title: WT_EDL_3805657

description:
Library name: 1088141_1_1
4133.9869.1088141.S33.W101102

tag: age

tag: age unit

tag: animal id

tag: fast time

value: Fasted 18h

value: M

tag: genotype

value: WT

value: Cdh15 (Mus musculus)

value: muscle

tag: tissue details


title: SJNHL019497_201496850182_R03C01

status: Public on Jan 13 2026

type: genomic

city: Memphis

first: Zhaoming

last: Wang

address: 262 Danny Thomas Place

country: USA

institute: St. Jude Children's Research Hospital

description:
201496850182_R03C01
blood from survivor of childhood cancer and control

hyb_protocol: Bisulfite-converted DNA was processed by following the Illumina Infinium Methylation Assay protocol for hybridization to MethylationEPIC BeadChips.

scan_protocol: Scanning used the Illumina HiScan system followed the Illumina Infinium Methylation Assay protocol.

data_processing: Genome-wide DNAm data were generated using Illumina Infinium MethylationEPIC BeadChip v1 (Illumina, San Diego, CA, USA), with DNA extracted from peripheral blood mononuclear cells (PBMCs) or saliva. Preprocessing was conducted using the minfi package in R, following established quality control procedures including a detection p-value ≤ 0.01. CpGs were excluded if they were located on sex chromosomes, contained single nucleotide polymorphisms (SNPs), or were previously identified as cross-reactive or non-specific. Quantile normalization was applied at the probe level to ensure comparability across samples.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA derived from blood samples from survivor of childhood cancer and community control

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA (250 ng per sample) were treated with bisulfite using the Zymo EZ DNA Methylation Kit under the following thermos-cycling conditions: 16 cycles: 95 degrees Celsius for 30 sec, 50 degrees Celsius for 1 hour. Following bisulfite treatment, DNA samples were desulphonated, column purified, then eluted using 12 µl of elution buffer (Zymo Research Corp.). Treating DNA with sodium bisulfite selectively converts cytosine to uracil but preserves 5-methylcytosine, which is immune from deamination.

tag: tissue

value: peripheral blood mononuclear cells

tag: Sex

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Non-Hodgkin lymphoma

tag: average dose to whole heart, cgy

tag: race group

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: Panc-1_control medium_replicate_1

type: RNA

city: Tokyo

first: Junjiro

last: Yoshida

address: 3-14-23 Kamiosaki, Shinagawa-ku

country: Japan

institute: Institute of Microbial Chemistry

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Ver.3.0 Microarray (Agilent, G4851C) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61×21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid 072363_D_F_20200924) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization was performed using Agilent GeneSpring GX 14.9.1.

molecule: total RNA

source_name: Panc-1, control medium, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the RNeasy Micro Kit (QIAGEN) according to the manufacturer’s instructions. RNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Conditioned medium (CAF) from pancreatic cancer-associated fibroblast cells (CAFs) was prepared by culturing the cells at a density of 1×10⁵ cells/mL in 10 cm dishes containing 1% dialyzed FBS (D-FBS) for 48 h, followed by centrifugation to remove debris. Panc-1, pancreatic cancer cell line, cells were cultured in control medium (DMEM with 1% D-FBS), CM of CAFs, or DMEM with 10% FBS for three consecutive cycles of 3 days culture.

tag: tumor

value: Pancreatic ductal adenocarcinoma

tag: cell line

tag: treatment

value: Control medium


title: SJHL018655_201496850182_R01C01

description:
201496850182_R01C01
blood from survivor of childhood cancer and control

tag: age

value: male

value: Hodgkin lymphoma

value: Black


title: Mouse Liver, Mtarc1 homozygous KO CDAHFD, Sample 6

type: SRA

city: Cambridge

first: Mark

last: Chaffin

state: MA

address: 75 Ames Street

department: Cardiovascular Disease Initiative

institute: Broad Institute of MIT and Harvard

description: Library name: 11072

library_source: transcriptomic

data_processing:
FASTQ files were trimmed for the Illumina universal adapter using cutadapt v3.5 and mapped to GENCODE M30 (GRCm39) reference using salmon 1.4.0 with the following parameters (-l A --validateMappings --gcBias --numGibbsSamples 20)
Gene counts were collapsed from the transcript to the gene level using the summarizeToGene() function in the R package tximeta.
Assembly: mm39
Supplementary files format and content: Tab delimited file containing the salmon estimated counts

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat# 74106, Qiagen) according to the manufacturer’s protocol
RNA samples were quantified using Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA). RNA sequencing libraries were prepared using the NEB Next Ultra II RNA Library Prep for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA).

treatment_protocol: Mice on choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD)  were treated for 2 weeks prior to RNA extraction

value: Liver

value: Mtarc1 Homozygous KO

tag: diet

value: CDAHFD


title: CUTRUN_cDC1_H3K9me3

city: New York City

first: Eduardo

last: Esteva

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

library_source: genomic

data_processing:
Basecalls performed using CASAVA
All the reads were mapped using bowtie2
Calculating insert size and standard deviation performed using Picard tools, Peak calling was performed using MACS
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Assembly: mm10
Supplementary files format and content: BigWig (coverage for mapped reads)
Library strategy: CUT&RUN

source_name: FL-BMDC

growth_protocol: The murine progenitor HoxB8-FL cell line (Redecke et al, PMC4131762) was maintained in the progenitor state by culturing in RPMI supplemented with 10% FCS, 10% B16-Flt3L supernatant, 1% L-glutamine, 1% penicillin-streptomycin, and 10 μM β-estradiol (Sigma-Aldrich). For FL-BMDC cultures, primary mouse bone marrow cells were plated in DMEM supplemented with 10% FBS, 10% B16-Flt3L supernatant, 1% L-glutamine, 1% sodium pyruvate, 1% MEM-NEAA, 1% penicillin-streptomycin, and 55 μM 2-mercaptoethanol. Cells were cultured at 37°C for 8 days without replating and collected by scraping the bottom of the well.

extract_protocol:
CUT&RUN was performed on ~3x105 sort-purified cells using the CUTANA ChIC/CUT&RUN Kit (Epicypher) according to manufacturer protocol. Briefly, cells were permeabilized with buffer containing 0.05% digitonin. After cells were bound to activated Concanavalin A (ConA)-coated beads, cells were bound with 4 μg of the following antibodies (or 0.5 μg for H3K4me3), which was used to guide cleavage by pAG-MNase: anti-histone H3K4me3 mixed monoclonal (Epicypher), anti-histone H3K4me1 polyclonal (Abcam), anti-histone H3K9me3 polyclonal (Abcam), anti-histone H3K27Ac (Abcam), and anti-histone H3K27me3 (Millipore).
Libraries were prepared with NEBNext Ultra II Library Prep Kit.

treatment_protocol: cDC1s, cDC2s and pDCs were purified from FL-BMDC cultures using a FACSAria II (BD Biosciences) at the Cytometry & Cell Sorting Laboratory at NYUSoM. Flow cytometry was performed on sorted samples to confirm purity > 95% for populations of interest. cDC1s = Live singlets CD11c+ MHC-II+ B220- CD11b+ CD24+, cDC2s = Live singlets CD11c+ MHC-II+ B220- CD11b+ CD24-, pDCs = Live singlets CD11c+ MHC-II- B220+ Siglec-H+.

value: FL-BMDC

tag: cell type


title: CUTRUN_undiff_H3K9me3

value: Undifferentiated


title: SJCNS018590_201496850117_R07C01

description:
201496850117_R07C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)


title: WT_EDL_3817948

city: Tarrytown

first: Michael

last: Stec

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

description:
Library name: 1088143_1_1
4133.9869.1088143.S33.W101102

data_processing:
OmicSoft Studio Server Version 10.0
Reads were mapped to mm10 using OmicSoft Studio RNA-seq pipeline (Parameters- Penalty=2, IndelPenalty=2, DetectIndels=True, MaxMiddleInsertionSize=12, MaxMiddleDeletionSize=1000 , MaxEndInsertionSize=12, MaxEndDeletionSize=12, MinDistalEndSize=3, ExcludeNonUniqueMapping=False, ReportCutoff=10, InsertSizeStandardDeviation=40, ExpectedInsertSize=300,  InsertOnSameStrand=False, InsertOnDifferentStrand=True)
Read count extraction and normalization were performed using OmicSoft Studio RNAseq-Pipeline (Parameters: AutoTrimUtr=True, CountStrandedReads=False, CountReverseStrandedReads=True)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts generated for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample
Supplementary files format and content: tab-delimited text file includes the annotation for each GeneID

molecule: polyA RNA

source_name: muscle

extract_protocol:
MagMax
KAPA_Stranded_mRNA-Seq

tag: age unit

value: days

tag: animal id

tag: fast time

value: Fasted 18h

tag: gender

value: M

tag: genotype

value: WT

tag: strain

tag: target gene

value: Cdh15 (Mus musculus)

value: muscle

tag: tissue details

value: EDL


title: SJNHL018777_201496850182_R02C01

description:
201496850182_R02C01
blood from survivor of childhood cancer and control

tag: tissue

value: peripheral blood mononuclear cells

tag: Sex

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Non-Hodgkin lymphoma

tag: average dose to whole heart, cgy

tag: race group

value: White

tag: base line visit start date


title: Mouse Liver, Mtarc1 homozygous KO CDAHFD, Sample 3

description: Library name: 11001

value: Liver

value: Mtarc1 Homozygous KO

tag: diet


title: Mouse Liver, Mtarc1 homozygous KO CDAHFD, Sample 2

description: Library name: 9988

value: CDAHFD


title: SJWLM018902_201496850117_R06C01

description:
201496850117_R06C01
blood from survivor of childhood cancer and control

tag: age

value: Wilms tumor

tag: base line visit finish

tag: age at death


title: WT_Tibialis_3793553

description:
Library name: 1088136_1_1
4133.9869.1088136.S33.W101102

tag: age unit

tag: animal id

tag: fast time

tag: gender

value: Tibialis


title: WT_EDL_3793543

description:
Library name: 1088138_1_1
4133.9869.1088138.S33.W101102

value: days

tag: genotype

tag: strain

tag: target gene

tag: tissue details


title: Cdh15 KO_Tibialis_3805666

description:
Library name: 1088135_1_1
4133.9869.1088135.S33.W101102

value: Fasted 18h

value: Cdh15 KO

tag: tissue


title: Mouse Liver, Mtarc1 heterozygous KO CDAHFD, Sample 6

description: Library name: 11071

value: Mtarc1 Heterozygous KO


title: CUTRUN_pDC_H3K4me3

value: FL-BMDC

tag: cell type

value: pDC


title: CUTRUN_pDC_H3K4me1


title: CUTRUN_cDC2_H3K4me1


title: Mouse Liver, Mtarc1 homozygous KO CDAHFD, Sample 4

description: Library name: 11067


title: CUTRUN_cDC1_H3K4me1


title: CUTRUN_cDC2_H3K4me3


title: Cdh15 KO_EDL_3817943

description:
Library name: 1088140_1_1
4133.9869.1088140.S33.W101102

value: M

value: Cdh15 (Mus musculus)

value: muscle

value: EDL


title: Mouse Liver, Mtarc1 heterozygous KO CDAHFD, Sample 4

description: Library name: 11002


title: SJEWS018616_201496850117_R01C01

description:
201496850117_R01C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: Sex

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Ewing sarcoma family of tumors

tag: average dose to whole heart, cgy

value: Other


title: CUTRUN_cDC1_H3K4me3


title: WT_Tibialis_3817948

description:
Library name: 1088131_1_1
4133.9869.1088131.S33.W101102

tag: age

value: WT


title: SJEWS018620_201496850117_R04C01

description:
201496850117_R04C01
blood from survivor of childhood cancer and control

value: male

tag: race group

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: Mouse Liver, Mtarc1 homozygous KO CDAHFD, Sample 5

description: Library name: 11070

value: Liver

value: Mtarc1 Homozygous KO

tag: diet

value: CDAHFD


title: SJNPC019801_201496850117_R02C01

description:
201496850117_R02C01
blood from survivor of childhood cancer and control

value: Carcinoma

value: Black


title: Mouse Liver, Mtarc1 heterozygous KO CDAHFD, Sample 5

description: Library name: 11063

tag: genotype

value: Mtarc1 Heterozygous KO


title: CUTRUN_undiff_H3K4me3

tag: cell line

value: Undifferentiated


title: Cdh15 KO_Tibialis_3805676

description:
Library name: 1088134_1_1
4133.9869.1088134.S33.W101102

tag: age unit

value: days

tag: animal id

tag: fast time

value: Fasted 18h

tag: gender

value: M

value: Cdh15 KO

tag: strain

tag: target gene

value: Cdh15 (Mus musculus)

value: muscle

value: Tibialis


title: Mouse Liver, Mtarc1 heterozygous KO CDAHFD, Sample 7

description: Library name: 11142

tag: tissue


title: Cdh15 KO_EDL_3793546

description:
Library name: 1088139_1_1
4133.9869.1088139.S33.W101102

tag: tissue details

value: EDL


title: SJRHB019583_201496850117_R03C01

description:
201496850117_R03C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: Sex

value: male

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Rhabdomyosarcoma

tag: average dose to whole heart, cgy


title: SJEWS018607_201496850117_R05C01

description:
201496850117_R05C01
blood from survivor of childhood cancer and control

tag: age

value: Ewing sarcoma family of tumors

tag: race group

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: Mouse Liver, Mtarc1 heterozygous KO CDAHFD, Sample 3

description: Library name: 9989

value: Liver

tag: genotype

tag: diet

value: CDAHFD


title: SJRB018829_201496850116_R07C01

description:
201496850116_R07C01
blood from survivor of childhood cancer and control

value: female

value: Retinoblastoma


title: Mouse Liver, Mtarc1 homozygous KO CDAHFD, Sample 1

description: Library name: 9975

value: Mtarc1 Homozygous KO


title: Cdh15 KO_EDL_3779417

description:
Library name: 1088137_1_1
4133.9869.1088137.S33.W101102

tag: age unit

value: days

tag: animal id

tag: fast time

value: Fasted 18h

tag: gender

value: M


title: SJNHL018775_201496850116_R08C01

description:
201496850116_R08C01
blood from survivor of childhood cancer and control

tag: tissue

value: Non-Hodgkin lymphoma


title: Mouse Liver, Mtarc1 heterozygous KO CDAHFD, Sample 2

description: Library name: 9968

value: Mtarc1 Heterozygous KO


title: SJRHB018847_201496850116_R05C01

description:
201496850116_R05C01
blood from survivor of childhood cancer and control

tag: Sex


title: RNA_SMC3KO_cDC1_CpGAB_02

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq, Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools, bedgraph to bigwig performed using bedGraphToBigWig v4
Assembly: mm10
Supplementary files format and content: BigWig (coverage for mapped reads)

growth_protocol: Primary mouse bone marrow cells were plated in DMEM supplemented with 10% FBS, 10% B16-Flt3L supernatant, 1% L-glutamine, 1% sodium pyruvate, 1% MEM-NEAA, 1% penicillin-streptomycin, and 55 μM 2-mercaptoethanol. Cells were cultured at 37°C for 8 days without replating and collected by scraping the bottom of the well. To induce recombination of the floxed Smc3 allele in FL-BMDC cultures from R26CreER/+ Smc3fl/fl mice, 4-hydroxytamoxifen (4-OHT) (Sigma-Aldrich) was spiked into cultures at day 3 of differentiation to a final concentration of 500 nM.

extract_protocol:
RNA was extracted from up to 5x104 sort-purified cells using the QIAGEN RNeasy Mini Kit and the accompanying RNase-Free DNase Set according to the manufacturer protocol.
cDNA libraries were prepared using the low input Clontech SMART-Seq HT with Nxt HT kit according to the manufacturer protocol.

treatment_protocol: For stimulated samples, FL-BMDC cultures were treated with 1 μM CpG-A/ODN2216 (InvivoGen) and 1 μM CpG-B/ODN1668 for 6 hours. Successful cDC activation was confirmed by flow cytometric analysis of CD69 upregulation. cDC1s, cDC2s and pDCs were purified from FL-BMDC cultures using a FACSAria II (BD Biosciences) at the Cytometry & Cell Sorting Laboratory at NYUSoM. Flow cytometry was performed on sorted samples to confirm purity > 95% for populations of interest. cDC1s = Live singlets CD11c+ MHC-II+ B220- CD11b+ CD24+, cDC2s = Live singlets CD11c+ MHC-II+ B220- CD11b+ CD24-, pDCs = Live singlets CD11c+ MHC-II- B220+ Siglec-H+.

value: FL-BMDC

tag: cell type

value: Rosa26CreER/+ Smc3fl/fl

tag: treatment

value: CpG-A+CpG-B


title: Mouse Liver, Mtarc1 heterozygous KO CDAHFD, Sample 1

description: Library name: 9929


title: Cdh15 KO_Tibialis_3793546

description:
Library name: 1088127_1_1
4133.9869.1088127.S33.W101102

value: Cdh15 KO

tag: strain

tag: target gene

value: Cdh15 (Mus musculus)

value: muscle

tag: tissue details

value: Tibialis


title: Mouse Liver, Wildtype CDAHFD, Sample 6

description: Library name: 11074

value: Liver

value: WT


title: RNA_SMC3KO_cDC2_CpGAB_01


title: SJNPC019503_201496850116_R03C01

description:
201496850116_R03C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: age

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Carcinoma

tag: average dose to whole heart, cgy

tag: race group

value: Black


title: RNA_SMC3KO_cDC2_CpGAB_02

tag: genotype


title: RNA_WT_cDC1_CpGAB_02


title: WT_Tibialis_3805673

description:
Library name: 1088132_1_1
4133.9869.1088132.S33.W101102

tag: age unit

value: days

tag: animal id

value: Fasted 18h

value: M


title: Mouse Liver, Wildtype CDAHFD, Sample 4

description: Library name: 11066

tag: diet

value: CDAHFD


title: SJNHL018780_201496850116_R04C01

description:
201496850116_R04C01
blood from survivor of childhood cancer and control

tag: tissue

value: Non-Hodgkin lymphoma

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: Cdh15 KO_Tibialis_3817943

description:
Library name: 1088128_1_1
4133.9869.1088128.S33.W101102

tag: fast time

tag: gender

value: Cdh15 KO

tag: strain


title: SJHL018657_201496850116_R06C01

description:
201496850116_R06C01
blood from survivor of childhood cancer and control

tag: age

tag: Sex

value: Hodgkin lymphoma


title: Cdh15 KO_Soleus muscle_3805676

description:
Library name: 1088122_1_1
4133.9869.1088122.S33.W101102

tag: target gene

value: Cdh15 (Mus musculus)

value: muscle

tag: tissue details

value: Soleus muscle


title: Mouse Liver, Wildtype CDAHFD, Sample 1

description: Library name: 9931

value: Liver

value: WT


title: WT_Tibialis_3805657

description:
Library name: 1088129_1_1
4133.9869.1088129.S33.W101102

value: Tibialis


title: CUTRUN_undiff_H3K4me1

tag: cell line

tag: cell type

value: Undifferentiated


title: Mouse Liver, Wildtype CDAHFD, Sample 3

description: Library name: 9993

tag: genotype


title: Mouse Liver, Wildtype control chow diet, Sample 5

description: Library name: 11123

value: Control chow diet


title: Cdh15 KO_Tibialis_3779417

description:
Library name: 1088125_1_1
4133.9869.1088125.S33.W101102

tag: age unit


title: SJCNS018583_201496850101_R06C01

description:
201496850101_R06C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Central nervous system (CNS)

tag: average dose to whole heart, cgy

tag: race group


title: WT_Tibialis_3793543

description:
Library name: 1088126_1_1
4133.9869.1088126.S33.W101102

value: days

tag: animal id

value: Fasted 18h

value: M

tag: tissue


title: WT_Soleus muscle_3817948

description:
Library name: 1088119_1_1
4133.9869.1088119.S33.W101102

tag: fast time

tag: gender


title: RNA_SMC3KO_cDC1_unstim_03

value: FL-BMDC

value: Rosa26CreER/+ Smc3fl/fl

tag: treatment

value: Unstimulated


title: Mouse Liver, Wildtype CDAHFD, Sample 5

description: Library name: 11068

tag: diet

value: CDAHFD


title: Cdh15 KO_Soleus muscle_3805666

description:
Library name: 1088123_1_1
4133.9869.1088123.S33.W101102

tag: age

value: Cdh15 KO

tag: strain

tag: target gene

value: Cdh15 (Mus musculus)

value: muscle

value: Soleus muscle


title: RNA_WT_cDC2_CpGAB_02

tag: cell type

value: CpG-A+CpG-B


title: RNA_WT_cDC2_CpGAB_01

tag: genotype


title: SJNBL018753_201496850116_R01C01

description:
201496850116_R01C01
blood from survivor of childhood cancer and control

tag: Sex

value: Neuroblastoma

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: RNA_SMC3KO_pDC_unstim_03

value: pDC


title: Mouse Liver, Wildtype control chow diet, Sample 3

description: Library name: 11099

value: Liver

value: WT

value: Control chow diet


title: SJALL019751_201496850116_R02C01

description:
201496850116_R02C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: male

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Acute lymphoblastic leukemia

tag: average dose to whole heart, cgy


title: RNA_SMC3KO_cDC1_CpGAB_01

tag: tissue

value: FL-BMDC

value: Rosa26CreER/+ Smc3fl/fl


title: WT_Soleus muscle_3793553

description:
Library name: 1088124_1_1
4133.9869.1088124.S33.W101102

tag: age unit

value: days

tag: animal id

tag: fast time

value: Fasted 18h

tag: gender

value: M

tag: tissue details


title: Mouse Liver, Wildtype control chow diet, Sample 2

description: Library name: 11131

tag: diet


title: Mouse Liver, Wildtype CDAHFD, Sample 2

description: Library name: 9977

value: CDAHFD


title: SJHL018650_201496850101_R08C01

description:
201496850101_R08C01
blood from survivor of childhood cancer and control

tag: age

value: female

value: Hodgkin lymphoma

tag: race group


title: SJALL019739_201496850101_R02C01

description:
201496850101_R02C01
blood from survivor of childhood cancer and control

tag: Sex

value: White


title: RNA_SMC3KO_cDC2_unstim_03

tag: cell type

tag: genotype

tag: treatment

value: Unstimulated


title: RNA_WT_cDC1_CpGAB_01

value: CpG-A+CpG-B


title: SJHIST018644_201496850101_R07C01

description:
201496850101_R07C01
blood from survivor of childhood cancer and control

tag: group

value: Histiocytosis

value: Black

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: WT_Soleus muscle_3805673

description:
Library name: 1088120_1_1
4133.9869.1088120.S33.W101102

value: WT

tag: strain

tag: target gene

value: Cdh15 (Mus musculus)

tag: tissue

value: muscle

value: Soleus muscle


title: WT_spleen_3793553

description:
Library name: 1088112_1_1
4133.9869.1088112.S33.W101102

source_name: spleen

tag: age unit

tag: animal id

tag: fast time

value: spleen


title: RNA_SMC3KO_cDC1_unstim_01

value: FL-BMDC

value: Rosa26CreER/+ Smc3fl/fl


title: SJHL018670_201496850096_R07C01

description:
201496850096_R07C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: male

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

tag: average dose to whole heart, cgy


title: WT_Soleus muscle_3805657

description:
Library name: 1088117_1_1
4133.9869.1088117.S33.W101102

tag: age

value: days

value: Fasted 18h

tag: gender

value: M

tag: tissue details


title: SJWLM018899_201496850101_R05C01

description:
201496850101_R05C01
blood from survivor of childhood cancer and control

tag: Sex

value: female

value: Wilms tumor

tag: race group

value: White


title: SJWLM018892_201496850101_R04C01

description:
201496850101_R04C01
blood from survivor of childhood cancer and control

tag: group

tag: base line visit start date


title: RNA_SMC3KO_pDC_unstim_01

tag: cell type

value: pDC

tag: genotype

tag: treatment

value: Unstimulated


title: Col291_4HT2

city: Freiburg

first: Ariane

last: Lehmann

address: Breisacher Strasse 153

department: IBSM

country: Germany

institute: Medical Center Freiburg

description: Library name: J_25

data_processing:
Sequence reads were trimmed for adapter sequences and low-quality sequences using trimmomatic (v 0.39) (parameters: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 HEADCROP:3 TRAILING:10 MINLEN:25)
Sequences were aligned using the STAR aligner (v 2.5.2b) (parameters: --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNmax 2 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --quantMode GeneCounts)
Raw counts were generated using STAR --quantMode GeneCounts
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file of raw counts for each sample

source_name: colon

growth_protocol: Organoids were generated and propagated as described before (Sato and Clevers, 2013; Sato et al., 2009; Yui et al., 2012, Reischmann et al., 2020)

extract_protocol:
RNA was extracted with the Universal RNA Purification KIT (EURX, E3598) according to manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cre recombination was induced in vitro with 4-Hydroxytamoxifen (3.5 µM) or organoids were treated with ethanol as controls for 24 hours. COL organoid RNA was isolated 3 days after Cre recombination.

tag: tissue

value: colon

tag: strain

value: colon epithelium organoids


title: SJHL018687_201496850096_R06C01

description:
201496850096_R06C01
blood from survivor of childhood cancer and control

value: Hodgkin lymphoma

tag: base line visit finish

tag: age at death


title: RNA_SMC3KO_cDC1_unstim_02


title: SJOS019519_201496850101_R03C01

description:
201496850101_R03C01
blood from survivor of childhood cancer and control

tag: age at cancer diagnosis

value: Osteosarcoma


title: Cdh15 KO_spleen_3805676

description:
Library name: 1088110_1_1
4133.9869.1088110.S33.W101102

tag: age unit

tag: animal id

tag: fast time

value: Cdh15 KO

tag: target gene

value: Cdh15 (Mus musculus)

value: spleen


title: WT_Soleus muscle_3793543

description:
Library name: 1088114_1_1
4133.9869.1088114.S33.W101102

tag: age

tag: gender

value: WT

value: muscle

tag: tissue details

value: Soleus muscle


title: RNA_SMC3KO_cDC2_unstim_02

value: FL-BMDC

value: Rosa26CreER/+ Smc3fl/fl


title: Mouse Liver, Wildtype control chow diet, Sample 4

description: Library name: 11121

value: Liver

tag: diet

value: Control chow diet


title: Mouse Liver, Wildtype control chow diet, Sample 1

description: Library name: 9927


title: RNA_WT_cDC2_unstim_03


title: Cdh15 KO_Soleus muscle_3817943

description:
Library name: 1088116_1_1
4133.9869.1088116.S33.W101102

value: days

value: Fasted 18h

value: M


title: Col312_4HT2

description: Library name: J_28

value: colon


title: Col287_4HT2

description: Library name: J_27

value: colon epithelium organoids


title: SJWLM018889_201496850096_R08C01

description:
201496850096_R08C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: Sex

value: male

tag: group

value: cancer survivor

tag: diagnostic group

value: Wilms tumor

tag: average dose to whole heart, cgy

tag: race group

value: White

tag: base line visit start date


title: SJWLM018879_201496850096_R05C01

description:
201496850096_R05C01
blood from survivor of childhood cancer and control

tag: tissue

value: female

tag: base line visit finish


title: SJALL018530_201496850096_R04C01

description:
201496850096_R04C01
blood from survivor of childhood cancer and control

tag: age at cancer diagnosis

value: Acute lymphoblastic leukemia

tag: age at death


title: WT_spleen_3805673

description:
Library name: 1088108_1_1
4133.9869.1088108.S33.W101102

tag: age unit

tag: animal id

tag: genotype

value: WT

tag: strain

value: Cdh15 (Mus musculus)

value: spleen


title: Cdh15 KO_Soleus muscle_3793546

description:
Library name: 1088115_1_1
4133.9869.1088115.S33.W101102

tag: age

tag: fast time

tag: gender

value: Cdh15 KO

tag: target gene

value: muscle

value: Soleus muscle


title: RNA_WT_cDC1_unstim_03

value: FL-BMDC

tag: cell type

tag: treatment

value: Unstimulated


title: Cdh15 KO_Soleus muscle_3779417

description:
Library name: 1088113_1_1
4133.9869.1088113.S33.W101102

value: days

value: Fasted 18h

value: M

tag: tissue details


title: SJNBL019405_201496850096_R03C01

description:
201496850096_R03C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: Sex

value: male

tag: group

tag: diagnostic group

value: Neuroblastoma

tag: average dose to whole heart, cgy

tag: race group


title: Col313_4HT2

description: Library name: J_24

tag: tissue

value: colon

value: colon epithelium organoids


title: Col290_4HT2

description: Library name: J_23


title: SJALL019734_201496850096_R02C01

description:
201496850096_R02C01
blood from survivor of childhood cancer and control

value: female

value: cancer survivor

tag: age at cancer diagnosis

value: Acute lymphoblastic leukemia

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: RNA_SMC3KO_cDC2_unstim_01

tag: genotype

value: Rosa26CreER/+ Smc3fl/fl


title: RNA_WT_cDC1_unstim_02


title: WT_spleen_3817948

description:
Library name: 1088107_1_1
4133.9869.1088107.S33.W101102

tag: age

tag: age unit

tag: animal id

tag: fast time

value: WT

tag: strain

value: Cdh15 (Mus musculus)

value: spleen


title: SJGCT018626_201496850101_R01C01

description:
201496850101_R01C01
blood from survivor of childhood cancer and control

value: Germ cell tumor

value: Black


title: RNA_SMC3KO_pDC_unstim_02

value: FL-BMDC

tag: cell type

value: pDC

tag: treatment

value: Unstimulated


title: Col286_4HT2

description: Library name: J_26


title: WT_spleen_3793543

description:
Library name: 1088102_1_1
4133.9869.1088102.S33.W101102

value: days

value: Fasted 18h

tag: gender

value: M

tag: target gene

tag: tissue details


title: Cdh15 KO_spleen_3805666

description:
Library name: 1088111_1_1
4133.9869.1088111.S33.W101102

value: Cdh15 KO


title: Col286_Ctrl2

description: Library name: J_19

value: colon

value: colon epithelium organoids

value: EtOH


title: RNA_WT_cDC2_unstim_01


title: RNA_WT_pDC_unstim_02


title: Cdh15 KO_spleen_3793546

description:
Library name: 1088103_1_1
4133.9869.1088103.S33.W101102


title: Col288_4HT2

description: Library name: J_22


title: RNA_WT_cDC2_unstim_02


title: Cdh15 KO_spleen_3817943

description:
Library name: 1088104_1_1
4133.9869.1088104.S33.W101102


title: Col287_Ctrl2

description: Library name: J_20


title: Col312_Ctrl2

description: Library name: J_21


title: Col291_Ctrl2

description: Library name: J_18


title: SJALL018523_201496850096_R01C01

description:
201496850096_R01C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: Sex

value: male

tag: group

value: cancer survivor

tag: diagnostic group

value: Acute lymphoblastic leukemia

tag: average dose to whole heart, cgy

tag: race group

value: White


title: SJHL018707_201496850030_R08C01

description:
201496850030_R08C01
blood from survivor of childhood cancer and control

tag: tissue

value: female

tag: age at cancer diagnosis

value: Hodgkin lymphoma

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: WT_lung_3793553

description:
Library name: 1088100_1_1
4133.9869.1088100.S33.W101102

source_name: lung

tag: age

tag: age unit

tag: animal id

tag: fast time

tag: genotype

value: WT

value: Cdh15 (Mus musculus)

value: lung


title: RNA_WT_cDC1_unstim_01

value: FL-BMDC

tag: cell type

tag: treatment

value: Unstimulated


title: Col313_Ctrl2

description: Library name: J_17

tag: strain


title: Cdh15 KO_spleen_3779417

description:
Library name: 1088101_1_1
4133.9869.1088101.S33.W101102

value: days

value: Fasted 18h

tag: gender

value: M

tag: target gene

value: spleen

tag: tissue details


title: SJNHL018766_201496850030_R06C01

description:
201496850030_R06C01
blood from survivor of childhood cancer and control

tag: Sex

tag: group

tag: diagnostic group

value: Non-Hodgkin lymphoma

tag: average dose to whole heart, cgy

tag: race group


title: Cdh15 KO_lung_3805676

description:
Library name: 1088098_1_1
4133.9869.1088098.S33.W101102

value: Cdh15 KO

tag: tissue


title: BMP2_Act2

city: Augusta

first: David

last: Maridas

state: GA

address: 1460 Laney Walker Blvd., CB2917

institute: Augusta University

description:
Library name: Sample 11
10X Genomics

data_processing:
DNBSEQTM Sequencing System and BGISEQ-500 platform
The PCR yield was then quantified by Qubit and samples were pooled together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe- Anchor Synthesis Sequencing Method. After filtering, the resulting reads were stored in FASTQ format.
All samples were processed using a bulk RNA-seq pipeline implemented in the bcbio-nextgen project (bcbio-nextgen,1.2.8-1c563f1). Gene expression was quantified using Salmon (version 0.14.2)
Assembly: Mouse mm10
Supplementary files format and content: csv files contain normalized counts for each samples
Supplementary files format and content: csv files contain DEG expressed genes from vehicle treatment with p-adj values under 0.05

growth_protocol: W20 are grown in DMEM supplemented with 10% FBS and with 100 U/ml penicillin-G and 100 mg/ml streptomycin

extract_protocol:
RNA was extracted after 6hr of treatment using TriZOL reagent. 1ug of RNA was used for construction of sequencing libraries
RNA libraries for RNA sequencing were prepared using Kapa mRNA HyperPrep

treatment_protocol: Confluent W20 cultures were serum-starved for 12hrs before being treated with vehicle (PBS), BMP2 (100ng/mL), Activin A (100ng/mL) or both ligands

tag: cell line

value: BMP2_Activin A

tag: replicate

value: replicate 2


title: RNA_WT_pDC_unstim_03

value: pDC


title: SJSTS018870_201496850030_R01C01

description:
201496850030_R01C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: age

value: male

value: cancer survivor

tag: age at cancer diagnosis

value: Soft tissue sarcoma

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: SJSTS019614_201496850030_R03C01

description:
201496850030_R03C01
blood from survivor of childhood cancer and control

value: female


title: Cdh15 KO_lung_3805666

description:
Library name: 1088099_1_1
4133.9869.1088099.S33.W101102

tag: age unit

tag: animal id

tag: fast time

tag: genotype

tag: strain

value: Cdh15 (Mus musculus)

value: lung


title: WT_lung_3805673

description:
Library name: 1088096_1_1
4133.9869.1088096.S33.W101102

value: days

tag: gender

value: WT

tag: target gene

tag: tissue details


title: SJHIST018643_201496850030_R04C01

description:
201496850030_R04C01
blood from survivor of childhood cancer and control

tag: Sex

tag: group

tag: diagnostic group

value: Histiocytosis

tag: average dose to whole heart, cgy

tag: race group


title: WT_lung_3805657

description:
Library name: 1088093_1_1
4133.9869.1088093.S33.W101102

tag: age

value: Fasted 18h

value: M

tag: tissue


title: Col286_4HT1

description: Library name: J_12

value: colon

tag: cell type

value: colon epithelium organoids

tag: treatment


title: BMP2_Act1

description:
Library name: Sample 10
10X Genomics

tag: cell line

value: BMP2_Activin A

tag: replicate

value: replicate 1


title: Col291_4HT

description: Library name: J_11


title: SJALL018516_201496850030_R07C01

description:
201496850030_R07C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: age at cancer diagnosis

value: Acute lymphoblastic leukemia

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: Col290_Ctrl2

description: Library name: J_16

tag: strain

tag: genotype

value: EtOH


title: Col287_4HT1

description: Library name: J_13


title: Col288_Ctrl2

description: Library name: J_15


title: WT_lung_3817948

description:
Library name: 1088095_1_1
4133.9869.1088095.S33.W101102

tag: age unit

tag: animal id

tag: fast time

tag: gender

tag: target gene

tag: tissue details


title: BMP2_Act3

description:
Library name: Sample 12
10X Genomics

value: replicate 3


title: Cdh15 KO_lung_3817943

description:
Library name: 1088092_1_1
4133.9869.1088092.S33.W101102

tag: age

value: Cdh15 KO

tag: tissue


title: SJALL018517_201496850030_R05C01

description:
201496850030_R05C01
blood from survivor of childhood cancer and control

tag: Sex

value: female

tag: group

value: cancer survivor

tag: diagnostic group

tag: average dose to whole heart, cgy

tag: race group

value: Black


title: Col313_4HT1

description: Library name: J_10

tag: cell type

tag: treatment


title: Cdh15 KO_lung_3793546

description:
Library name: 1088091_1_1
4133.9869.1088091.S33.W101102

value: days

tag: strain

value: Cdh15 (Mus musculus)

value: lung


title: Act3

description:
Library name: Sample 9
10X Genomics

tag: cell line

value: Activin A

tag: replicate


title: Act2

description:
Library name: Sample 8
10X Genomics

value: replicate 2


title: SJCNS019760_201496850030_R02C01

description:
201496850030_R02C01
blood from survivor of childhood cancer and control

tag: age at cancer diagnosis

value: Central nervous system (CNS)

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: RNA_WT_pDC_unstim_01

value: FL-BMDC

value: pDC

tag: genotype

value: Unstimulated


title: SJRHB018840_201496710057_R07C01

description:
201496710057_R07C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: age

value: Rhabdomyosarcoma


title: WT_lung_3793543

description:
Library name: 1088090_1_1
4133.9869.1088090.S33.W101102

tag: age unit

tag: animal id

tag: fast time

value: Fasted 18h

tag: gender

value: M

value: WT

tag: target gene

tag: tissue

tag: tissue details


title: Col312_4HT1

description: Library name: J_14

value: colon

tag: cell type

value: colon epithelium organoids

tag: treatment


title: Col290_4HT1

description: Library name: J_9

tag: strain


title: BMP2_rep3

description:
Library name: Sample 6
10X Genomics

tag: cell line

tag: replicate

value: replicate 3


title: SJHL018679_201496710057_R06C01

description:
201496710057_R06C01
blood from survivor of childhood cancer and control

tag: Sex

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Hodgkin lymphoma

tag: average dose to whole heart, cgy

tag: race group

tag: base line visit start date


title: Act1

description:
Library name: Sample 7
10X Genomics

value: Activin A

value: replicate 1


title: WT_liver_3793553

description:
Library name: 1088088_1_1
4133.9869.1088088.S33.W101102

source_name: liver

tag: age

tag: age unit

value: days

tag: animal id

tag: fast time

tag: genotype

value: Cdh15 (Mus musculus)

value: liver


title: BMP2_rep1

description:
Library name: Sample 4
10X Genomics


title: Col312_Ctrl1

description: Library name: J_7

tag: tissue

tag: cell type

value: EtOH


title: Col291_Ctrl1

description: Library name: J_4

tag: strain

tag: treatment


title: Col286_Ctrl1

description: Library name: J_5


title: Col288_4HT1

description: Library name: J_8


title: SJWLM018877_201496710057_R05C01

description:
201496710057_R05C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Wilms tumor

value: White

tag: base line visit finish

tag: age at death


title: Cdh15 KO_liver_3805676

description:
Library name: 1088086_1_1
4133.9869.1088086.S33.W101102

value: Fasted 18h

tag: gender

value: M

value: Cdh15 KO

tag: target gene

tag: tissue details


title: BMP2_rep2

description:
Library name: Sample 5
10X Genomics

tag: cell line

tag: replicate

value: replicate 2


title: Cdh15 KO_lung_3779417

description:
Library name: 1088089_1_1
4133.9869.1088089.S33.W101102

value: lung


title: Col287_Ctrl1

description: Library name: J_6

value: colon

value: colon epithelium organoids


title: SJOS019812_201496710057_R02C01

description:
201496710057_R02C01
blood from survivor of childhood cancer and control

tag: Sex

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Osteosarcoma

tag: average dose to whole heart, cgy

tag: race group

tag: base line visit start date


title: SJHL018673_201496710057_R08C01

description:
201496710057_R08C01
blood from survivor of childhood cancer and control

tag: tissue

tag: age

value: Hodgkin lymphoma


title: SJALL017887_201496710057_R01C01

description:
201496710057_R01C01
blood from survivor of childhood cancer and control

value: male

value: Acute lymphoblastic leukemia


title: WT_liver_3817948

description:
Library name: 1088083_1_1
4133.9869.1088083.S33.W101102

tag: age unit

value: days

tag: animal id

tag: fast time

tag: genotype

value: WT

tag: strain

value: Cdh15 (Mus musculus)

value: liver


title: Veh1

description:
Library name: Sample 1
10X Genomics

tag: treatment

value: Vehicle

value: replicate 1


title: Veh3

description:
Library name: Sample 3
10X Genomics

tag: cell line

value: replicate 3


title: SJALL019034_201496710057_R04C01

description:
201496710057_R04C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: White

tag: base line visit finish

tag: age at death


title: WT_liver_3805673

description:
Library name: 1088084_1_1
4133.9869.1088084.S33.W101102

value: Fasted 18h

tag: gender

value: M

tag: target gene

tag: tissue details


title: Cdh15 KO_liver_3805666

description:
Library name: 1088087_1_1
4133.9869.1088087.S33.W101102

value: Cdh15 KO


title: SJRHB019580_201496710057_R03C01

description:
201496710057_R03C01
blood from survivor of childhood cancer and control

tag: Sex

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Rhabdomyosarcoma

tag: average dose to whole heart, cgy


title: WT_liver_3805657

description:
Library name: 1088081_1_1
4133.9869.1088081.S33.W101102

tag: age

tag: age unit

tag: tissue


title: Col313_Ctrl1

description: Library name: J_3

value: colon

tag: cell type

value: colon epithelium organoids

tag: genotype

value: EtOH


title: Veh2

description:
Library name: Sample 2
10X Genomics

tag: treatment

tag: replicate

value: replicate 2


title: Tet2_cko_Pvi_2

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

country: China

institute: Tongji university

description: Library name: Sample 4

data_processing:
Illumina Casava1.7 software used for basecalling.
The resulting clean reads were saved in FASTQ format and subsequently aligned to the reference genome using HISAT2. The clean reads were aligned against the reference coding gene set using Bowtie2
Genes expression level is quantified through RSEM.
Differential expression analysis was carried out utilizing DESeq2, which identified genes with statistically significant differences at a threshold of Q < 0.05.
Assembly: GRCm38.84
Supplementary files format and content: FPKM ( Fragments Per Kilobase Million) and read counts for each Sample

source_name: Intestinal epithelial cells

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Intestinal epithelial cells

tag: strain


title: Tet2_cko_Pvi_1

description: Library name: Sample 3


title: SJWLM018875_201496710043_R07C01

description:
201496710043_R07C01
blood from survivor of childhood cancer and control

value: Wilms tumor

tag: race group

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: SJALL018438_201496710043_R06C01

description:
201496710043_R06C01
blood from survivor of childhood cancer and control

tag: Sex

value: Acute lymphoblastic leukemia


title: Cdh15 KO_liver_3817943

description:
Library name: 1088080_1_1
4133.9869.1088080.S33.W101102

value: days

tag: animal id

tag: fast time

tag: gender

tag: target gene

value: Cdh15 (Mus musculus)

value: liver

tag: tissue details


title: Ctrl_Pvi_2

description: Library name: Sample 2

value: Ctrl


title: Col290_Ctrl1

description: Library name: J_2


title: SJALL004739_201496710043_R08C01

description:
201496710043_R08C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: age

tag: group

tag: age at cancer diagnosis

tag: diagnostic group

tag: average dose to whole heart, cgy

value: White


title: Col288_Ctrl1

description: Library name: J_1

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: Ctrl_Pvi_1

description: Library name: Sample 1

tag: strain


title: Pooled library

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: Library name: 1

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
STARsolo (version 2.7.10a) was used to perform sample demultiplexing, alignment of reads and UMI counting, with options  --soloUMIdedup=1MM_Directional --soloUMIfiltering="-" --soloCBmatchWLtype=1MM --outSAMmapqUnique=60 --quantMode=GeneCounts --soloType=CB_UMI_Simple --soloCBstart=1 --soloCBlen=14 –soloUMIstart=15 --soloUMIlen=14 –soloBarcodeReadLength=0 –outFilterMultimapNmax=1 --soloStrand=Forward --soloMultiMappers=Unique. A hybrid reference comprising human and mouse genomes (hg38 and mm39), supplemented by construct sequences Cre, tdTomato, Ighv-MOG and LMP1 (https://www.ncbi.nlm.nih.gov/gene/3783750) was created and the mouse gene models from Ensembl release 110 were used. The sample barcode whitelist Set D was used.
Assembly: mm39
Supplementary files format and content: Counts_Table.tsv: TSV file (tab separated values) including read counts for each sample and gene (ENSEMBL ID release 110).
Supplementary files format and content: Sample_Info.tsv: TSV file (tab separated values) including sample barcodes used to demultiplex the samples using read 1 sequences, as well as metadata on the demultiplexed samples.

source_name: B cells

growth_protocol: Animals were bred and maintained in the animal facility of the Department of Biomedicine, University of Basel, Switzerland. Mice used have a transgenic B cell receptor specific for MOG, and some have tamoxifen-inducible expression of the EBV protein LMP1

extract_protocol:
RNA extracted with Zymo quick-RNA MicroPrep kit according to the manufactuer's instructions
Library preparation was performed starting with 30 ng of total RNA of each sample using the HS BRB-seq Library Preparation Kit (Cat. #10891; Alithea Genomics, Epalinges, Switzerland). Subsequently, 14 ng of cDNA was used for tagmentation. An additional PCR (5 cycles) was carried out following the BRB-seq protocol, employing the Equinox Library Amplification Kit (Cat. #7K0014-096; Watchmaker Genomics, Boulder, CO, USA).
Final libraries were sequenced on an AVITI platform (Element Biosciences, San Diego, CA, USA) with the AVITI 2×75 Sequencing Kit Cloudbreak FS High Output (Cat. #860-00015) in paired-end mode (29 bp read 1 / 121 bp read 2), applying a PMG shift of 2 during run setup.

treatment_protocol: TE671 cells stably transfected with MOG, with or without transient transfection with CD40L, or control non-expressing cells were cultured in T25 flasks. B cells from tamoxifen treated animals were then added for 4 hours, or for 24 hours, then retrieved and lysed in Lysis buffer from Zymo kit

value: B cells


title: mSCADD1_RNA

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

description: Library name: 22L001457

data_processing:
STAR index was prepared by rsem-prepare-reference (RSEM  version 1.3.3).
Paired-end RNA-seq reads were aligned to the reference genome (Mus musculus GRCm38 dna primary assembly) by STAR  (version 2.7.6a) with the annotation (GRCm38.101.gtf) and with the parameter –quantMode GeneCounts.
Transcript per million (TPM) was calculated by rsem-calculate-expression with the parameters --paired-end --strandedness none.
Assembly: GRCm38
Supplementary files format and content: ReadsPerGene.out.tab
Supplementary files format and content: rsem.genes.results

growth_protocol: WT (BALB_cJ) and SCADD (BALB_cBYJ) were maintained on standard chow diet in a temperature-controlled environment on a 12/12 h light-dark cycle. Food and water were available ad libitum.

extract_protocol:
Total RNA was extracted from 20 mg of frozen liver tissue using the Quick-RNA Miniprep Kit (Zymo Research), following the manufacturer’s protocol. RNA concentration was determined with the Qubit RNA Broad Range assay kit (Thermo Fisher), and RNA integrity was assessed using the Bioanalyzer 6000 Nano Chip (Agilent).
RNA libraries were prepared using the NEBNext RNA Library Prep Kit for Illumina sequencing.

value: male

value: 8 weeks

value: SCADD


title: WT_liver_3793543

description:
Library name: 1088078_1_1
4133.9869.1088078.S33.W101102

tag: age unit

value: Fasted 18h

value: M

value: WT


title: mSCADD2_RNA

description: Library name: 22L001458

tag: Sex


title: SJWLM019668_201496710043_R04C01

description:
201496710043_R04C01
blood from survivor of childhood cancer and control

value: cancer survivor

tag: race group

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: SJHL019321_201496710043_R03C01

description:
201496710043_R03C01
blood from survivor of childhood cancer and control

value: Hodgkin lymphoma


title: SJMEL019799_201496710043_R02C01

description:
201496710043_R02C01
blood from survivor of childhood cancer and control

value: female

value: Melanoma


title: WT_kidney_3793553

description:
Library name: 1088076_1_1
4133.9869.1088076.S33.W101102

source_name: kidney

value: days

tag: animal id

tag: fast time

tag: gender

tag: target gene

value: kidney

tag: tissue details


title: mSCADD3_RNA

description: Library name: 22L001459

value: liver

tag: age


title: Cdh15 KO_liver_3779417

description:
Library name: 1088077_1_1
4133.9869.1088077.S33.W101102

value: Cdh15 KO

value: Cdh15 (Mus musculus)

tag: tissue


title: SJNHL017931_201496710043_R01C01

description:
201496710043_R01C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: group

tag: age at cancer diagnosis

tag: diagnostic group

value: Non-Hodgkin lymphoma

tag: average dose to whole heart, cgy

value: White


title: Cdh15 KO_kidney_3805676

description:
Library name: 1088074_1_1
4133.9869.1088074.S33.W101102

tag: age unit

tag: genotype

tag: strain


title: mWT3_RNA

description: Library name: 22L001456

tag: Sex

value: male

value: 8 weeks


title: mWT2_RNA

description: Library name: 22L001455


title: MULTI_CTRL_del TB_GEX

description:
Library name: MULTI_CTRL_del TB_GEX
snRNA-seq

library_source: transcriptomic single cell

data_processing:
Fastq files were processed with 10x Genomics Cell Ranger arc 2.0.0 software using "count" pipeline; reads aligned to mm10 reference genome (cellranger version 2020, bulild A, based on GRCm38)
QC; dimensionality reduction; normalization and scaling were performed with Seurat v.4.3.0 and Signac version 1.9.0.
Assembly: mm10
Supplementary files format and content: per_barcode_metrics.csv: barcode-level metadata
Supplementary files format and content: atac_fragments.tsv.gz: chromatin-level read data
Supplementary files format and content: filtered_feature_barcode_matrix.h5: multi-assay counts

molecule: nuclear RNA

growth_protocol: Primary mouse bone marrow cells from control and ΔTB mice were plated in DMEM supplemented with 10% FBS, 10% B16-Flt3L supernatant, 1% L-glutamine, 1% sodium pyruvate, 1% MEM-NEAA, 1% penicillin-streptomycin, and 55 μM 2-mercaptoethanol. Cells were cultured at 37°C for 7 days without replating and collected by scraping the bottom of the well.

extract_protocol:
2.5x104 pDCs from each genotype and stimulation condition were sorted on FACSAria II (BD Biosciences) at the Cytometry & Cell Sorting Laboratory at NYUGSoM and pooled together. pDCs = Live singlets CD11c+ MHC-II- B220+ Siglec-H+.
Nuclei were isolated according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (GEX) protocol (10X Genomics) using an optimized 4 minutes of lysis. Libraries were prepared according to the 10X Genomics Single Cell Multiome ATAC Kit.

treatment_protocol: On day 7, FL-BMDC cultures were stimulated with 1 μM CpG-A/ODN2216 (InvivoGen) for 6 hours or left unstimulated.

value: FL-BMDC

tag: cell type

value: pDC

value: Control, del TB

tag: treatment

value: Unstimulated, CpG-A


title: CITE_HTO

description:
Library name: CITE_HTO
Hashtag-derived oligonucleotide (HTO)
HTO library: The R1/R2 files correspond to Read 1 and Read 2 of a paired-end sequencing run and the I1/I2 files refer to the Index Read 1 and Index Read 2 for dual-index barcodes.

library_source: other

data_processing:
alignment using cellranger count v6.0.1
single-cell analyses using Seurat v5.3.0
demultiplexing using HTODemux
QC filtering extracting singlets, removing cells with greater than 2.5 percent mitochondrial genes, removing cells with less than 750 features, and removing cells with more than 4250 features
Leiden clustering
Assembly: mm10
Supplementary files format and content: tab-separated files, matrix files, and Rds files
Supplementary files format and content: features.tsv.gz,matrix.mtx.gz
Library strategy: CITE-seq

molecule: other

extract_protocol:
Spleens from each genotype and treatment group (n=2 per condition) were pooled, and single cell suspensions were stained with fluorophore-conjugated antibodies as well as TotalSeqB hashtag antibodies specific against mouse CD45 and MHC-I (BioLegend) to maintain sample identity (B0301 = Control untreated, B0302 = Control LPS+profilin, B0303 = Smc3ΔDC untreated, B0304 = Smc3ΔDC LPS+profilin. Successful cDC activation was confirmed by flow cytometric analysis of CD86 upregulation. Cell sorting was performed on FACSAria II (BD Biosciences) at the Cytometry & Cell Sorting Laboratory at NYUGSoM. 6,500 (B0301-0303) or 4,000 (B0304) cDC1s (Live singlets IgD- TCR-β- NK1.1- CD11c+ MHC-II+ XCR1+ SIRPα-) and 8,500 cDC2s (Live singlets IgD- TCR-β- NK1.1- CD11c+ MHC-II+ XCR1- SIRPα+) from each sample were sorted and pooled together in 50 μl PBS containing 10% FBS.
The resulting cell mixture was prepared according to the 10X Genomics protocol at the Genome Technology Center at NYUGSoM.

treatment_protocol: Mice were injected i.v. with 100 ng profilin and 2.5 μg LPS (Invivogen) in 200 μl PBS, and spleens were collected from mice 6 hours after challenge. Spleens were minced and digested in 1 mg/ml collagenase D (Roche) and 20 μg/ml DNaseI (Roche) in RPMI supplemented with 10% FCS for 30 min at 37°C. Digested splenic tissue was subjected to red blood cell (RBC) lysis (BioLegend).

value: spleen

value: cDC

value: Control and Smc3 del DC

value: Untreated and LPS+profilin

tag: library type

value: Antibody Capture

tag: hto

value: TotalSeq-B0301 anti-mouse Hashtag 1, TotalSeq-B0302 anti-mouse Hashtag 2, TotalSeq-B0303 anti-mouse Hashtag 3, TotalSeq-B0304 anti-mouse Hashtag 4


title: SJEWS018618_201496710043_R05C01

description:
201496710043_R05C01
blood from survivor of childhood cancer and control

value: female

value: cancer survivor

value: Ewing sarcoma family of tumors

tag: race group

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: MULTI_CTRL_del TB_ATAC

description:
Library name: MULTI_CTRL_del TB_ATAC
snATAC-seq

library_source: genomic single cell

tag: tissue


title: Cdh15 KO_liver_3793546

description:
Library name: 1088079_1_1
4133.9869.1088079.S33.W101102

tag: age

value: days

tag: animal id

tag: fast time

value: Fasted 18h

tag: gender

value: M

value: Cdh15 KO

tag: target gene

value: Cdh15 (Mus musculus)

value: liver

tag: tissue details


title: Cdh15 KO_kidney_3805666

description:
Library name: 1088075_1_1
4133.9869.1088075.S33.W101102

tag: age unit

tag: genotype

tag: strain

value: kidney


title: CITE_GEX

description:
Library name: CITE_GEX
polyA RNA
GEX library: The R1/R2 files correspond to Read 1 and Read 2 of a paired-end sequencing run and the I1/I2 files refer to the Index Read 1 and Index Read 2 for dual-index barcodes.

tag: cell type

tag: treatment

value: Gene Expression


title: WT_kidney_3805673

description:
Library name: 1088072_1_1
4133.9869.1088072.S33.W101102

value: WT


title: SJALL018471_201496710015_R07C01

description:
201496710015_R07C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: Sex

tag: group

tag: age at cancer diagnosis

tag: diagnostic group

value: Acute lymphoblastic leukemia

tag: average dose to whole heart, cgy

value: Black


title: CUTRUN_H3K27me3_SMC3KO_CpGB_02

description: Library name: Sample 6

data_processing:
Data processing was performed with nf-core/cutandrun pipelipe with default parameters except: --spikein_genome K12-MG1655 --normalisation_mode Spikein --use_control false
Briefly, reads were adapter/quality-trimmed (Trim Galore 0.6.6/Cutadapt 5.1, pipeline default) and aligned with Bowtie2 2.4.4 to the mouse reference (mm10) and the spike-in reference (E. coli K-12 MG1655). Low-quality alignments were filtered (default MAPQ ≥ 20) and standard mm10 blacklists bundled with the pipeline were used. Spike-in normalization was applied across samples using the E. coli mapping rates (nf-core “Spikein” mode). Genome-wide tracks (bigWig) were generated from paired-end fragments (extended to full fragment length by default).
Pipeline versions: nextflow: 25.04.7, nf-core/cutandrun: 3.2.2
Assembly: mm10
Supplementary files format and content: bigwig files with CUT&RUN normalized coverage
Library strategy: CUT&RUN

growth_protocol: Primary mouse bone marrow cells were plated in DMEM supplemented with 10% FBS, 10% B16-Flt3L supernatant, 1% L-glutamine, 1% sodium pyruvate, 1% MEM-NEAA, 1% penicillin-streptomycin, and 55 μM 2-mercaptoethanol. Cells were cultured at 37°C for 8 days without replating and collected by scraping the bottom of the well. To induce recombination of the floxed Smc3 allele in FL-BMDC cultures from R26CreER/+ Smc3fl/fl mice, and as a control for cultures from R26CreER/+ mice, 4-hydroxytamoxifen (4-OHT) (Sigma-Aldrich) was spiked into cultures at day 3 of differentiation to a final concentration of 500 nM.

extract_protocol:
CUT&RUN was performed on ~1.4-2x105 sort-purified cells using the CUTANA ChIC/CUT&RUN Kit (Epicypher) according to manufacturer protocol. Briefly, cells were permeabilized with buffer containing 0.05% digitonin. After cells were bound to activated Concanavalin A (ConA)-coated beads, cells were bound with 4 μg anti-histone H3K27me3 (Millipore), which was used to guide cleavage by pAG-MNase. After cleavage, 0.5ng E. coli spike-in DNA was added to the Stop Buffer for sequencing data normalization.
Libraries were prepared with NEBNext Ultra II Library Prep Kit.

treatment_protocol: For stimulated samples, FL-BMDC cultures were treated with 1 μM CpG-B/ODN1668 for 6 hours. cDCs were purified from FL-BMDC cultures using a FACSAria II (BD Biosciences) at the Cytometry & Cell Sorting Laboratory at NYUSoM. Flow cytometry was performed on sorted samples to confirm purity > 95% for populations of interest. cDCs = Live singlets CD11c+ MHC-II+ B220-.

tag: tissue

value: FL-BMDC

value: cDC

value: Rosa26CreER/+ Smc3fl/fl

value: CpG-B


title: mWT1_RNA

description: Library name: 22L001454

value: male

tag: age

value: 8 weeks


title: mSCADD2B_input

description: Library name: 25L002459

data_processing:
Paired-end sequencing reads were trimmed by cutadapt  (version 3.5) with the parameters -a CTGTCTCTTATA -A CTGTCTCTTATA -a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=20 and mapped to the reference genome (Mus musculus GRCm38 dna primary assembly) using bowtie2  (version 2.5.1). Reads were filtered by samtools  (version 1.17) with the parameter -q 12.
ChIP-seq coverage (bigwig) files created in R (version 4.1.2) using the Bioconductor packages ShortRead (version 1.52.0) and rtracklayer (version 1.54.0) on the unique fragments (read pairs). Coverages were normalized by the total number of fragments and multiplied by a million.
ChIP-seq peaks were called using Homer  (version 4.10) findPeaks with parameters -style histone -fragLength 150 -inputFragLength 150 using input libraries as control. Peaks overlapping black list regions were filtered out using bedtools (version 2.31.0) and the black list (mm10-blacklist.v2 ).
Assembly: GRCm38
Supplementary files format and content: BED peak files
Supplementary files format and content: BW bigwig coverage

extract_protocol:
We used a native ChIP approach. For this 40-60 mg of frozen liver tissue was homogenized via a tissue grinder. After lysis, the nuclei pellet was digested with 20 U MNase for 15 min at 20 °C.
Libraries from purified DNA were prepared using the NEBNext Ultra II DNA Library Prep kit following the manufacturer’s instructions. After PCR enrichment of adaptor-ligated DNA, libraries were size selected at 150-700 bp in length using AMPure XP beads (Beckman Coulter) following the instructions of SPRIselect User Guide. Libraries were controlled via BioAnalyzer (Agilent) measurements using the High Sensitivity DNA

value: SCADD

tag: antibody


title: CUTRUN_H3K27me3_SMC3KO_CpGB_01

description: Library name: Sample 5


title: WT_kidney_3817948

description:
Library name: 1088071_1_1
4133.9869.1088071.S33.W101102

value: days

tag: animal id

tag: fast time

value: Fasted 18h

value: M


title: mSCADD1B_input

description: Library name: 25L002458

value: liver


title: CUTRUN_H3K27me3_SMC3WT_CpGB_02

description: Library name: Sample 4


title: SJCNS018596_201496710015_R06C01

description:
201496710015_R06C01
blood from survivor of childhood cancer and control

value: cancer survivor

value: Central nervous system (CNS)

tag: race group

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: SJEWS018622_201496710015_R05C01

description:
201496710015_R05C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: female

value: Ewing sarcoma family of tumors


title: SJALL018953_201496710015_R03C01

description:
201496710015_R03C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: mWT2B_input

description: Library name: 25L002457

tag: genotype

value: WT


title: mSCADD2B_H4K16pr

description: Library name: 25L002455

value: H4K16pr (Thermo Fisher, #PA5-112557)

tag: chip input


title: Cdh15 KO_kidney_3817943

description:
Library name: 1088068_1_1
4133.9869.1088068.S33.W101102

tag: age unit

tag: gender

value: Cdh15 KO

tag: strain

tag: target gene

value: Cdh15 (Mus musculus)

value: kidney

tag: tissue details


title: mWT1B_input

description: Library name: 25L002456

tag: Sex

value: male

value: 8 weeks


title: SJALL019750_201496710015_R02C01

description:
201496710015_R02C01
blood from survivor of childhood cancer and control

tag: tissue

tag: group

tag: age at cancer diagnosis

tag: diagnostic group

tag: average dose to whole heart, cgy


title: SJALL019051_201496710015_R04C01

description:
201496710015_R04C01
blood from survivor of childhood cancer and control

tag: age

tag: race group


title: mSCADD1B_H4K16pr

description: Library name: 25L002454

value: SCADD

tag: antibody


title: SJALL018439_201496710015_R08C01

description:
201496710015_R08C01
blood from survivor of childhood cancer and control

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: CTCF - mESC treated with DNMTi rep3

first: Bongmin

last: Bae

address: 16 Divinity Ave

institute: Harvard University

description:
Library name: CTCF_DNMTi_3
DNMTi_3_genome1 and DNMTi_3_genome2

data_processing:
Adapters sequences were automatically detected and trimmed using TrimGalore. Reads were mapped to CAST SNP-masked GRCm39 genome using bowtie2 --local -X 2000. PCR duplicates were removed using Picard MarkDuplicates. Allele-specific reads were parsed using SNPsplit (v 0.6.0). Peak calling was performed using MACS2 or SICER2 callpeak inputing un-split bam files. Peaks from each bam file were merged and converted to saf format for its use in FeatureCounts. Read counts were performed by featureCounts -p --countReadPairs using SNP split bam files. Parental biased read enrichment was assessed in R using DEseq2. For visualization purposes, bam files were converted to bigwig files with CPM normalization.
Assembly: GRCm39
Supplementary files format and content: bigwig files
Library strategy: CUT&Tag

source_name: F1.2-3 mESC

growth_protocol: Cortices from E16 embryos were carefully collected into cortical neuron plating media (Neurobasal supplemented with 2% B27, 2% FBS and 1X glutamine). Tissues were mechanically triturated into the plating media by pipetting up and down with 1000μL micropipette tips. Cell suspensions were filtered through a 40 μm cell strainer. Dissociated cells were plated onto Poly-D-lysine coated plates with plating media. Next day, media was replaced with cortical neuron maintenance media (Neurobasal supplemented with 2% B27 and 1X glutamine) and kept at 37°C with 5% CO2 until use. / NPCs were plated onto Geltrex coated plates at a density of 50,000 cells/mL (e.g. in 12 well plates 50,000 cells with 1 mL media, and in 6 well plates 100,000 cells in 2 mL media), and incubated for 3-4 hours to allow cell adherence. Transduction was performed at 7500 genomic particles per cell. Next day, NPC media was fed to keep multipotent state of the NPCs. After 48h of transduction, cells were replated onto new Geltrex coated plates with blasticidin-supplemented media. The next day, neuron differentiation was induced by replating NPCs onto PDL coated plates with cortical neuron media with blasticidin. The following day, cell culture media was optionally replaced to fresh cortical neuron media to enhance neuronal differentiation.   / Mouse ESCs were grown on 0.2% gelatin coated plate in ESC media (DMEM supplemented with 10 mM HEPES, 0.11 mM β-mercaptoethanol, 1× NEAA, 2 mM L-glutamine, 15% FBS, and 1000 U/mL LIF). For drug treatment, 5 μM GSK-3484862 was added to treatment groups and volume matched DMSO was added to controls.

extract_protocol:
Cells were gently washed with PBS and scraped into 1 ml PBS. An aliquot equivalent of 600,000 cells were used for each CUT&Tag sample. Cells were collected by centrifugation for 4 min at 300xg and supernatant was discarded.
Cells were resuspended in lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 0.5 mM spermidine, 1.5 mM MgCl, 0.1 mM EDTA, and 0.25% IGEPAL CA-630) and incubated for 5 min on ice. Lysis was assisted mechanically by gently pipetting up and down 10 times with 1000 μL tips.  Successful lysis was confirmed by Typan blue staining and inspection under a light microscope. Nuclei were collected by centrifugation for 4 min at 800xg. Nuclei pellet was washed with CUT&Tag wash buffer and resuspended in 1.5 mL wash buffer. All the procedures were performed according to manufacturer’s guides. Concanavalin A beads were conditioned by washing with 1.6 mL 1X CUT&Tag binding buffer two times. Prepared beads were resuspended in binding buffer and slowly added to the nuclei suspension. For each sample, 20 μL of beads were used. Nuclei binding was performed for 10 min at room temperature in a rotator. Beads-bound nuclei were collected using a magnetic stand and clear supernatant was discarded. Beads were resuspended in 50 μL ice-cold CUT&Tag antibody buffer and desired amount of antibody was added (2 μL CTCF antibody). Suspension was gently mixed by vortexing. Primary antibody binding was performed overnight at 4°C. After a quick spin, beads were cleared on a magnetic stand and supernatant was discarded. Beads were resuspended in 100 μL of 1:100 diluted secondary antibody in CUT&Tag Dig-Wash buffer and incubated for 1h at room temp with rotation. After secondary antibody binding, three washes with 1 mL CUT&Tag Dig-Wash buffer were performed. Beads were resuspended in 1:100 diluted CUT&Tag transposomes in CUT&Tag Dig-300 buffer and incubated on an orbital rotator for 60 min at room temperature. After transposome binding, beads were washed three times with Dig-300 buffer. Tagmentation was induced by incubating beads in 125 μL of CUT&Tag tagmentation buffer for 1h at 37°C. After tagmentation, total DNA was extracted using columns. Purified DNA was PCR amplified using proper index primers. Then, the PCR reaction was purified using SPRI beads. Samples were pooled equimolar. Sequencing was performed PE150.

tag: cell line

value: F1.2-3 mESC

tag: genotype

tag: treatment


title: SJOS017934_201496710015_R01C01

description:
201496710015_R01C01
blood from survivor of childhood cancer and control

value: Osteosarcoma


title: WT_heart_3793553

description:
Library name: 1088064_1_1
4133.9869.1088064.S33.W101102

source_name: heart

tag: age unit

value: days

tag: animal id

tag: fast time

value: Fasted 18h

tag: gender

value: M

tag: strain

tag: target gene

value: heart


title: Cdh15 KO_heart_3805666

description:
Library name: 1088063_1_1
4133.9869.1088063.S33.W101102

tag: tissue

tag: tissue details


title: CUTRUN_H3K27me3_SMC3WT_US_01

description: Library name: Sample 1

value: FL-BMDC

tag: cell type

value: cDC

value: Unstimulated


title: Cdh15 KO_kidney_3793546

description:
Library name: 1088067_1_1
4133.9869.1088067.S33.W101102

tag: age


title: mWT2B_H4K16pr

description: Library name: 25L002453

value: liver

tag: Sex

value: WT

tag: antibody

tag: chip input


title: Cdh15 KO_kidney_3779417

description:
Library name: 1088065_1_1
4133.9869.1088065.S33.W101102

value: Cdh15 KO


title: WT_kidney_3805657

description:
Library name: 1088069_1_1
4133.9869.1088069.S33.W101102

value: Cdh15 (Mus musculus)


title: SJALL018479_201492570152_R08C01

description:
201492570152_R08C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Acute lymphoblastic leukemia

tag: average dose to whole heart, cgy

tag: race group

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: CTCF - mESC treated with DNMTi rep1

description:
Library name: CTCF_DNMTi_1
DNMTi_1_genome1 and DNMTi_1_genome2

tag: cell line

value: F1.2-3 mESC

tag: genotype

tag: treatment


title: SJALL018473_201492570152_R07C01

description:
201492570152_R07C01
blood from survivor of childhood cancer and control

tag: tissue

value: female


title: CUTRUN_H3K27me3_SMC3WT_US_02

description: Library name: Sample 2

tag: cell type


title: mSCADD2A_H4K16bu

description: Library name: 22L006673

value: male

tag: age

value: 8 weeks

value: SCADD

value: H4K16bu (in-house)


title: mWT1B_H4K16pr

description: Library name: 25L002452

tag: Sex

value: H4K16pr (Thermo Fisher, #PA5-112557)


title: CUTRUN_H3K27me3_SMC3WT_CpGB_01

description: Library name: Sample 3

value: FL-BMDC

value: cDC

value: CpG-B


title: CTCF - mESC treated with DNMTi rep2

description:
Library name: CTCF_DNMTi_2
DNMTi_2_genome1 and DNMTi_2_genome2


title: mSCADD1A_H4K16bu

description: Library name: 22L006672

value: liver

tag: antibody


title: WT_heart_3805673

description:
Library name: 1088060_1_1
4133.9869.1088060.S33.W101102

tag: age unit

value: days

tag: animal id

tag: fast time

value: Fasted 18h

tag: gender

value: M

value: WT

tag: strain

tag: target gene

value: heart

tag: tissue details


title: CTCF - mESC treated with DMSO rep3

description:
Library name: CTCF_DMSO_3
DMSO_3_genome1 and DMSO_3_genome2

value: DMSO


title: WT_heart_3817948

description:
Library name: 1088059_1_1
4133.9869.1088059.S33.W101102

value: Cdh15 (Mus musculus)


title: Cdh15 KO_heart_3805676

description:
Library name: 1088062_1_1
4133.9869.1088062.S33.W101102

value: Cdh15 KO


title: CTCF - mESC treated with DMSO rep2

description:
Library name: CTCF_DMSO_2
DMSO_2_genome1 and DMSO_2_genome2

value: F1.2-3 mESC


title: SJGCT019237_201492570152_R03C01

description:
201492570152_R03C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Germ cell tumor

tag: average dose to whole heart, cgy

tag: race group

value: White

tag: base line visit start date

tag: base line visit finish


title: WT_heart_3805657

description:
Library name: 1088057_1_1
4133.9869.1088057.S33.W101102

tag: age

tag: genotype

tag: tissue


title: mWT2A_H4K16bu

description: Library name: 22L006671

tag: Sex

value: male

value: 8 weeks

tag: antibody

value: H4K16bu (in-house)

tag: chip input


title: SJCNS010133_201492570152_R02C01

description:
201492570152_R02C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)

tag: age at death


title: Cdh15 KO_heart_3793546

description:
Library name: 1088055_1_1
4133.9869.1088055.S33.W101102

tag: age unit

value: days

tag: animal id

tag: fast time

value: Fasted 18h

tag: gender

tag: strain


title: Cdh15 KO_heart_3817943

description:
Library name: 1088056_1_1
4133.9869.1088056.S33.W101102

value: M

tag: target gene

tag: tissue details


title: SJALL018405_201492570152_R05C01

description:
201492570152_R05C01
blood from survivor of childhood cancer and control

tag: group

tag: age at cancer diagnosis

tag: diagnostic group

value: Acute lymphoblastic leukemia

tag: average dose to whole heart, cgy

tag: race group


title: SJALL018935_201492570152_R04C01

description:
201492570152_R04C01
blood from survivor of childhood cancer and control

tag: tissue

tag: age

tag: base line visit start date

tag: base line visit finish


title: CTCF - mESC treated with DMSO rep1

description:
Library name: CTCF_DMSO_1
DMSO_1_genome1 and DMSO_1_genome2

tag: cell line

tag: genotype

tag: treatment

value: DMSO


title: H3K27ac - NPC neuron treated with LV-E105 rep2

description:
Library name: H3K27ac_E105_2
H3K27ac_E105_2

source_name: NPC-derived neuron

tag: cell type

value: NPC-derived neuron

value: E105 gRNA


title: H3K27ac - NPC neuron treated with LV-Scrb rep2

description:
Library name: H3K27ac_Scrb_2
H3K27ac_Scrb_2

value: Scrb gRNA


title: mSCADD1A_H4K16ac

description: Library name: 22L006668

value: liver

tag: Sex

value: SCADD

tag: antibody

value: H4K16ac (Merck Millipore, #17-10101)

tag: chip input


title: H3K27ac - NPC neuron treated with LV-E105 rep1

description:
Library name: H3K27ac_E105_1
H3K27ac_E105_1


title: mWT2A_H4K16ac

description: Library name: 22L006667

value: WT


title: WT_heart_3793543

description:
Library name: 1088054_1_1
4133.9869.1088054.S33.W101102

tag: age unit

tag: animal id

tag: fast time

tag: gender

tag: strain

tag: target gene

value: Cdh15 (Mus musculus)

value: heart

tag: tissue details


title: mWT1A_H4K16bu

description: Library name: 22L006670

tag: tissue

value: male

tag: age

value: 8 weeks


title: SJCNS018565_201492570152_R06C01

description:
201492570152_R06C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Central nervous system (CNS)

tag: average dose to whole heart, cgy

tag: race group

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: mSCADD2A_H4K16ac

description: Library name: 22L006669

tag: Sex

tag: genotype

tag: antibody

tag: chip input


title: SJCNS018574_201114530005_R08C01

description:
201114530005_R08C01
blood from survivor of childhood cancer and control


title: mWT1A_H4K16ac

description: Library name: 22L006666


title: Cdh15 KO_heart_3779417

description:
Library name: 1088053_1_1
4133.9869.1088053.S33.W101102

tag: age unit

value: days

tag: animal id

tag: fast time

value: Fasted 18h

tag: gender

value: M

value: Cdh15 KO

tag: strain


title: colon, gdT cells, batch 2

first: Jakob

last: Arnold

address: Breisacher Str. 66

institute: Uniklinik Freiburg

description: Library name: colon_gdT_FLASHseq_2

data_processing:
Sequencing reads from FLASH-Seq were pre-processed using BBDUK from the BBMAP suite (v39.06) for trimming and Trimmomatic PE (CROP:75 MINLEN:50, v0.39) for cropping. Cleaned reads were aligned to the Gencode hg38 reference genome (v46) using the STAR aligner (v2.7.11b) with parameters --limitSjdbInsertNsj 2000000 and --outFilterIntronMotifs RemoveNoncanonicalUnannotated. Primary alignments were retained using SAMtools (v1.13). Gene expression was quantified with featureCounts (v2.0.6) using the parameters -p -t exon -g gene_name --fracOverlap 0.25 and the Gencode primary assembly annotation (v46). For V(D)J and C (V(D)JC) repertoire analysis, raw sequencing reads were processed with MiXCR (v4.6.0) using its Smart-seq2 wrapper function and the built-in RepSeq.io reference library (v4.0)39. Sequencing reads from the 10x Genomics platform were processed using CellRanger’s (v8.0.0) multi pipeline to quantify gene expression and antibody-derived hashtag counts. Alignment was performed with the pre-built hg38 reference (v2020-A). TCR libraries from 10x Genomics sequencing were analyzed with MiXCR’s analyze 10x-sc-xcr-vdj wrapper function, leveraging the built-in reference library for annotation.
Assembly: PBMC (10x Genomics): GENCODE v32; colon (FLASHseq): GENCODE v46
Supplementary files format and content: FLASH-Seq output files: counts.mtx.gz, cells.tsv.gz and genes.tsv.gz; 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz and MiXCR output files: clones.tsv.gz

extract_protocol:
For isolation of intestinal lymphocytes from biopsies, samples were mechanically homogenized using a 70 µm cell strainer, washed with PBS and cryopreserved in 90% FBS and 10% DMSO. On the day of the experiment, frozen cells were thawed in RPMI-1640, centrifuged at 400×g for 5 minutes, and washed once with PBS. Cells were stained with a viability stain (BD Horizon, Fixable Viability Stain 780), antibodies against CD3E (PE/Cynanine7, SK7, BioLegend) and TCR γδ (PE, REA591, Miltenyi Biotec). Viable TCRγδ+ T cells were sorted into 384-well plates using MoFlo Astrios EQ (Beckman Coulter). For blood samples, those collected in EDTA tubes and were diluted 1:1 with phosphate-buffered saline (PBS) and overlaid in a 2:1 ratio on Ficoll (Ficoll Paque PLUS, GE Healthcare Life Sciences). Samples were centrifuged at 800×g for 20 minutes at room temperature (RT) with no acceleration or braking. The buffy coat was collected, washed with PBS, and centrifuged at 500×g for 10 minutes (RT, maximum acceleration and braking). Cells were cryopreserved at -80°C in freeze in 90% FBS and 10% DMSO. On the day of the experiment, frozen PBMCs were thawed in RPMI-1640, centrifuged at 400×g for 5 minutes, and washed once. Cells were stained with a viability dye, anti-CD3E, anti-TCRγδ, anti-Vδ1, and anti-Vδ2 antibodies. Viable Vδ2+ and Vδ1+ γδ T cells were sorted into BSA-coated 1.5 mL Eppendorf tubes using a MoFlo Astrios EQ sorter (Beckman Coulter).
cDNA synthesis and library preparation of sorted gut γδ T cells were conducted using the FLASH-Seq protocol as described previously (PMID: 35637419; PMCID: PMC9546769). Library concentration and size were assessed before normalization to 1.9 nM. Sequencing was performed on an Illumina NextSeq550 High Output flow cell (75-8-8-75) with a target of approximately 125,000 reads per cell. Single-cell RNA sequencing of blood-derived Vd1+ and Vd2+ T cells was performed using 10x Genomics with feature barcoding technology, allowing for multiplexing of cell samples from different donors to reduce costs and minimize technical variability. Hashtag oligonucleotides were obtained pre-conjugated in TotalSeq-C (5′ chemistry) formats from BioLegend. Cells were stained with barcoded antibodies during the staining step before FACS sorting. Antibodies were used at a concentration of 1 µg per million cells, as recommended by the manufacturer (BioLegend) for flow cytometry applications. After staining, cells were washed twice in PBS containing 2% BSA and 0.01% Tween 20, followed by centrifugation (400×g, 5 minutes, 4 °C) and supernatant exchange. After the final wash, cells were resuspended in PBS, filtered through 40-μm cell strainers, and prepared for sorting. Sorted Vd1+ and Vd2+ T cells were processed using the 10x Genomics single-cell 5′ V(D)J workflow according to the manufacturer’s instructions. Single-cell TCR libraries were generated using the following primers: First PCR: 1 μM forward primer (5′-GATCTACACTCTTTCCCTACACGACGC-3′) and 1 μM of each reverse primer (5′-ATCCCA GAATCGTGTTGCTC-3′, and 5′- CCCACTGGGAGAGATGACAA-3′). Second PCR: 1 μM forward primer (5′-GATCTACACTCTTTCCCTACACGACGC -3′) and 1 μM of each reverse primer (5′-GGGGAAACATCTGCATCAAG-3′ and 5′-GACAAAAACGGATGGTTTGG-3′). Libraries were pooled in appropriate quantities to achieve the desired sequencing depth, following 10x Genomics guidelines, and sequenced using NovaSeq 6000.

tag: tissue

value: colon

tag: cell type

value: gd T cells

tag: library type

value: mRNA

tag: batch


title: H3K27ac - NPC neuron treated with LV-Scrb rep1

description:
Library name: H3K27ac_Scrb_1
H3K27ac_Scrb_1

value: NPC-derived neuron

tag: treatment

value: Scrb gRNA


title: mRNAseq - mESC treated with DNMTi rep3

description:
Library name: mRNAseq_DNMTi_3
DNMTi_3_genome1 and DNMTi_3_genome2

data_processing:
Adapters sequences were automatically detected and trimmed using TrimGalore. Reads were mapped to CAST SNP-masked GRCm39 genome using STAR –sjdbGTFfile Mus_musculus.GRCm39.110.gtf --sjdbOverhang 149 --alignEndsType EndToEnd. PCR duplicates were removed using Picard MarkDuplicates. Allele-specific reads were parsed using SNPsplit (v 0.6.0). Read counts were performed by featureCounts -p –countReadPairs -t exon -g gene_id -a Mus_musculus.GRCm39.110.gtf and using SNP split bam files. Parental biased read enrichment was assessed in R using DEseq2.
Assembly: GRCm39
Supplementary files format and content: bigwig files

growth_protocol: Cortices from E16 embryos were carefully collected into cortical neuron plating media (Neurobasal supplemented with 2% B27, 2% FBS and 1X glutamine). Tissues were mechanically triturated into the plating media by pipetting up and down with 1000μL micropipette tips. Cell suspensions were filtered through a 40 μm cell strainer. Dissociated cells were plated onto Poly-D-lysine coated plates with plating media. Next day, media was replaced with cortical neuron maintenance media (Neurobasal supplemented with 2% B27 and 1X glutamine) and kept at 37°C with 5% CO2 until use. / NPCs were plated onto Geltrex coated plates at a density of 50,000 cells/mL (e.g. in 12 well plates 50,000 cells with 1 mL media, and in 6 well plates 100,000 cells in 2 mL media), and incubated for 3-4 hours to allow cell adherence. Transduction was performed at 7500 genomic particles per cell. Next day, NPC media was fed to keep multipotent state of the NPCs. After 48h of transduction, cells were replated onto new Geltrex coated plates with blasticidin-supplemented media. The next day, neuron differentiation was induced by replating NPCs onto PDL coated plates with cortical neuron media with blasticidin. The following day, cell culture media was optionally replaced to fresh cortical neuron media to enhance neuronal differentiation. / Mouse ESCs were grown on 0.2% gelatin coated plate in ESC media (DMEM supplemented with 10 mM HEPES, 0.11 mM β-mercaptoethanol, 1× NEAA, 2 mM L-glutamine, 15% FBS, and 1000 U/mL LIF). For drug treatment, 5 μM GSK-3484862 was added to treatment groups and volume matched DMSO was added to controls.

extract_protocol:
RNA was extracted using Trizol (Thermo Fisher Scientifics) method. DNA was removed from the samples using Turbo DNase (Thermo Fisher Scientifics).
Library preparation was performed using rRNA depletion strategy / mESC library preparation was performed using poly(A) selection strategy

tag: cell line

value: F1.2-3 mESC


title: mSCADD2A_H3K9ac

description: Library name: 22L006665

value: liver

value: male

tag: age

value: SCADD

value: H3K9ac (abcam, ab4441)


title: SJWLM017959_201492570152_R01C01

description:
201492570152_R01C01
blood from survivor of childhood cancer and control

data_processing: Genome-wide DNAm data were generated using Illumina Infinium MethylationEPIC BeadChip v1 (Illumina, San Diego, CA, USA), with DNA extracted from peripheral blood mononuclear cells (PBMCs) or saliva. Preprocessing was conducted using the minfi package in R, following established quality control procedures including a detection p-value ≤ 0.01. CpGs were excluded if they were located on sex chromosomes, contained single nucleotide polymorphisms (SNPs), or were previously identified as cross-reactive or non-specific. Quantile normalization was applied at the probe level to ensure comparability across samples.

extract_protocol: Genomic DNA (250 ng per sample) were treated with bisulfite using the Zymo EZ DNA Methylation Kit under the following thermos-cycling conditions: 16 cycles: 95 degrees Celsius for 30 sec, 50 degrees Celsius for 1 hour. Following bisulfite treatment, DNA samples were desulphonated, column purified, then eluted using 12 µl of elution buffer (Zymo Research Corp.). Treating DNA with sodium bisulfite selectively converts cytosine to uracil but preserves 5-methylcytosine, which is immune from deamination.

value: peripheral blood mononuclear cells

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Wilms tumor

tag: average dose to whole heart, cgy

tag: race group

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: SJALL018487_201114530005_R07C01

description:
201114530005_R07C01
blood from survivor of childhood cancer and control

tag: Sex

value: Acute lymphoblastic leukemia

value: White


title: MeWo, GFP control, biological replicate#3

city: Taipei City

first: han-ying

last: cheng

address: No. 155, Sec. 2, Linong St., Beitou Dist.

department: Institute of clincal medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: Library name: MeWo_ctrl_3

data_processing:
Quality Control & Trimming: Raw reads were processed using CLC Genomics Workbench 25.0.3 (tool: Trim Sequences 3.0). Low-quality bases (limit 0.01) and ambiguous nucleotides (max 2) were trimmed. To remove bias, the first 12 nucleotides were removed from the 5' end. Illumina adapters were automatically trimmed via the "New trim adapter list".
Alignment Strategy (Species-specific): Trimmed reads were mapped using the "RNA-Seq Analysis 2.9" tool with the following references: For Human samples (MeWo): Mapped to Homo sapiens (GRCh38.p14) with annotations from Ensembl release 113. For Mouse samples (3T3): Mapped to Mus musculus (GRCm39) with annotations from Ensembl release 112.
Mapping Parameters: Alignment was performed with consistent parameters for all samples: Mismatch cost = 2, Insertion/Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8. The library was defined as Strand specific (Reverse).
Expression Calculation: Gene expression values were calculated based on unique gene reads. The final processed files contain "Unique gene reads" (raw counts), TPM, and RPKM values.
Assembly: GRCm39, GRCh38.p14
Supplementary files format and content: Tab-delimited text files
Supplementary files format and content: Each file contains gene expression quantification results. Full column list: Name, Chromosome, Region, Expression value, TPM, RPKM, Exons, Gene ID, Gene length, ENSEMBL, Biotype, Unique gene reads, Total gene reads, Transcripts annotated, Uniquely identified transcripts, Exon length, Unique exon reads, Total exon reads, Ratio of unique to total (exon reads), Unique exon-exon reads, Total exon-exon reads, Unique intron reads, Total intron reads, Ratio of intron to total gene reads.

source_name: MeWo

extract_protocol:
Total RNA was extracted from cells using TRIzol Reagent (Invitrogen) following the manufacturer's instructions. 1μg of total RNA was used for construction of sequencing liberaries.
RNA liberaries for RNA-seq were prepared by Illumina Stranded mRNA Prep kit following manufeacture's protocals

value: MeWo

tag: genotype

value: GFP-control expression


title: MeWo, GFP control, biological replicate#2

description: Library name: MeWo_ctrl_2


title: mRNAseq - mESC treated with DNMTi rep2

description:
Library name: mRNAseq_DNMTi_2
DNMTi_2_genome1 and DNMTi_2_genome2


title: mSCADD1A_H3K9ac

description: Library name: 22L006664

tag: tissue

value: 8 weeks

tag: antibody

tag: chip input


title: mWT2A_H3K9ac

description: Library name: 22L006663

value: WT


title: colon, gdT cells, batch 1

description: Library name: colon_gdT_FLASHseq_1

value: colon

tag: cell type

value: gd T cells

tag: library type

value: mRNA

tag: batch


title: SJALL018433_201114530005_R05C01

description:
201114530005_R05C01
blood from survivor of childhood cancer and control

tag: age


title: SJCNS018584_201114530005_R06C01

description:
201114530005_R06C01
blood from survivor of childhood cancer and control

tag: group

value: Central nervous system (CNS)


title: mRNAseq - mESC treated with DMSO rep2

description:
Library name: mRNAseq_DMSO_2
DMSO_2_genome1 and DMSO_2_genome2

tag: cell line

value: F1.2-3 mESC

tag: treatment

value: DMSO


title: mSCADD2A_input

description: Library name: 22L006661

value: liver

value: male

value: SCADD


title: SJSTS019623_201114530005_R04C01

description:
201114530005_R04C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: female

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Soft tissue sarcoma

tag: average dose to whole heart, cgy


title: MeWo, EML4-ALK expression, biological replicate#3

description: Library name: MeWo_EML4-ALK_3

value: MeWo

value: EML4-ALK expression


title: RNAseq - NPC neuron LV-E105 rep3

description:
Library name: RNAseq_E105_3
dif3E105_3.genome1 and dif3E105_3.genome2

source_name: NPC-derived neurons

value: NPC-derived neurons


title: mWT1A_H3K9ac

description: Library name: 22L006662

value: 8 weeks

value: WT

value: H3K9ac (abcam, ab4441)


title: MeWo, EML4-ALK expression, biological replicate#2

description: Library name: MeWo_EML4-ALK_2


title: SJALL018409_201114530005_R02C01

description:
201114530005_R02C01
blood from survivor of childhood cancer and control

source_name: genomic DNA derived from blood samples from survivor of childhood cancer and community control

value: Acute lymphoblastic leukemia

tag: race group

value: White

tag: base line visit start date

tag: base line visit finish


title: mWT2A_input

description: Library name: 22L006659

tag: Sex

tag: genotype


title: mRNAseq - mESC treated with DMSO rep1

description:
Library name: mRNAseq_DMSO_1
DMSO_1_genome1 and DMSO_1_genome2

value: F1.2-3 mESC


title: mSCADD1A_input

description: Library name: 22L006660

tag: tissue

tag: antibody


title: MeWo, EML4-ALK expression, biological replicate#1

description: Library name: MeWo_EML4-ALK_1


title: mRNAseq - mESC treated with DNMTi rep1

description:
Library name: mRNAseq_DNMTi_1
DNMTi_1_genome1 and DNMTi_1_genome2


title: MeWo, GFP control, biological replicate#1

description: Library name: MeWo_ctrl_1

value: GFP-control expression


title: SJWLM017958_201114530005_R01C01

description:
201114530005_R01C01
blood from survivor of childhood cancer and control

value: Wilms tumor

tag: age at death


title: mWT1A_input

description: Library name: 22L006658

value: liver

value: male


title: RNAseq - NPC neuron LV-E105 rep2

description:
Library name: RNAseq_E105_2
dif3E105_2.genome1 and dif3E105_2.genome2

tag: cell type


title: SJGCT019238_201114530005_R03C01

description:
201114530005_R03C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Germ cell tumor

value: Black