Day10 EBs Batch3

description:
27_S36
QSER1/TET1 DKO_EB_2_Batch3


title: RNA-seq #3 of QSER1/TET1 DKO Day10 EBs Batch3

description:
31_S40
QSER1/TET1 DKO_EB_3_Batch3


title: RNA-seq #1 of QSER1/TET1 DKO Day10 EBs Batch3

description:
23_S32
QSER1/TET1 DKO_EB_1_Batch3


title: RNA-seq #1 of WT Day10 EBs Batch3

description:
20_S29
WT_EB_1_Batch3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019806_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018497_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019764_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #3 of H1 QSER1/TET1 DKO hESCs Batch3

description:
6_S15
QSER1/TET1 DKO_ES_3_Batch3

source_name: H1 human embryonic stem cells (hESCs)

value: H1 hESCs


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJLM018726_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #2 of TET1 KO Day10 EBs Batch3

description:
26_S35
TET1KO_EB_2_Batch3


title: RNA-seq #3 of H1 TET1 KO hESCs Batch3

description:
3_S12
TET1KO_ES_3_Batch3


title: RNA-seq #1 of H1 QSER1/TET1 DKO hESCs Batch3

description:
4_S13
QSER1/TET1 DKO_ES_1_Batch3


title: RNA-seq #2 of H1 TET1 KO hESCs Batch2

description:
HT18-P6_IGO_09130_8_S14
TET1KO_ES_2_Batch2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019709_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #3 of TET1 KO Day10 EBs Batch3

description:
30_S39
TET1KO_EB_3_Batch3


title: RNA-seq #1 of QSER1 KO Day10 EBs Batch3

description:
21_S30
QSER1KO_EB_1_Batch3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019793_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019763_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML018559_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #1 of H1 QSER1 KO hESCs Batch1

description:
Q22_P3
QSER1KO_ES_1_Batch1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS018619_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJLGG001217_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #2 of H1 WT hESCs Batch1

description:
H1_P12_18
WT_ES_2_Batch1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018543_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #1 of H1 WT hESCs Batch1

description:
H1_P12_17
WT_ES_1_Batch1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019843_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019847_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019779_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #2 of H1 QSER1/TET1 DKO hESCs Batch3

description:
5_S14
QSER1/TET1 DKO_ES_2_Batch3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019790_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #3 of H1 WT hESCs Batch2

description:
H1-WT_IGO_09130_1_S7
WT_ES_3_Batch2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018904_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018533_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018907_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #1 of H1 TET1 KO hESCs Batch2

description:
HT18-P4_IGO_09130_7_S13
TET1KO_ES_1_Batch2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019797_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #3 of H1 QSER1 KO hESCs Batch3

description:
2_S11
QSER1KO_ES_3_Batch3


title: Methyl caputre seq #1 on H1 QSER1 KOpm hESCs

description:
Methyl capture sequencing
QT66_P3_IGO_10762_1_S10

library_source: genomic

data_processing:
Raw reads alignment and CpG methylation call were performed by Bismark v0.13.0.
Genome_build: hg19
Supplementary_files_format_and_content: methylcall files are in .txt format

growth_protocol: H1 hESCs were maintained in the chemically defined feeder-free, serum-free E8 condition (Thermo Fisher Scientific, A1517001) on polystyrene plates coated with human recombinant vitronectin (Thermo Fisher Scientific, A14700) at 37°C with 5% CO2. hESCs were dissociated with 0.5 mM EDTA and split every 3–4 days at a 1:10–1:15 ratio. 10 µM Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Selleck Chemicals, S1049) was added into the culture medium when passaging or thawing cells. Cells were routinely confirmed to be mycoplasma-free by the MSKCC Antibody and Bioresource Core Facility. All experiments were approved by the Tri-SCI Embryonic Stem Cell Research Oversight Committee (ESCRO).

extract_protocol:
DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines. Two biological replicates for each genotype were submitted to the MSKCC Integrated Genomics Operation Core for library prep and sequencing.
After PicoGreen quantification and quality control by Agilent BioAnalyzer, 480-490ng of genomic DNA were sheared using a LE220-plus Focused-ultrasonicator (Covaris catalog # 500569). Sequencing libraries were prepared using the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) without PCR amplification. Post-ligation cleanup proceeded according to Illumina’s instructions with 110 µL Sample Purification Mix from the TruSeq Methyl Capture EPIC LT Library Prep Kit (Illumina catalog # FC-151-1002). After purification, 4 samples were pooled equimolar and methylome regions were captured using EPIC oligos. Capture pools were bisulfite converted and amplified with 11 cycles of PCR. Pools were sequenced on a HiSeq 4000 in a 100bp/100bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina). The average number of read pairs per sample was 29 million.
TruSeq Methyl Capture EPIC Library Prep Kit from Illumina

treatment_protocol: No treatments were applied prior to genomic DNA extraction

tag: genotype/variation


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB018825_G1]

description: blood from survivor of childhood cancer


title: RNA-seq #2 of H1 QSER1 KO hESCs Batch1

description:
Q22_P4
QSER1KO_ES_2_Batch1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL006049_G2]

description: blood from survivor of childhood cancer


title: RNA-seq #5 of H1 WT hESCs Batch3

description:
1_S10
WT_ES_5_Batch3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018671_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS019838_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019809_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB019834_G1]

description: blood from survivor of childhood cancer


title: Methyl caputre seq #2 on H1 QSER1/DNMT3B DKO hESCs

description:
Methyl capture sequencing
QD19_P4_IGO_10762_8_S58

value: Inactivating mutations in QSER1 and DNMT3B


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB019819_G1]

description: blood from survivor of childhood cancer


title: Methyl caputre seq #1 on H1 DNMT3B KO hESCs

description:
Methyl capture sequencing
D5_P3_IGO_10762_5_S55

value: Inactivating mutation in DNMT3B


title: Methyl caputre seq #1 on H1 QSER1/DNMT3B DKO hESCs

description:
Methyl capture sequencing
QD19_P3_IGO_10762_7_S57


title: Methyl caputre seq #2 on H1 QSER1/TET1 DKO hESCs

description:
Methyl capture sequencing
QT23_P4_IGO_10762_4_S13


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS019768_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018894_G1]

description: blood from survivor of childhood cancer


title: Methyl caputre seq #1 on H1 QSER1/TET1 DKO hESCs

description:
Methyl capture sequencing
QT23_P3_IGO_10762_3_S12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018505_G1]

description: blood from survivor of childhood cancer


title: Methyl caputre seq #1 on H1 WT hESCs

description:
Methyl capture sequencing
H1-WT-Cont_IGO_09589_1_S44


title: Methyl caputre seq #1 on H1 QSER1 KO hESCs

description:
Methyl capture sequencing
Q22_IGO_09589_4_S47


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018915_G1]

description: blood from survivor of childhood cancer


title: Input sample from QSER1-FLAG/TET1-V5 QSER1 KO H1 hESCs

data_processing:
FASTQ files were aligned using BWA 0.7.17.
Peak identification was performed using nonduplicate reads with Model-based Analysis of ChIP-Seq data (MACS14 1.4.2).
Genome_build: hg19
Supplementary_files_format_and_content: peak files in .txt format

extract_protocol:
ChIP-seq was performed as follows. Cells were cross-linked with 1% formaldehyde (Sigma, F1635) at 37 °C for 15 minutes and quenched with 0.125 M glycine for 5 minutes at room temperature. Fixed cells were scraped off the plates in cold PBS buffer and washed twice in cold PBS buffer. Cell pellets were obtained by centrifugation at 3,000 RPM for 5 minutes at 4 °C and frozen in liquid nitrogen immediately before transferring to the −80 °C freezer. ~25 million cells were used for one ChIP reaction. Cell pellets were thawed on ice, resuspended in 1 ml SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8) containing proteinase and phosphatase inhibitor for one reaction in an Eppendorf tube and incubated on ice for 10 minutes. Sonication was performed on a Branson Sonifier 250 with a 20% amplitude setting for 5.5 minutes (10 seconds on/off pulsing). Sonication products were spun down at 14,000 RPM at 4 °C for 10 minutes and 1 ml supernatant containing chromatin and DNA were transferred to a falcon tube containing 9 ml ChIP dilution buffer (0.01% SDS, 1.1% TritonX-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8, 167 mM NaCl) with proteinase and phosphatase inhibitor. 50 μl of Dynabeads (Life Technologies, 10009D) were added to samples and incubated at 4 °C with rotation for 1 hour. After pre-clearing, Dynabeads beads were removed and 200 μl of sample were collected as 2% input separately. 5 μg antibodies were added to the pre-cleared samples for overnight incubation at 4 °C with rotation. 200 μl Dynabeads were added into one ChIP reaction and incubated for 4–6 hours at 4 °C with rotation. Dynabeads were collected by centrifugation with 3,000 RPM at 4 °C for 5 minutes and washed in 1 ml low salt buffer (0.1% SDS, 1% TritonX-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl) for 5 minutes at 4 °C with rotations. Then beads were washed in 1 ml high salt buffer (0.1% SDS, 1% TritonX-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, 500 mM NaCl) twice and TE buffer (10 mM Tris-HCl pH 8, 1 mM EDTA) twice for 5 minutes at 4 °C with rotation. After the last wash, beads were resuspended in 250 μl elution buffer (1% SDS, 0.1 M NaHCO3) and incubated in a thermomixer: 850 RPM for 15 minutes at 60 °C. Supernatant were collected and added with 5 M NaCl for overnight decrosslinking at 65 °C. 10 μl 0.5 M EDTA, 20 μl 1 M Tris-HCl pH6.5 and 1 μl proteinase K (20 mg/ml) were added to decrosslinked product and incubated for 1 hour at 45 °C. DNA was isolated by using QIAquick PCR purification kit (Qiagen, 28104).
Libraries were prepared using the NEBNext® Ultra II DNA Library Prep Kit (NEB, E7103S) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1; NEB, E7335S). Samples were pooled and submitted to MSKCC Integrated Genomics Operation core for quality control and sequencing as follows. After PicoGreen quantification and quality control by Agilent BioAnalyzer, pooled libraries were run over one lane of a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina). The loading concentration was 2nM and a 5% spike-in of PhiX was added to the run to increase diversity and for quality control purposes. The lane yielded ~269M reads.

treatment_protocol: No treatments were applied prior to chromatin isolation and fixation.

tag: chip antibody


title: Methyl caputre seq #2 on H1 QSER1 KOpm hESCs

description:
Methyl capture sequencing
QT66_P4_IGO_10762_2_S11


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019714_G1]

description: blood from survivor of childhood cancer

tag: gender


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT018636_G1]

description: blood from survivor of childhood cancer

tag: age


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003607_G1]

description: blood from survivor of childhood cancer


title: Input sample from HUES8 WT hESCs #2

description: 44_Input_ES_WT2_TS19_A12_IGO_09116_18_S9

source_name: HUES8 human embryonic stem cells (hESCs)

tag: cell line

value: HUES8 hESCs


title: RNA-seq #4 of H1 WT hESCs Batch2

description:
KI36-WT_IGO_09130_2_S8
WT_ES_4_Batch2

tag: genotype


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS019836_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines


title: Input sample from H1 WT hESCs #2


title: Input sample from QSER1 KO H1 hESCs #1


title: Input sample from H1 WT hESCs #1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT018631_G1]

description: blood from survivor of childhood cancer

tag: alkylating agent,classic


title: Methyl caputre seq #2 on H1 DNMT3B KO hESCs

description:
Methyl capture sequencing
D5_P4_IGO_10762_6_S56


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018483_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids


title: Methyl caputre seq #2 on H1 TET1 KO hESCs

description:
Methyl capture sequencing
TET1KO_IGO_09589_2


title: Input sample from QSER1 KO H1 hESCs #2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019735_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins


title: Input sample from QSER1-FLAG/TET1-V5 WT H1 hESCs


title: Methyl caputre seq #1 on H1 TET1 KO hESCs

description:
Methyl capture sequencing
HT18_P3_IGO_09083_4_S33


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB018841_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004732_G1]

description: blood from survivor of childhood cancer

tag: asparaginase enzymes


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019784_G1]

description: blood from survivor of childhood cancer

tag: antimetabolites


title: Methyl caputre seq #2 on H1 QSER1 KO hESCs

description:
Methyl capture sequencing
Q22_P4_IGO_09798_4


title: BCOR ChIP-seq on H1 QSER1 KO hESCs

description:
processed data file: Q22_BCOR_IGO_10642_6_S6_input_peaks.bed
Q22_BCOR_IGO_10642_6_S6

value: BCOR

tag: input

value: Input sample from QSER1 KO H1 hESCs #2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018796_G1]

description: blood from survivor of childhood cancer

tag: brainrt

tag: chestrt


title: Input sample from QSER1/TET1 DKO H1 hESCs

value: Inactivating mutations in QSER1 and TET1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019731_G1]

description: blood from survivor of childhood cancer

value: Female

tag: abdominalrt

tag: pelvicrt


title: Methyl caputre seq #2 on H1 WT hESCs

description:
Methyl capture sequencing
H1-WT_IGO_09083_1_S30

tag: genotype/variation


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS003252_G1]

description: blood from survivor of childhood cancer

tag: gender

value: Male


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS018815_G1]

description: blood from survivor of childhood cancer

tag: age


title: Input sample from HUES8 WT hESCs #1

description: 43_Input_ES_WT1_TS18_A12_IGO_09116_17_S8

tag: cell line

tag: chip antibody


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018461_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018431_G1]

description: blood from survivor of childhood cancer

tag: alkylating agent,classic


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019745_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS018858_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins


title: DNMT3B ChIP-seq #2 on H1 QSER1/TET1 DKO hESCs

description:
processed data file: DNMT3B_QTDKO_input_peaks.bed
QT23_3B_IGO_11142_8_S44

tag: genotype

value: Input sample from QSER1/TET1 DKO H1 hESCs


title: DNMT3B ChIP-seq #1 on H1 QSER1/TET1 DKO hESCs

description:
processed data file: DNMT3B_QTDKO_input_peaks.bed
DNMT3B_QT23_IGO_10964_9_S9


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS017951_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids

tag: asparaginase enzymes


title: DNMT3A ChIP-seq #1 on H1 QSER1/TET1 DKO hESCs

description:
processed data file: DNMT3A_QTDKO_input_peaks.bed
DNMT3A_QT23_IGO_10964_6_S6

tag: input


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017888_G1]

description: blood from survivor of childhood cancer

tag: antimetabolites

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019730_G1]

description: blood from survivor of childhood cancer

tag: chestrt

tag: abdominalrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB019827_G1]

description: blood from survivor of childhood cancer

tag: pelvicrt


title: DNMT3A ChIP-seq #2 on H1 QSER1/TET1 DKO hESCs

description:
processed data file: DNMT3A_QTDKO_input_peaks.bed
QT23_3A_IGO_11142_4_S40


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS017897_G1]

description: blood from survivor of childhood cancer

tag: gender


title: H3K4me3 ChIP-seq #2 on H1 QSER1 KO hESCs

description:
processed data file: QSER1KO_K4_input_peaks.bed
QSER1KO_K4_P4

value: Input sample from QSER1 KO H1 hESCs #1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019749_G1]

description: blood from survivor of childhood cancer

tag: age


title: H3K4me3 ChIP-seq #1 on H1 QSER1 KO hESCs

description:
processed data file: QSER1KO_K4_input_peaks.bed
QSER1KO_K4_P3

tag: cell line


title: H3K27me3 ChIP-seq #2 on H1 QSER1 KO hESCs

description:
processed data file: QSER1KO_K27_input_peaks.bed
QSER1KO_K27_P4

tag: chip antibody


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL018740_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines


title: EZH2 ChIP-seq on H1 QSER1 KO hESCs

description:
processed data file: Q22_EZH2_IGO_10642_4_S4_input_peaks.bed
Q22_EZH2_IGO_10642_4_S4


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB018838_G1]

description: blood from survivor of childhood cancer

tag: alkylating agent,classic


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018785_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017890_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL017903_G1]

description: blood from survivor of childhood cancer


title: H3K27me3 ChIP-seq #1 on H1 QSER1 KO hESCs

description:
processed data file: QSER1KO_K27_input_peaks.bed
QSER1KO_K27_P3

tag: genotype


title: old mice CD8+ Thymocytes (CD8N) Rep1

type: RNA

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: old mice CD8+ Thymocytes (CD8N) Rep1

hyb_protocol: Slides were hybridized to  Whole Mouse Genome Microarray 4x44K v2 (Agilent) according to manufacturer’s protocols

scan_protocol: The hybridized chips were scanned with SureScan Microarray Scanner D (Agilent) and the expression level was determined with Agilent Feature Extraction software 11.5.1.1.

data_processing:
Data are extracted with Agilent Feature Extraction Software. The data were further processed with ExAtlas. See https://lgsun.irp.nia.nih.gov/exatlas for details.
The data is normalized with the following method:
(1) Take values from the columns gProcessedSignal, rProcessedSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 24 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr (adjust to UMR).

organism: Mus musculus

source_name: old mice CD8+ Thymocytes (CD8N)

label_protocol: RNA was labeled using Quick Amp Labeling two-color kit (Agilent)

extract_protocol: RNA extraction: For each array sample, the RNA was prepared from the purified thymocytes and splenocytes. The cells were processed by using the RNEasy Mini Kit (Qiagen, Valencia, CA) as the manufacturer’s instructions. Probes used were Cy3 which labeled samples and Cy5 which labeled control sample. The last one is home made. It was mixed with 50% CD4 and CD8 resting T cells and 50% stimulated T cells with anti-CD3 and anti-CD28 antibodies. Quality and quantity of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Experiments were done with C57BL/6 wild type mice obtained from Jackson Laboratory. Gropus of young mice (N = 13, age 8 wk) and old mice (N = 22, age 79 - 121 wk) included both males and females. All mice were maintained  in plastic cages under pathogen free conditions at the animal facility of National Institute on Aging at a temperature of 20-26 °C under a 12-h light-dark cycle. They were carried for and used in accordance with the National Institute of Health Guide for the Care and Use of Laboratory Animals. Mice with evidence of disease (e.g., dermatosis, gross tumors…) were not uzed in this study. Thymocyte isolation: Freshly-extracted thymi from mice of various ages were dissociated in RPMI using some syringe and forceps. Cell clumps were broken up with repeated pipetting and then poured through 70μm nylon mesh cell strainers (BD Falcon, Bedford, MA) to remove connective tissue and any remaining clumps.  The cells were washed once to remove fat cells. The remaining thymocyte population, which reflects the actual interactive environment of the thymus, was counted, washed twice in RPMI followed by PBS. Splenocyte isolation: Spleens were removed from mice and were homogenized into a single-cell suspension using RPMI buffer. Red blood cells were lysed by resuspending spleen cells in ammonium chloride-Potassium (ACK) lysis buffer and incubating for 5 min. Splenocytes were washed and resuspended in PBS buffer. B cells were removed using magnetic beads with anti-CD19 antibodies. The remaining cells were counted, washed twice in RPMI followed by PBS. Cell staining, and sorting: For mature thymocytes, CD4+ and CD8+ T cells were sorted based on Lin- (to exclude other lineages) CD44-low expression. Concerning splenocytes, CD4+ T cells were surface stained with fluorescent antibodies to CD4, CD44 and CD62L and CD8+T cells with fluorescent antibodies to CD8, CD44, and CD62L. Naïve CD4+and CD8+T-cell populations from young and old animals were sorted based on CD44low⁄ CD62Lhi expression on the BD FACS Aria.

tag: cell  type

value: old mice CD8+ Thymocytes (CD8N)

source_name: Mix of resting and activated mouse T cells

tag: biomaterial provider

value: Home-made

tag: extract protocol

value: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit.


title: H3K36me3 ChIP-seq #2 on H1 QSER1 KO hESCs

description:
processed data file: H3K36me3_Q22_input_peaks.bed
me3_Q22_2_IGO_10964_20_S20

tag: input

value: Input sample from QSER1-FLAG/TET1-V5 QSER1 KO H1 hESCs


title: H3K36me2 ChIP-seq #2 on H1 QSER1 KO hESCs

description:
processed data file: H3K36me2_Q22_input_peaks.bed
me2_Q22_2_IGO_10964_16_S16

value: Inactivating mutation in QSER1


title: old mice CD4+ Thymocytes (CD4N) Rep2

description: old mice CD4+ Thymocytes (CD4N) Rep2

source_name: old mice CD4+ Thymocytes (CD4N)

value: old mice CD4+ Thymocytes (CD4N)


title: old mice CD8+ Thymocytes (CD8N) Rep3

description: old mice CD8+ Thymocytes (CD8N) Rep3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST011273_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS017932_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017885_G1]

description: blood from survivor of childhood cancer

tag: age

tag: anthracyclines


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019848_G1]

description: blood from survivor of childhood cancer

tag: alkylating agent,classic

tag: corticosteroids


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017886_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018774_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018579_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018521_G1]

description: blood from survivor of childhood cancer


title: H3K36me3 ChIP-seq #1 on H1 QSER1 KO hESCs

description:
processed data file: H3K36me3_Q22_input_peaks.bed
me3_Q22_IGO_10964_19_S19

tag: cell line

value: H1 hESCs

tag: genotype

tag: chip antibody


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL017906_G1]

description: blood from survivor of childhood cancer


title: old mice naive CD8+ cells in spleen (SP8) Rep3

tag: cell  type

tag: biomaterial provider

tag: extract protocol


title: old mice CD8+ Thymocytes (CD8N) Rep2

description: old mice CD8+ Thymocytes (CD8N) Rep2


title: old mice CD4+ Thymocytes (CD4N) Rep1

description: old mice CD4+ Thymocytes (CD4N) Rep1


title: old mice CD4+ Thymocytes (CD4N) Rep3

description: old mice CD4+ Thymocytes (CD4N) Rep3


title: DNMT3B ChIP-seq #1 on H1 QSER1 KO hESCs

description:
processed data file: DNMT3B_QSER1KO_input_peaks.bed
Q22_DNMT3B_IGO_10642_2_S2

tag: input


title: DNMT3B ChIP-seq #2 on H1 QSER1 KO hESCs

description:
processed data file: DNMT3B_QSER1KO_input_peaks.bed
QT66_3B_IGO_11142_6_S42


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML017891_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL017920_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS017900_G1]

description: blood from survivor of childhood cancer

tag: age

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018765_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins


title: H3K36me2 ChIP-seq #1 on H1 QSER1 KO hESCs

description:
processed data file: H3K36me2_Q22_input_peaks.bed
me2_Q22_IGO_10964_15_S15

tag: cell line

tag: genotype

tag: chip antibody


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS018823_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018908_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017869_G1]

description: blood from survivor of childhood cancer


title: old mice naive CD8+ cells in spleen (SP8) Rep1

tag: cell  type

tag: biomaterial provider

tag: extract protocol


title: old mice naive CD8+ cells in spleen (SP8) Rep2


title: DNMT3A ChIP-seq #2 on H1 QSER1 KO hESCs

description:
processed data file: DNMT3A_QSER1KO_input_peaks.bed
QT66_3A_IGO_11142_2_S38

tag: input


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMEL017913_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNPCA018729_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: old mice naive CD4+ cells in spleen (SP4) Rep3


title: DNMT3A ChIP-seq #1 on H1 QSER1 KO hESCs

description:
processed data file: DNMT3A_QSER1KO_input_peaks.bed
DNMT3A_QT66_IGO_10964_4_S4


title: old mice naive CD4+ cells in spleen (SP4) Rep2


title: DNMT3A ChIP-seq #2 on H1 TET1 KO hESCs

description:
processed data file: DNMT3A_TET1KO_input_peaks.bed
HT18_3A_IGO_11142_3_S39

value: Inactivating mutation in TET1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB018830_G1]

description: blood from survivor of childhood cancer

tag: age

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids


title: TET1-V5 ChIP-seq #2 on H1 QSER1 KO hESCs

description:
processed data file: TET1_QSER1KO_input_peaks.bed
QFTV_Q38_KO_IGO_11142_12_S48

tag: cell line

tag: genotype

tag: chip antibody


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB017944_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB017940_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST017902_G1]

description: blood from survivor of childhood cancer


title: TET1-V5 ChIP-seq #1 on H1 QSER1 KO hESCs

description:
processed data file: TET1_QSER1KO_input_peaks.bed
QFTV_Q38_KO_IGO_10964_2_S2

tag: input


title: old mice naive CD4+ cells in spleen (SP4) Rep1

tag: cell  type

tag: biomaterial provider

tag: extract protocol


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017889_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt


title: young mice CD8+ Thymocytes (CD8N) Rep2

description: young mice CD8+ Thymocytes (CD8N) Rep2

source_name: young mice CD8+ Thymocytes (CD8N)

value: young mice CD8+ Thymocytes (CD8N)


title: QSER1-FLAG ChIP-seq #2 on H1 TET1 KO hESCs

description:
processed data file: QSER1_TET1KO_input_peaks.bed
QF3A_T25_KO_IGO_11142_10_S46


title: DNMT3B ChIP-seq #2 on H1 TET1 KO hESCs

description:
processed data file: DNMT3B_TET1KO_input_peaks.bed
HT18_3B_IGO_11142_7_S43


title: young mice CD8+ Thymocytes (CD8N) Rep1

description: young mice CD8+ Thymocytes (CD8N) Rep1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL017919_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018573_G1]

description: blood from survivor of childhood cancer

tag: age

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids


title: young mice CD4+ Thymocytes (CD4N) Rep1

description: young mice CD4+ Thymocytes (CD4N) Rep1

source_name: young mice CD4+ Thymocytes (CD4N)

value: young mice CD4+ Thymocytes (CD4N)


title: young mice CD4+ Thymocytes (CD4N) Rep3

description: young mice CD4+ Thymocytes (CD4N) Rep3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT017901_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins


title: QSER1-FLAG ChIP-seq #1 on H1 TET1 KO hESCs

description:
processed data file: QSER1_TET1KO_input_peaks.bed
QF3A_T25_KO_IGO_10642_10_S10

tag: cell line

tag: genotype

tag: chip antibody

tag: input


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS018802_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids


title: DNMT3B ChIP-seq #1 on H1 TET1 KO hESCs

description:
processed data file: DNMT3B_TET1KO_input_peaks.bed
DNMT3B_HT18_IGO_10964_8_S8


title: young mice naive CD8+ cells in spleen (SP8) Rep1

tag: cell  type

tag: biomaterial provider

tag: extract protocol


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJLM017912_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS018868_G1]

description: blood from survivor of childhood cancer

tag: age

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB017945_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017883_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS017899_G1]

description: blood from survivor of childhood cancer


title: young mice CD4+ Thymocytes (CD4N) Rep2

description: young mice CD4+ Thymocytes (CD4N) Rep2


title: DNMT3A ChIP-seq #1 on H1 TET1 KO hESCs

description:
processed data file: DNMT3A_TET1KO_input_peaks.bed
DNMT3A_HT18_IGO_10964_5_S5

tag: cell line

tag: genotype

tag: chip antibody

tag: input


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017925_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids


title: young mice CD8+ Thymocytes (CD8N) Rep3

description: young mice CD8+ Thymocytes (CD8N) Rep3

tag: cell  type

tag: biomaterial provider

tag: extract protocol


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018918_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018688_G1]

description: blood from survivor of childhood cancer

tag: age

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: H3K4me1 ChIP-seq #2 on HUES8 WT hESCs

description:
processed data file: H3K4me1_input_peaks.bed
41_6D_ES_WT2_H3K4me1_TS15_A12_IGO_09116_15_S6

value: HUES8 hESCs

value: Wild type sequence

value: Input sample from HUES8 WT hESCs #1 and #2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS017935_G1]

description: blood from survivor of childhood cancer

value: Female

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins


title: young mice naive CD8+ cells in spleen (SP8) Rep2


title: H3K4me1 ChIP-seq #1 on HUES8 WT hESCs

description:
processed data file: H3K4me1_input_peaks.bed
39_5D_ES_WT1_H3K4me1_TS13_A12_IGO_09116_13_S4

tag: cell line

tag: genotype

tag: chip antibody

tag: input


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018499_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids


title: young mice naive CD4+ cells in spleen (SP4) Rep1

tag: cell  type

tag: biomaterial provider

tag: extract protocol


title: young mice naive CD4+ cells in spleen (SP4) Rep2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017954_G1]

description: blood from survivor of childhood cancer

tag: gender

value: Male

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018919_G1]

description: blood from survivor of childhood cancer

tag: age

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: young mice naive CD8+ cells in spleen (SP8) Rep3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL017921_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins


title: H3K27me3 ChIP-seq #2 on H1 WT hESCs

description:
processed data file: H1_K27_input_peaks.bed
H1_K27_P4

tag: cell line

tag: genotype

tag: chip antibody

tag: input

value: Input sample from H1 WT hESCs #1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017870_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids


title: H3K27me3 ChIP-seq #1 on H1 WT hESCs

description:
processed data file: H1_K27_input_peaks.bed
H1_K27_P3


title: old mice CD8+ Thymocytes (CD8N) Rep4

description: young mice CD8+ Thymocytes (CD8N) Rep1

hyb_protocol: Slides were hybridized to  Whole Mouse Genome Microarray 8x60K (Agilent) according to manufacturer’s protocols

data_processing:
Data are extracted with Agilent Feature Extraction Software. The data were further processed with ExAtlas. See https://lgsun.irp.nia.nih.gov/exatlas for details.
The data is normalized with the following method:
(1) Take values from the columns gProcessedSignal, rProcessedSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 12 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr (adjust to UMR).

tag: cell  type

tag: biomaterial provider

tag: extract protocol


title: old mice CD8+ Thymocytes (CD8N) Rep5

description: young mice CD8+ Thymocytes (CD8N) Rep2


title: H3K27ac ChIP-seq #1 on HUES8 WT hESCs

description:
processed data file: H3K27ac_input_peaks.bed
40_5E_ES_WT_H3K27ac_TS14_A12_IGO_09116_14_S5


title: EZH2 ChIP-seq on H1 WT hESCs

description:
processed data file: H1_EZH2_IGO_10642_3_S3_input_peaks.bed
H1_EZH2_IGO_10642_3_S3

value: Input sample from H1 WT hESCs #2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017956_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017926_G1]

description: blood from survivor of childhood cancer

tag: age

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017960_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins


title: young mice naive CD4+ cells in spleen (SP4) Rep3


title: young mice CD8+ Thymocytes (CD8N) Rep4

description: young mice naive CD8+ cells in spleen (SP8) Rep1


title: young mice CD4+ Thymocytes (CD4N) Rep4

description: young mice naive CD4+ cells in spleen (SP4) Rep3


title: H3K27ac ChIP-seq #2 on HUES8 WT hESCs

description:
processed data file: H3K27ac_input_peaks.bed
42_6E_ES_WT2_H3K27ac_TS16_A12_IGO_09116_16_S7

tag: cell line

tag: genotype

tag: chip antibody

tag: input


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017881_G1]

description: blood from survivor of childhood cancer

tag: vinca alkaloids


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB017946_G1]

description: blood from survivor of childhood cancer

tag: gender


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017930_G1]

description: blood from survivor of childhood cancer

tag: asparaginase enzymes


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018504_G1]

description: blood from survivor of childhood cancer

tag: antimetabolites


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB017941_G1]

description: blood from survivor of childhood cancer

tag: brainrt


title: old mice CD8+ Thymocytes (CD8N) Rep6

description: young mice CD8+ Thymocytes (CD8N) Rep3

tag: cell  type

value: old mice CD8+ Thymocytes (CD8N)

tag: biomaterial provider

tag: extract protocol


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS017950_G1]

description: blood from survivor of childhood cancer

tag: age

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: H3K36me2 ChIP-seq #1 on H1 WT hESCs

description:
processed data file: H3K36me2_H1_input_peaks.bed
me2_H1_IGO_10964_13_S13

value: Input sample from QSER1-FLAG/TET1-V5 WT H1 hESCs


title: old mice CD4+ Thymocytes (CD4N) Rep6

description: young mice CD4+ Thymocytes (CD4N) Rep3

value: Home-made

value: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit.


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018797_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJLM018727_G1]

description: blood from survivor of childhood cancer


title: old mice CD4+ Thymocytes (CD4N) Rep4

description: young mice CD4+ Thymocytes (CD4N) Rep1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL017907_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB017939_G1]

description: blood from survivor of childhood cancer


title: H3K4me3 ChIP-seq #1 on H1 WT hESCs

description:
processed data file: H1_K4_input_peaks.bed
H1_K4_P3

tag: cell line

tag: genotype

tag: chip antibody

tag: input


title: old mice naive CD8+ cells in spleen (SP8) Rep4

description: young mice naive CD8+ cells in spleen (SP8) Rep3


title: MSC-ATRA3

city: Guang zhou

first: qi

last: Lou

state: Guang dong

address: china guangzhou

institute: sun yen san university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.3 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MSC

growth_protocol: MSCs were cultured at 37°C in 5% CO2, 5% O2 with DMEM low-glucose medium containing 20% fetal bovine serum, 2% penicillin-streptomycin and 10 µM ROCK inhibitor

extract_protocol:
RNAs were extracted from two biological replicates of cultured from wild-type BMSC incubated with control and 1μM ATRA , digested with DNAse I (AM2222, Ambion) and purified with Rneasy MinElute Spin Columns (Qiagen)
TruePrepTM DNA library Prep Kit V2 (Vazyme, TD503) was used to prepare RNA seq library following the manufacturer’s protocol

treatment_protocol: Treated with DMSO or ATRA for 48h respectively

tag: cell type

value: BM-MSCs

tag: strain

tag: treatment

value: ATRA


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017923_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: vinca alkaloids

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017962_G1]

description: blood from survivor of childhood cancer

tag: age

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017955_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins


title: H3K36me3 ChIP-seq #2 on H1 WT hESCs

description:
processed data file: H3K36me3_H1_input_peaks.bed
me3_H1_2_IGO_10964_18_S18

tag: cell line

value: H1 hESCs

tag: genotype

tag: chip antibody

tag: input


title: old mice naive CD4+ cells in spleen (SP4) Rep4

description: young mice naive CD8+ cells in spleen (SP8) Rep2

tag: cell  type

tag: biomaterial provider

tag: extract protocol


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018911_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: vinca alkaloids

tag: asparaginase enzymes

tag: antimetabolites


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCA017893_G1]

description: blood from survivor of childhood cancer

tag: age

tag: brainrt

tag: chestrt

tag: abdominalrt


title: MSC-ATRA1

tag: cell type

tag: strain

tag: treatment


title: H3K36me3 ChIP-seq #1 on H1 WT hESCs

description:
processed data file: H3K36me3_H1_input_peaks.bed
me3_H1_IGO_10964_17_S17

tag: cell line

tag: genotype


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017957_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017963_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: vinca alkaloids


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS017952_G1]

description: blood from survivor of childhood cancer

tag: asparaginase enzymes

tag: antimetabolites


title: H3K36me2 ChIP-seq #2 on H1 WT hESCs

description:
processed data file: H3K36me2_H1_input_peaks.bed
me2_H1_2_IGO_10964_14_S14

tag: chip antibody

tag: input


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS017898_G1]

description: blood from survivor of childhood cancer

tag: age

tag: brainrt

tag: chestrt

tag: abdominalrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL017917_G1]

description: blood from survivor of childhood cancer


title: MSC-DMSO2

tag: cell type

tag: strain

tag: treatment

value: DMSO


title: old mice CD4+ Thymocytes (CD4N) Rep5

description: young mice CD4+ Thymocytes (CD4N) Rep2

tag: cell  type

value: old mice CD4+ Thymocytes (CD4N)

tag: biomaterial provider

tag: extract protocol


title: young mice naive CD8+ cells in spleen (SP8) Rep4

description: young mice naive CD4+ cells in spleen (SP4) Rep2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL017918_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins

tag: pelvicrt


title: MSC-DMSO1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017961_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: vinca alkaloids

tag: asparaginase enzymes

tag: antimetabolites


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041935_G1]

description: blood from survivor of childhood cancer

tag: age

tag: brainrt

tag: chestrt


title: QSER1-FLAG ChIP-seq #2 on H1 WT hESCs

description:
processed data file: QSER1_WT_input_peaks.bed
QF3A_WT_IGO_11142_9_S45

tag: cell line

tag: genotype

tag: chip antibody

tag: input


title: SV Single-Cell RNA-Seq

city: Yayoi, Bunkyo-ku

first: Yoshiakira

last: Kanai

state: Tokyo

country: Japan

institute: The University of Tokyo

data_processing:
Sequence reads in Fastq format were generated from Illunina basecalls using Illumina's bcl2fastq (version 2.17).
Sequence reads were aligned to Ensembl GRCh38 genome build and gene models retrieved from Ensembl 91 using STAR (v 2.5.2b).
Aligned reads were counted whithin exons using subread (verion 1.4.6)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: counts of genes

source_name: Sertoli valve of W/Wv mouse

growth_protocol: 7-week-old W/Wv mice were purchased from SLC Japan.

extract_protocol:
RNA-Seq libraries were prepared following the iCELL8 Single-Cell protocol (WaferGen Biosystems).
Nextera XT Library Preparation (Illumina) adapted for iCELL8 Single-Cell libraries (WaferGen Biosystems)

tag: strain

value: W/Wv mouse

tag: tissue

value: testis


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041894_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: abdominalrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017929_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins

tag: pelvicrt


title: young mice naive CD4+ cells in spleen (SP4) Rep4

description: young mice naive CD4+ cells in spleen (SP4) Rep1

tag: cell  type

tag: biomaterial provider

tag: extract protocol


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018515_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: age

tag: vinca alkaloids

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt


title: DNMT3B ChIP-seq #2 on H1 WT hESCs

description:
processed data file: DNMT3B_WT_input_peaks.bed
H1_3B_IGO_11142_5_S41

tag: cell line

tag: genotype

value: Wild type sequence

tag: chip antibody

tag: input


title: H3K4me3 ChIP-seq #2 on H1 WT hESCs

description:
processed data file: H1_K4_input_peaks.bed
H1_K4_P4


title: SE_Combi_2

city: Utrecht

first: Frank

last: van Leeuwen

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

data_processing:
Raw data (raw reads) of FASTQ format were processed through fastp
alignment to reference genome (hg38) using the Spliced Transcripts Alignment to a Reference (STAR) software
FeatureCounts was used to count the read numbers mapped of each gene.
FPKM of each gene was calculated

source_name: ALL-cell line

growth_protocol: Cells were grown in RPMI (Invitrogen, Thermo Fisher Scientific, Breda, the Netherlands), supplemented with 10% fetal bovine serum (FBS, Greiner Bio-One, Essen, Germany) and 1% penicillin/streptomycin solution (P/S) (Invitrogen) at a cell density between 0.25 and 3x106 cells per milliliter.

extract_protocol:
mRNA was purified from cell cultures using a RNeasy minikit (#74106, Qiagen).
RNA sequencing and data analysis was performed by NovoGene (Cambridge, UK) on triplicate samples.
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

treatment_protocol: Nalm6 and Sem cells were either left untreated or treated for 24 h 10um Ibrutinib, 0,5 IU/ml Asparaginase or a combination of both drugs

value: Sem

tag: treatment

value: 10uM Ibrutinib and 1 IU/ml Asparaginase


title: SE_Combi_3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS042766_G1]

description: blood from survivor of childhood cancer

value: Female

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: chestrt

tag: abdominalrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL017904_G1]

description: blood from survivor of childhood cancer

value: Male

tag: epipodophyllotoxins

tag: pelvicrt


title: DNMT3B ChIP-seq #1 on H1 WT hESCs

description:
processed data file: DNMT3B_WT_input_peaks.bed
DNMT3B_WT_IGO_10964_7_S7


title: MSC-ATRA2

tag: cell type

tag: strain


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042744_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: age

tag: vinca alkaloids

tag: asparaginase enzymes


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042689_G1]

description: blood from survivor of childhood cancer

tag: antimetabolites

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS042714_G1]

description: blood from survivor of childhood cancer


title: BCOR ChIP-seq on H1 WT hESCs

description:
processed data file: H1_BCOR_IGO_10642_5_S5_input_peaks.bed
H1_BCOR_IGO_10642_5_S5

tag: cell line

tag: genotype

tag: chip antibody

value: BCOR

tag: input

value: Input sample from H1 WT hESCs #2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003458_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids


title: DNMT3A ChIP-seq #1 on H1 WT hESCs

description:
processed data file: DNMT3A_WT_input_peaks.bed
DNMT3A_WT_IGO_10964_3_S3

value: Input sample from QSER1-FLAG/TET1-V5 WT H1 hESCs


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042696_G1]

description: blood from survivor of childhood cancer

tag: epipodophyllotoxins

tag: chestrt

tag: abdominalrt


title: SE_Asn_3

tag: treatment

value: 1 IU/ml Asparaginase


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB018831_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: pelvicrt


title: SE_Asn_2


title: TET1-V5 ChIP-seq #2 on H1 WT hESCs

description:
processed data file: TET1_WT_input_peaks.bed
QFTV_Q14_WT_IGO_11142_11_S47


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017922_G1]

description: blood from survivor of childhood cancer

tag: age

tag: vinca alkaloids


title: MSC-DMSO3

tag: cell type

tag: strain


title: SE_Combi_1

tag: cell line


title: DNMT3A ChIP-seq #2 on H1 WT hESCs

description:
processed data file: DNMT3A_WT_input_peaks.bed
H1_3A_IGO_11142_1_S37

tag: genotype


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042086_G1]

description: blood from survivor of childhood cancer

tag: asparaginase enzymes

tag: antimetabolites

tag: brainrt


title: TET1-V5 ChIP-seq #1 on H1 WT hESCs

description:
processed data file: TET1_WT_input_peaks.bed
QFTV_Q14_WT_IGO_10964_1_S1

tag: chip antibody

tag: input


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043130_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins


title: SE_Ibr_3

tag: treatment

value: 10uM Ibrutinib


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041929_G1]

description: blood from survivor of childhood cancer

tag: gender

tag: chestrt

tag: abdominalrt

tag: pelvicrt


title: QSER1-FLAG ChIP-seq #1 on H1 WT hESCs

description:
processed data file: QSER1_WT_input_peaks.bed
QF3A_T90_WT_IGO_10642_9_S9


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042653_G1]

description: blood from survivor of childhood cancer

tag: age

tag: vinca alkaloids


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042765_G1]

description: blood from survivor of childhood cancer


title: SE_Ibr_2

tag: cell line


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042704_G1]

description: blood from survivor of childhood cancer

tag: asparaginase enzymes


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042662_G1]

description: blood from survivor of childhood cancer

tag: antimetabolites


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042496_G1]

description: blood from survivor of childhood cancer

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT042716_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041942_G1]

description: blood from survivor of childhood cancer


title: SE_Asn_1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041022_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042497_G1]

description: blood from survivor of childhood cancer


title: SE_Ctr_1

value: untreated


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041851_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB041689_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041002_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041891_G1]

description: blood from survivor of childhood cancer


title: SE_Ibr_1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042105_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041856_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042486_G1]

description: blood from survivor of childhood cancer


title: SE_Ctr_3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS042127_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041979_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005343_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL040973_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041958_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042761_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019655_G1]

description: blood from survivor of childhood cancer


title: SE_Ctr_2


title: N6_Asn_3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041963_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041236_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT042487_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042652_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041030_G1]

description: blood from survivor of childhood cancer


title: N6_Combi_3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042064_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042100_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004196_G1]

description: blood from survivor of childhood cancer


title: N6_Combi_2


title: N6_Combi_1


title: N6_Ctr_3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042004_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005347_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041908_G1]

description: blood from survivor of childhood cancer


title: N6_Ctr_1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS041986_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041198_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042618_G1]

description: blood from survivor of childhood cancer


title: N6_Asn_2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042026_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS040991_G1]

description: blood from survivor of childhood cancer


title: N6_Asn_1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041461_G1]

description: blood from survivor of childhood cancer


title: N6_Ibr_2


title: N6_Ibr_3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041208_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041970_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042096_G1]

description: blood from survivor of childhood cancer


title: N6_Ibr_1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041972_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041435_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041292_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041254_G1]

description: blood from survivor of childhood cancer


title: C3

first: yaqiong

last: li

address: youanmenwai

institute: Capital Medical University

data_processing:
Image processing and base recognition were performed using Solexa pipeline software (Illumina, version 1.8).
The RNA sequencing reads were aligned to the human reference genome GRCh37 (also known as hg19) using HISAT2 (version 2.1.0) with default parameters.
The normalized expression value, fragments per kilobase of transcript per million mapped reads (FPKM), was calculated for each gene using StringTie (version 1.3.3).
FPKM at the gene level and transcript level were calculated using Ballgown (version 2.8.4). Differentially expressed genes with a fold change≥1.5, p-value ≤ 0.05 and FPKM≥0.5 were screened and retained in groups.
Gene Set Enrichment Analysis (GSEA) for the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analysis was analysed using GSEA (version 2.2.4).
Genome_build: GRCh37
Supplementary_files_format_and_content: The Express file format is xlsx, which analyses the expression of gene and transcript; the Diff_express file format is xlsx, which analyses all differentially expressed genes /transcripts and differentially expressed genes /transcripts; the Pathway_Report file format includes doc, pdf, png, html, xls, txt, which analyses the upregulated and downregulated pathways of differentially expressed genes; the GO_Report file format includes doc, pdf, png, html, xls, txt, which analyses the upregulated and downregulated  differentially expressed genes; the Plots file format includes pdf, png, txt, which analyses differentially expressed genes; the GSEA file format includes pdf, png, xls, html, which analyses differentially expressed genes in biological processes, cellular components,molecular functions and KEGG pathway.

source_name: hepatocyte-like cells

growth_protocol: hASCs from lean donors (body mass index, BMI<24k/m2) and obese donors (BMI>30 kg/m2) were separately cultured and differentiated to HLCs. Briefly, hASCs were plated  on collagen I-coated dishes and cultured in DMEM/F-12 (Invitrogen, Grand Island, NY, USA)supplemented with 10% foetal bovine serum (FBS) (Gibco, Rockville, MD, USA), 100 U/ml penicillin and 100 µg/ml streptomycin (Invitrogen) at 37°C with 5% CO2. Once the cells reached 90% confluence, they were washed twice with PBS and incubated with serum-free DMEM/F-12 medium for 48 hrs. The cells were incubated with DMEM/F-12 containing 0.5 mg/ml  bovine serum albumin (BSA; Sigma-Aldrich, St. Louis, MO, USA) and 100 ng/ml activin A (Peprotech, Rocky Hill, NJ, USA) for 72 hrs; 1% insulin–transferrin–selenium (ITS) (Sigma-Aldrich) was added to the medium beginning at the second day. At day 5, the medium was changed to MEM/NEAA (Invitrogen), supplemented with 0.5 mg/ml BSA, 1% ITS, 20 ng/ml bone morphogenetic protein 2 (BMP2) (Peprotech) and 30 ng/ml fibroblast growth factor 4 (FGF4) (Peprotech) for 5 days. At day 10, the cells were further treated with 20 ng/ml hepatocyte growth factor (HGF) (Peprotech) for 5 days and with 20 ng/ml HGF, 10 ng/ml oncostatin M (OSM) (Peprotech) plus 106 M dexamethasone (DEX) (Sigma-Aldrich) treatment for another 5 days. The differentiation media were changed every 2 days. Once the hASC-HLCs were differentiated, these cells were harvested.

extract_protocol:
RNA was harvested using Trizol reagent and the KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used with 1-2 ug of total RNA for the construction of sequencing libraries.
Approximately 1-2 µg of total RNA isolated from each independent biological sample was processed with a Ribo-Zero Magnetic Gold kit (Epicentre Biotechnologies) to reduce ribosomal RNA abundance. Sequencing libraries were then constructed using the KAPA Stranded RNA-Seq Library Prep kit (Illumina). The quality of the constructed sequencing libraries was analysed using an Agilent 2100 Bioanalyzer. Quantitative real-time PCR was performed to quantify the sequencing libraries, and the mixed different sample libraries were sequenced using an Illumina HiSeq 4000 platform.

tag: cell type

value: adipose stem cell-derived hepatocyte-like cells

tag: passages

tag: donor diagnosis

value: lean control


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL041039_G1]

description: blood from survivor of childhood cancer

tag: anthracyclines

tag: alkylating agent,classic


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018944_G1]

description: blood from survivor of childhood cancer

tag: corticosteroids

tag: epipodophyllotoxins


title: C2


title: N6_Ctr_2

tag: treatment


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS001304_G2]

description: blood from survivor of childhood cancer

tag: gender

tag: chestrt


title: FD4

value: obese


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042539_G1]

description: blood from survivor of childhood cancer

tag: abdominalrt

tag: pelvicrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019306_G1]

description: blood from survivor of childhood cancer

tag: age

tag: vinca alkaloids


title: FD1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041918_G1]

description: blood from survivor of childhood cancer

tag: asparaginase enzymes


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042115_G1]

description: blood from survivor of childhood cancer

tag: antimetabolites


title: C1


title: FD3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041229_G1]

description: blood from survivor of childhood cancer

tag: brainrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041917_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041953_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST042002_G1]

description: blood from survivor of childhood cancer


title: VDr81

city: New Haven

first: Marc

last: Hammarlund

state: Connecticut

address: 295 Congress Ave

department: Genetics

institute: Yale University

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
VDr81_ATGACAGG

data_processing:
fastq files were aligned to the WS274 genome using STAR on default settings, and duplicate reads were removed using samtools markup
BAM files resulting from the alignments were summarized to genes using the featureCounts tool
Genome_build: WS274
Supplementary_files_format_and_content: tab-delimited text file includes raw counts from featureCounts

organism: Caenorhabditis elegans

source_name: FACS C. elegans neurons

growth_protocol:
Worms were grown on 8P nutrient agar 150 mm plates seeded with E. coli strain NA22
Sorting protocol: Fluorescence Activated Cell Sorting (FACS) was performed on a BD FACSAria™ III equipped with a 70-micron diameter nozzle. Cells were sorted into Trizol reagent LS

extract_protocol:
RNA was isolated using chloroform extraction
Libraries were prepared using Tecan SoLo Ovation RNAseq library

tag: tissue/cell type

value: FACS isolated VD Neurons


title: VDr77

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
VDr77_AACTCGGA


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042109_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018957_G1]

description: blood from survivor of childhood cancer


title: VDr79

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
VDr79_ACAACAGC


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041257_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041944_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019468_G1]

description: blood from survivor of childhood cancer


title: VDr78

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
VDr78_GTCGAGAA


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018985_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041873_G1]

description: blood from survivor of childhood cancer


title: Refr29

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
Refr29_ATGACAGG

value: FACS isolated all viable-cell reference


title: Refr28

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
Refr28_AACGCCTT


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041971_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041455_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041186_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042080_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041875_G1]

description: blood from survivor of childhood cancer


title: Rab3r12

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
Rab3r12_GTCGAGAA

value: FACS isolated Pan-Neuronal reference sample


title: Refr27

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
Refr27_CCTATACC


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019044_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042087_G1]

description: blood from survivor of childhood cancer


title: Rab3r10

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
Rab3r10_CGTCTAAC


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042507_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041325_G1]

description: blood from survivor of childhood cancer


title: Rab3r11

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
Rab3r11_AACTCGGA


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019049_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM041025_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018987_G1]

description: blood from survivor of childhood cancer


title: PVDr63

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
PVDr63_TAGGAGCT

value: FACS isolated PVD Neurons


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018974_G1]

description: blood from survivor of childhood cancer


title: Refr30

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
Refr30_GCACACAA


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS019512_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJST042112_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019128_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019486_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018943_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019348_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019069_G1]

description: blood from survivor of childhood cancer


title: PVDr62

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
PVDr62_AGGCAATG


title: DDr84

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
DDr84_CTCCTAGT

value: FACS isolated DD Neurons


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS019604_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL019430_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019131_G1]

description: blood from survivor of childhood cancer


title: AWBr54

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AWBr54_TCGTGCAT

value: FACS isolated AWB Neurons


title: DDr86

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
DDr86_GACTACGA


title: Rab3r1

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
Rab3r1_CGCTACAT


title: Rab3r7

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
Rab3r7_AATCCAGC


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS019602_G1]

description: blood from survivor of childhood cancer

value: Female


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019305_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML018553_G1]

description: blood from survivor of childhood cancer

value: Male


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018982_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019496_G1]

description: blood from survivor of childhood cancer


title: AWBr52

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AWBr52_CCACATTG


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019472_G1]

description: blood from survivor of childhood cancer


title: AWBr51

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AWBr51_CAACACAG


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019134_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018941_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019473_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018420_G1]

description: blood from survivor of childhood cancer


title: DDr83

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
DDr83_GCACACAA


title: AWAr20

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AWAr20_CTAAGACC

value: FACS isolated AWA Neurons


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS018614_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019250_G1]

description: blood from survivor of childhood cancer


title: AWBr53

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AWBr53_TAGTGCCA


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019263_G1]

description: blood from survivor of childhood cancer


title: AWBr50

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AWBr50_TGCTGTGA


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019150_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB019587_G1]

description: blood from survivor of childhood cancer


title: AWAr19

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AWAr19_ACGGACTT


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019641_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018510_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS001207_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018668_G1]

description: blood from survivor of childhood cancer


title: AWAr18

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AWAr18_AATCCAGC


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019456_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML019107_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS001204_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019017_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019359_G1]

description: blood from survivor of childhood cancer


title: AWAr17

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AWAr17_CGCTACAT


title: AVGr45

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AVGr45_TGACAACC

value: FACS isolated AVG Neurons


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST019244_G1]

description: blood from survivor of childhood cancer


title: AVGr43

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AVGr43_ACGCTTCT


title: AVEr42

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AVEr42_AAGGACCA

value: FACS isolated AVE Neurons


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019175_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018680_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019271_G1]

description: blood from survivor of childhood cancer


title: ASGr16

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
ASGr16_CCAACACT

value: FACS isolated ASG Neurons


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGICT018824_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019056_G1]

description: blood from survivor of childhood cancer


title: AVGr44

description:
Library built using SoLo Ovation RNAseq kit from Tecan Genomics
AVGr44_CTATCCAC


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL006047_G2]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018952_G1]

description: blood from survivor of childhood cancer