title: RNA_SMC3KO_pDC_CpGA_18h_03

data_processing:
Adapters were trimmed using Trimmomatic
reads were alligned using Star
reads quantified using featureCount
count normalization and differential expression performed using DEseq2
Assembly: mm10
Supplementary files format and content: counts.raw.csv.gz; comma-delimited un-normalized counts by sample matrix

source_name: FL-BMDC

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 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: pDCs were sorted from 4-OHT-treated 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. pDCs = Live singlets CD11c+ MHC-II- B220+ Siglec-H+. Purified pDCs were stimulated with 1 μM CpG-A/ODN2216 (InvivoGen) for 6 hours and 18 hours or left unstimulated as a control for 6 hours. Successful pDC activation was confirmed by flow cytometric analysis of CD69 upregulation.

value: FL-BMDC

value: R26CreER/+ Smc3fl/fl

tag: treatment

value: CpG-A (18h)


title: ATAC_IRF7KO_HoxB8_pDC_02

status: Public on Jan 13 2026

type: SRA

city: New York City

first: Eduardo

last: Esteva

state: New York

address: 550 1st Ave

country: USA

institute: NYU Grossman School of Medicine

library_source: genomic

data_processing:
Illumina bcl2fastq
Seq-N-Slide
Reads were trimmed using Trimmomatic
Aligned using BowTie 2
Duplicates removed using sambamba
Peak calling performed using MACS2
Assembly: mm10
Supplementary files format and content: Bigwigs

molecule: genomic DNA

organism: Mus musculus

growth_protocol: The murine progenitor HoxB8-FL cell line (Redecke et al, 2013, 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). To induce progenitor differentiation into mature DCs, the cells were washed twice and replated in RPMI supplemented with 10% charcoal-stripped serum, 10% B16-Flt3L supernatant, 1% L-glutamine, and 1% penicillin-streptomycin in the absence of estrogen.

extract_protocol:
Cells were washed with PBS and immediately processed as previously described (Buenostro et al, 2015, PMC4374986).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cas9 ribonucleoproteins (RNPs) were prepared by incubating 250 pmol sgRNAs (targeting either Ifnar1, Irf7, Spib or Irf8), 250 pmol CD45 sgRNA, 75 pmol S. pyogenes Cas9 Nuclease V3, and 100 pmol Alt-R Cas9 electroporation enhancer (all from IDT) together for 15 min at room temperature. Control Cas9-RNPs were prepared containing 250 pmol non-targeting control crRNA and 250 pmol tracrRNA instead of 250 pmol targeting sgRNA. HoxB8-FL cells (1x106) were resuspended in 100 μl Opti-MEM I reduced serum medium (Thermo Fisher Scientific), to which Cas9-RNPs were added. Cells were electroporated with 4D-Nucleofector X Unit (Lonza) using program CM-137. Transfected HoxB8-FL progenitors cells were passaged every other day until day 6 post transfection, then differentiated into mature DCs. Successful transfection was confirmed by loss of CD45 expression, and successful targeting was confirmed by flow cytometric staining for the intended target. Cell sorting was performed on 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. pDC = Live singlets CD45- CD11c+ SigH+ CD11b- MHCII-, DC = Live singlets CD45-.

tag: cell line

tag: cell type

value: pDC

tag: genotype


title: RNA_SMC3KO_pDC_CpGA_18h_02

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: ATAC_IRF8KO_spleen_pDC_01

source_name: spleen

treatment_protocol: Spleens were minced and digested with 150 μg/ml Liberase TL (Roche) in PBS for 30 min at 37°C, then passed through a 100 μm cell strainer. The splenic DC fraction was enriched by collecting the interface of a bovine serum albumin density gradient. Cell sorting was performed on 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. pDC = Live singlets IgD- NK1.1- TCR-β- CD11b- CX3CR1- CD11c+ B220int Siglec-H+.

value: spleen


title: RNA_WT_pDC_CpGA_18h_02


title: SJCNS041944_201496860143_R08C01

type: genomic

city: Memphis

first: Zhaoming

last: Wang

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description:
201496860143_R08C01
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

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.

value: peripheral blood mononuclear cells

tag: age

tag: Sex

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: RNA_WT_pDC_CpGA_18h_03


title: ATAC_SpiBKO_HoxB8_pDC_02

value: Spib{delta}


title: RNA_SMC3KO_pDC_CpGA_6h_02

value: CpG-A (6h)


title: SJMEL042542_201496860143_R04C01

description:
201496860143_R04C01
blood from survivor of childhood cancer and control

value: Melanoma

value: Black


title: RNA_WT_pDC_CpGA_18h_01


title: SJCNS041972_201496860143_R06C01

description:
201496860143_R06C01
blood from survivor of childhood cancer and control


title: RNA_SMC3KO_pDC_CpGA_18h_01


title: SJCNS041937_201496860143_R05C01

description:
201496860143_R05C01
blood from survivor of childhood cancer and control


title: SJALL041435_201496860143_R03C01

description:
201496860143_R03C01
blood from survivor of childhood cancer and control

value: male

value: Acute lymphoblastic leukemia


title: SJALL018944_201496860143_R01C01

description:
201496860143_R01C01
blood from survivor of childhood cancer and control


title: SJALL041254_201496860143_R02C01

description:
201496860143_R02C01
blood from survivor of childhood cancer and control


title: RNA_SMC3KO_pDC_CpGA_6h_03


title: SJRHB042115_201496860072_R05C01

description:
201496860072_R05C01
blood from survivor of childhood cancer and control

value: Rhabdomyosarcoma


title: SJCNS041914_201496860143_R07C01

description:
201496860143_R07C01
blood from survivor of childhood cancer and control


title: SJCNS041953_201496860072_R08C01

description:
201496860072_R08C01
blood from survivor of childhood cancer and control


title: SJHL019306_201503670004_R01C01

description:
201503670004_R01C01
blood from survivor of childhood cancer and control

value: Hodgkin lymphoma


title: RNA_SMC3KO_pDC_CpGA_6h_01

value: FL-BMDC

value: R26CreER/+ Smc3fl/fl


title: RNA_WT_pDC_CpGA_6h_03

value: pDC


title: RNA_SMC3KO_pDC_unstim_6h_03

value: Unstimulated (6h)


title: RNA_WT_pDC_CpGA_6h_02


title: SJTALL005069_201496860072_R07C01

description:
201496860072_R07C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells


title: RNA_WT_pDC_CpGA_6h_01


title: RNA_SMC3KO_pDC_unstim_6h_01


title: SJEWS001304_201496860072_R06C01

description:
201496860072_R06C01
blood from survivor of childhood cancer and control

value: female

value: Ewing sarcoma family of tumors


title: RNA_SMC3KO_pDC_unstim_6h_02


title: SJALL042539_201496860072_R04C01

description:
201496860072_R04C01
blood from survivor of childhood cancer and control

value: cancer survivor


title: SJCNS041918_201496860065_R08C01

description:
201496860065_R08C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)

value: White


title: RNA_WT_pDC_unstim_6h_03


title: SJOS042109_201496860065_R06C01

description:
201496860065_R06C01
blood from survivor of childhood cancer and control

value: Osteosarcoma


title: RNA_L929_SEV8h_03

data_processing:
Seq-N-Slide
Illumina bcl2fastq
Sequence reads adapter and quality trimmed using Trimmomatic
Trimmed reads aligned to mm10/GrCM38 using STAR
Count extraction performed using featureCounts
Count normalization and differential expression testing using DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each Sample

growth_protocol: The mouse fibroblast NCTC clone 929 (L929) cell line (ATCC CCL-1) was cultured in DMEM supplemented with 10% FBS, 1% L-glutamine, 1% sodium pyruvate, and 1% penicillin-streptomycin.

extract_protocol:
RNA was extracted from fibroblasts lysed in TRIzol Reagent (Thermo Fisher Scientific) using the Direct-zol RNA Miniprep kit (Zymo Research) 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: L929 fibroblasts (3x105) were infected with 80 HAU Sendai virus (SEV) in 2 ml of culture media or left uninfected as a control. At 4, 8, or 16 hours after infection, fibroblasts were collected by trypsinization. Successful infection was confirmed by intracellular staining for the SEV hemagglutinin-neuraminidase.

value: Sendai virus (8h)


title: SJALL041455_201496860072_R03C01

description:
201496860072_R03C01
blood from survivor of childhood cancer and control


title: SJALL041229_201496860072_R02C01

description:
201496860072_R02C01
blood from survivor of childhood cancer and control


title: SJALL018957_201496860072_R01C01

description:
201496860072_R01C01
blood from survivor of childhood cancer and control


title: RNA_L929_SEV4h_03

value: Sendai virus (4h)


title: RNA_L929_SEV8h_02


title: SJHIST042002_201496860065_R05C01

description:
201496860065_R05C01
blood from survivor of childhood cancer and control

value: Histiocytosis


title: RNA_WT_pDC_unstim_6h_01


title: SJALL041873_201496850124_R07C01

description:
201496850124_R07C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: SJST042112_201496850124_R08C01

description:
201496850124_R08C01
blood from survivor of childhood cancer and control

value: Other malignancy


title: RNA_L929_SEV4h_02


title: SJALL041257_201496860065_R03C01

description:
201496860065_R03C01
blood from survivor of childhood cancer and control


title: RNA_L929_SEV8h_01


title: SJCNS042527_201496860065_R04C01

description:
201496860065_R04C01
blood from survivor of childhood cancer and control

value: Black


title: RNA_L929_SEV4h_01


title: RNA_L929_SEV16h_02

value: Sendai virus (16h)


title: SJCNS041917_201496860065_R07C01

description:
201496860065_R07C01
blood from survivor of childhood cancer and control


title: SJCNS041971_201496850124_R06C01

description:
201496850124_R06C01
blood from survivor of childhood cancer and control


title: SJALL018985_201496860065_R02C01

description:
201496860065_R02C01
blood from survivor of childhood cancer and control


title: RNA_L929_SEV16h_01


title: SJNHL019468_201496860065_R01C01

description:
201496860065_R01C01
blood from survivor of childhood cancer and control

value: Non-Hodgkin lymphoma


title: RNA_WT_pDC_unstim_6h_02

value: FL-BMDC

value: pDC


title: RNA_L929_CTRL_03

value: Uninfected


title: SJALL040945_201496850124_R02C01

description:
201496850124_R02C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: female


title: RNA_L929_SEV16h_03


title: SJCNS041969_201496850124_R05C01

description:
201496850124_R05C01
blood from survivor of childhood cancer and control

value: male

value: cancer survivor


title: D3BP

city: nanjing

first: guoyong

last: yin

address: hanzhong road 104

country: China

institute: The First Affiliated Hospital of Nanjing Medical University

library_source: transcriptomic single cell

data_processing:
Primary analysis of raw read data (scRNA-seq) Raw reads were processed to generate gene expression profiles using CeleScope v1.15.0 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCm38 (mm10) transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to exons with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis.  Quality control, dimension-reduction and clustering (Scanpy) Scanpy v1.8.1 [2] was used for quality control, dimensionality reduction and clustering under Python 3.7. For each sample dataset, we filtered expression matrix by the following criteria: 1) cells with gene count less than 200 or with top 2% gene count were excluded; 2) cells with top 2% UMI count were excluded; 3) cells with mitochondrial content  5% were excluded; 4) genes expressed in less than 5 cells were excluded. After filtering, 129,277 cells were retained for the downstream analyses, with on average 1638.71 genes and 4942.63 UMIs per cell. The raw count matrix was normalized by total counts per cell and logarithmically transformed into normalized data matrix. Top 2000 variable genes were selected by setting flavor = ‘seurat’. Principle Component Analysis (PCA) was performed on the scaled variable gene matrix, and top 16 principle components were used for clustering and dimensional reduction. Cells were separated into 24 clusters by using Louvain algorithm and setting resolution parameter at 1.2. Cell clusters were visualized by using Uniform Manifold Approximation and Projection (UMAP).
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCm38 (mm10) ensembl release 99
Supplementary files format and content: matrix files

source_name: spinal cord

extract_protocol:
The  spinal cord tissues of  mice were collected, and the tissue dissociation solution was used to form single-cell suspension, and CD45+ cells were sorted by magnetic beads
RT & Amplification & Library Construction Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) [1]. Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: spinal cord

value: CD45+ cells


title: SJALL041186_201496850124_R03C01

description:
201496850124_R03C01
blood from survivor of childhood cancer and control

value: White


title: SJALL019044_201496850124_R01C01

description:
201496850124_R01C01
blood from survivor of childhood cancer and control


title: D7BP


title: ChIP_cDC_input

data_processing:
Data was processed with chipseq-nextflow version 2.0.0 with parameters --paired_end --narrow_peak.
Briefly, mapping was done by bwa mem v0.7.17-r1188 to the reference mm10 genome, and the peak calling was done by MACS2 v2.2.7.1 in narrow-peak regime.
Inputs for normalization were specified in the samplesheet for the nextflow pipeline according to the software documentation.
Assembly: mm10
Supplementary files format and content: MACS2 peaks in .narrowPeak format

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). To induce progenitor differentiation into mature DCs, the cells were washed twice and replated in RPMI supplemented with 10% charcoal-stripped serum, 10% B16-Flt3L supernatant, 1% L-glutamine, and 1% penicillin-streptomycin in the absence of estrogen.

extract_protocol:
Sort-purified cells (~3.5-4.5x106) were cross-linked with 1% methanol-free formaldehyde in PBS for 8 min followed by quenching with 0.125 M glycine for 5 min. Cells were lysed and nuclei isolated using the Covaris TruCHIP Kit, and chromatin was sheared using a Covaris M220 ultrasonicator. ChIP was performed using 4 μg of rabbit anti-CTCF polyclonal antibody (Millipore) or rabbit anti-mouse/human Rad21 polyclonal antibody (Abcam) and Dynabeads Protein A (Thermo Fisher Scientific).
Libraries were prepared using the KAPA HyperPrep Kit (Roche). As a control, libraries were also prepared from non-immunoprecipitated “input” DNA from each cell type.

treatment_protocol: HoxB8-FL-derived cDCs and pDCs were sorted 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+ CD11b+ B220-, pDCs = Live singlets CD11c+ MHC-II- B220+ Siglec-H+.

value: cDC


title: RNA_L929_CTRL_01


title: RNA_L929_CTRL_02


title: SJSTS042513_201496850124_R04C01

description:
201496850124_R04C01
blood from survivor of childhood cancer and control

value: Wilms tumor


title: SJALL041875_201496850010_R05C01

description:
201496850010_R05C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: SJALL042507_201496850010_R04C01

description:
201496850010_R04C01
blood from survivor of childhood cancer and control


title: SJNHL042080_201496850010_R06C01

description:
201496850010_R06C01
blood from survivor of childhood cancer and control


title: D3BN


title: SJALL041325_201496850010_R03C01

description:
201496850010_R03C01
blood from survivor of childhood cancer and control


title: SJALL018974_201496850010_R01C01

description:
201496850010_R01C01
blood from survivor of childhood cancer and control


title: ChIP_pDC_input


title: SJALL018987_201503670102_R06C01

description:
201503670102_R06C01
blood from survivor of childhood cancer and control


title: ChIP_undiff_Rad21

value: Undifferentiated


title: SJALL019049_201503670102_R04C01

description:
201503670102_R04C01
blood from survivor of childhood cancer and control


title: ATAC_L929_SEV8h_02

data_processing:
Mapping was done with nf-core/atacseq version 2.1.2. Briefly, sequencing reads were mapped to the reference genome (mm10) using the Bowtie2 (v2.5.1) and duplicate reads were removed using Picard tools (v.3.1.1). Low quality mapped reads were removed from the analysis. The read per million (RPM) normalized BigWig files were generated using BEDTools (v.2.31.1) and the bedGraphToBigWig tool (2.9 bbi v.4).
Assembly: mm10
Supplementary files format and content: bigwig files with ATAC-Seq normalized coverage (RPM)

extract_protocol:
1x105 cells were washed with PBS and immediately processed as previously described (Buenostro et al, 2015, PMC4374986).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: L929 fibroblasts (3x105) were infected with 80 HAU Sendai virus (SEV) in 2 ml of culture media or left uninfected as a control. 8 hours later fibroblasts were collected by trypsinization. Successful infection was confirmed by intracellular staining for the SEV hemagglutinin-neuraminidase.

value: fibroblast

value: Sendai virus (8h)


title: ChIP_pDC_CTCF


title: ATAC_L929_CTRL_02

value: Uninfected (8h)


title: ATAC_L929_CTRL_01


title: ChIP_undiff_input


title: ATAC_L929_SEV8h_01


title: HiC_L929_SEV8h

data_processing:
Hi-C data was processed with distiller-nf version 0.3.4 with default parameters, except parsing options: "--walks-policy all" added to parse complex walks from reads.
Only pairs with both reads mapped with MAPQ>=30 were considered for the final contact matrices.
https://github.com/open2c/distiller-nf
Assembly: mm10
Supplementary files format and content: mcool files with merged replicates

extract_protocol:
Cells were cross-linked for 10 min in 1 ml of 2% methanol-free formaldehyde (Thermo Fisher Scientific) in PBS + 3% BSA. Crosslinking was reversed by addition of glycine (Thermo Fisher Scientific) to 0.125 M for 5 min, followed by incubation on ice for 15 min.
Libraries were prepared using the Arima Hi-C kit according to manufacturer protocol.

treatment_protocol: In each well, L929 fibroblasts (3x105) were infected with 80 HAU Sendai virus (SEV) in 2 ml of culture media or left uninfected as a control. 8 hours later fibroblasts were collected by trypsinization and pooled to achieve 5x106 cells per condition. Successful infection was confirmed by intracellular staining for the SEV hemagglutinin-neuraminidase.


title: SJALL004836_201496850010_R07C01

description:
201496850010_R07C01
blood from survivor of childhood cancer and control

value: Black


title: D7BN


title: SJNHL042087_201496850010_R08C01

description:
201496850010_R08C01
blood from survivor of childhood cancer and control

value: Non-Hodgkin lymphoma


title: ChIP_pDC_Rad21

value: pDC


title: ChIP_cDC_CTCF


title: HiC_L929_CTRL


title: SJHL019260_201503470042_R07C01

description:
201503470042_R07C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Hodgkin lymphoma


title: ChIP_cDC_Rad21


title: HiC_Irf8KO_02

data_processing:
Hi-C data was processed with distiller-nf version 0.3.3 with default parameters.
Only pairs with both reads mapped with MAPQ>=30 were considered for the final contact matrices.
https://github.com/open2c/distiller-nf
Assembly: mm10
Supplementary files format and content: mcool files with merged replicates

extract_protocol:
Sorted cells (3-5x106 per sample) were cross-linked for 10 min in 1 ml of 2% methanol-free formaldehyde (Thermo Fisher Scientific) in PBS + 3% BSA. Crosslinking was reversed by addition of glycine (Thermo Fisher Scientific) to 0.125 M for 5 min, followed by incubation on ice for 15 min.
Libraries were prepared using the Arima Hi-C kit according to manufacturer protocol.

treatment_protocol: HoxB8-FL-derived cDCs and pDCs were sorted 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+ CD11b+ B220-, pDCs = Live singlets CD11c+ MHC-II- B220+ Siglec-H+. Purified pDCs were stimulated with 1 μM CpG-A/ODN2216 (InvivoGen) for 6 hours. All other populations were left unstimulated for the same duration of time. Successful pDC activation was confirmed by flow cytometric analysis of CD69 upregulation. Cas9 ribonucleoproteins (RNPs) were prepared by incubating 250 pmol IRF8 sgRNA, 250 pmol CD45 sgRNA, 75 pmol S. pyogenes Cas9 Nuclease V3, and 100 pmol Alt-R Cas9 electroporation enhancer (all from IDT) together for 15 min at room-temperature. Hoxb8-FL cells (1x106) were resuspended in 100 μl Opti-MEM I reduced serum medium (Thermo Fisher Scientific), to which Cas9-RNPs were added. Cells were electroporated with 4D-Nucleofector X Unit (Lonza) using program CM-137. Transfected HoxB8-FL cells were passaged every other day until day 6 post transfection, at which point Hoxb8-FL progenitors were differentiated into mature DCs. Successful transfection was confirmed by loss of CD45 expression. Cell sorting was performed on 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. DC = Live singlets CD45-


title: SJSTS019602_201503670102_R07C01

description:
201503670102_R07C01
blood from survivor of childhood cancer and control

value: female

value: Soft tissue sarcoma


title: SJNHL019486_201503670102_R03C01

description:
201503670102_R03C01
blood from survivor of childhood cancer and control

value: male

value: cancer survivor


title: SJCNS019128_201503670102_R05C01

description:
201503670102_R05C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)

value: White


title: HiC_pDC_CpGA_02

value: CpG-A


title: SJALL019038_201503470042_R02C01

description:
201503470042_R02C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: SJWLM041025_201496850010_R02C01

description:
201496850010_R02C01
blood from survivor of childhood cancer and control

value: Wilms tumor


title: SJNHL018787_201503670102_R01C01

description:
201503670102_R01C01
blood from survivor of childhood cancer and control


title: HiC_cDC_unstim_02

value: cDC

value: Unstimulated


title: HiC_pDC_CpGA_01


title: SJALL018943_201503470033_R08C01

description:
201503470033_R08C01
blood from survivor of childhood cancer and control


title: Donor 6, Active-HIV

city: Amsterdam

first: Neeltje

last: Kootstra

address: Meibergdreef 9

country: Netherlands

institute: AmsterdamUMC

description: Library name: Sample 16

data_processing:
Data-preprocessing was performed using the RNA sequencing PLUS workflow by Single Cell Discoveries. Raw sequencing reads were mapped to the human reference genome (GRCh38, Ensembl 98) using STARsolo (v2.7.10b).
Assembly: Human genome GRCh38, Ensembl 98)
Supplementary files format and content: tab-delimited text file contains mapped read counts for each sample

molecule: polyA RNA

growth_protocol: Peripheral blood monocytes were isolated from buffy coats of healthy blood bank donors by Lymphoprep density gradient centrifugation, followed by Percoll gradient steps. Monocytes were differentiated into monocyte-derived dendritic cells in the presence of IL-4 (500 U/ml) and GM-CSF (800 U/ml) for 6 days in RPMI supplemented with 10% FCS, penicillin (10 U/ml), streptomycin (10 mg/ml), and L-glutamine (2 mM).

extract_protocol:
Isolated cells were resuspended in buffer PKD (Qiagen) and incubated with proteinase K (0.1 μg/sample) for 1 hour at 50°C. Cells were then lysed using TriPure™ Isolation Reagent. Samples were subseqeuntly processed for bulk RNA sequencing using the RNA Sequencing PLUS workflow by Single Cell Discoveries (Utrecht, The Netherlands).
Libraries were constructed using the RNA sequencing PLUS workflow by Single Cell Discoveries. Libraries were sequenced to a depth of approximately 20 million raw reads per sample using single-end 75 bp (1×75) chemistry on an Illumina NovaSeq X Plus.

treatment_protocol: DCs were infected with HIV-GKOVSV-G (MOI 0.3) for 5 day

value: dendritic cell

value: HIV-infected


title: HiC_undiff_unstim_02

value: Undifferentiated


title: ChIP_undiff_CTCF


title: HiC_cDC_unstim_01


title: Donor 6, Latent-HIV

description: Library name: Sample 17


title: SJNHL019496_201503470042_R03C01

description:
201503470042_R03C01
blood from survivor of childhood cancer and control

value: Non-Hodgkin lymphoma


title: SJOS019512_201503470042_R05C01

description:
201503470042_R05C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Osteosarcoma


title: SJHL019348_201503470042_R06C01

description:
201503470042_R06C01
blood from survivor of childhood cancer and control

value: Hodgkin lymphoma


title: Donor 6, Uninfected

description: Library name: Sample 18

value: Uninfected


title: SJALL019069_201503670102_R02C01

description:
201503670102_R02C01
blood from survivor of childhood cancer and control

value: female


title: Donor 5, Latent-HIV

description: Library name: Sample 14


title: SJHL019305_201503470033_R07C01

description:
201503470033_R07C01
blood from survivor of childhood cancer and control

value: cancer survivor


title: Donor 5, Uninfected

description: Library name: Sample 15


title: HiC_pDC_unstim_01

value: pDC


title: SJWLM018906_201503470042_R01C01

description:
201503470042_R01C01
blood from survivor of childhood cancer and control

value: Black


title: SJALL018982_201503470042_R04C01

description:
201503470042_R04C01
blood from survivor of childhood cancer and control

value: White


title: HiC_pDC_unstim_02


title: Donor 4, Unexposed

description: Library name: Sample 12


title: HiC_Irf8KO_01


title: HiC_SMC3KO_pDC_02

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 Rosa26CreER/+ 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:
Sorted cells (1-5x106 per sample) were cross-linked for 10 min in 1 ml of 2% methanol-free formaldehyde (Thermo Fisher Scientific) in PBS + 3% BSA. Crosslinking was reversed by addition of glycine (Thermo Fisher Scientific) to 0.125 M for 5 min, followed by incubation on ice for 15 min.
Libraries were prepared using the Arima Hi-C kit according to manufacturer protocol.

treatment_protocol: cDCs and pDCs were sorted from 4-OHT-treated 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-, pDCs = Live singlets CD11c+ MHC-II- B220+ Siglec-H+.

value: FL-BMDC

value: R26CreER/+ Smc3fl/fl


title: Donor 4, Active-HIV

description: Library name: Sample 10


title: HiC_undiff_unstim_01


title: SJHL019257_201503470033_R05C01

description:
201503470033_R05C01
blood from survivor of childhood cancer and control


title: Donor 4, Latent-HIV

description: Library name: Sample 11


title: Donor 3, Active-HIV

description: Library name: Sample 7


title: Donor 5, Active-HIV

description: Library name: Sample 13


title: HiC_SMC3KO_pDC_01


title: Donor 3, Latent-HIV

description: Library name: Sample 8


title: SJNHL019473_201503470033_R06C01

description:
201503470033_R06C01
blood from survivor of childhood cancer and control


title: SJNBL019430_201503470033_R02C01

description:
201503470033_R02C01
blood from survivor of childhood cancer and control

value: Neuroblastoma


title: SJCNS019131_201503470033_R03C01

description:
201503470033_R03C01
blood from survivor of childhood cancer and control

value: male

value: Central nervous system (CNS)


title: Donor 3, Unexposed

description: Library name: Sample 9

value: dendritic cell


title: HiC_SMC3KO_cDC_01

value: cDC


title: SJSTS019604_201503470033_R04C01

description:
201503470033_R04C01
blood from survivor of childhood cancer and control

value: Soft tissue sarcoma


title: Donor 1, Unexposed

description: Library name: Sample 3


title: Donor 1, Active-HIV

description: Library name: Sample 1

value: HIV-infected


title: SJAML018553_201503470033_R01C01

description:
201503470033_R01C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Acute myeloid leukemia


title: SJGCT019225_201503470042_R08C01

description:
201503470042_R08C01
blood from survivor of childhood cancer and control

value: Germ cell tumor


title: HiC_SMC3KO_cDC_02


title: HiC_WT_cDC_02


title: mut3A_NTC_30d

city: Solna

first: Maria

last: Needhamsen

address: Solnavagen 1

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

description: Library name: mRNA-seq_Sample 40

data_processing:
The RAW RNA sequence files were used to extract the fastq data, which underwent quality control checks using the multiqc software to prepare them for alignment 25. Subsequently, the resulting fastqc files were aligned and annotated using the STAR aligner and Stringtie software 26, incorporating human hg38 refseq information from UCSC. Finally, the analysis of the count matrix was carried out using bash and Python and reads were mapped to the human reference genome hg19 assembly. To filter out low-expressed transcripts, we have considered all the transcripts that have at least one count per transcript across all the samples.  The counts were normalized by CPM using the TMM method and log2 fold change (logFC) was calculated based on the normalized CPM counts. We chose logFC ≥ 2 or logFC < -2 and adjusted p value < 0.05 as the screening criteria.
Assembly: hg19
Supplementary files format and content: Comma-delimited file includes raw counts for each sample
Supplementary files format and content: Comma-delimited file includes CPM values for each sample

growth_protocol: Human embryonic kidney HEK293T cells were maintained in Dulbecco’s Modified Eagle Medium (Sigma Aldrich, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (Sigma Aldrich), 4 mM L-glutamine (Sigma Aldrich), 100 U/ml penicillin and 100 µg/ml streptomycin (Sigma Aldrich). Cells were incubated at 37◦C in a humidified 5% CO2-containing atmosphere

extract_protocol:
To enrich the EGFP+ cells, FACS sorting was performed after 72 h and the sorted cells were subjected directly for DNA, RNA and protein extraction using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Venlo, Netherlands).
The RNA-seq libraries were constructed according to the manufacturer’s protocol using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, CA, USA).

treatment_protocol: HEK293T cells were transfected using Lipofectamine 3000 Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. Briefly, cells were seeded in 6 well plates and were transfected the day after at around 80% of confluency. The transfection cocktail was prepared as follows: 4µg of the plasmid DNA, 5 µl Lipofectamine™ 3000 Reagent, 5 µl P3000™ Reagent (2 µL/µg DNA) and Opti-MEM™ Medium (Invitrogen).

value: epithelial-like cell

value: dCas9-DNMT3A with R882H mutation , non targeted guide RNA (NTC), day30


title: Donor 2, Latent-HIV

description: Library name: Sample 5


title: HiC_WT_pDC_02

value: pDC


title: Donor 2, Active-HIV

description: Library name: Sample 4


title: SJRHB019587_201503470031_R08C01

description:
201503470031_R08C01
blood from survivor of childhood cancer and control

value: female

value: cancer survivor

value: Rhabdomyosarcoma


title: HiC_WT_pDC_01

value: FL-BMDC


title: Donor 1, Latent-HIV

description: Library name: Sample 2


title: Non transfected cells (NT)_30d_rep1

description: Library name: mRNA-seq_Sample 41

value: Non transfected cells, day30


title: Non transfected cells (NT)_30d_rep2

description: Library name: mRNA-seq_Sample 42


title: CRISPRoff_NTC_30d

description: Library name: mRNA-seq_Sample 39

value: DNMT3A_DNMT3L_dCas9_BFP_KRAB (CRISPRoff), non targeted guide RNA (NTC), day30


title: SJNHL019472_201503470031_R07C01

description:
201503470031_R07C01
blood from survivor of childhood cancer and control

value: Non-Hodgkin lymphoma

value: White


title: Donor 2, Unexposed

description: Library name: Sample 6

value: dendritic cell

value: Uninfected


title: 3A_NTC_30d

description: Library name: mRNA-seq_Sample 38

value: dCas9_DNMT3A, non targeted guide RNA (NTC), day30


title: 3A3L_NTC_30d

description: Library name: mRNA-seq_Sample 37

value: dCas9_DNMT3A_DNMT3L, non targeted guide RNA (NTC), day30


title: SJCNS019134_201503470031_R06C01

description:
201503470031_R06C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Central nervous system (CNS)


title: HiC_WT_cDC_01

value: cDC


title: SJALL018941_201503470031_R05C01

description:
201503470031_R05C01
blood from survivor of childhood cancer and control

value: male

value: Acute lymphoblastic leukemia


title: dDNMT3A_BACH2_g8_30d_rep2

description: Library name: mRNA-seq_Sample 35

value: epithelial-like cell

value: dCas9_dDNMT3A, BACH2 targeted guide RNA8 ,day30


title: 3A3A_NTC_30d

description: Library name: mRNA-seq_Sample 36

value: dCas9_DNMT3A_DNMT3A, non targeted guide RNA (NTC), day30


title: brain, E2

data_processing:
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0[3] and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference_x0002_based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM[6] software
Assembly: Ensembl_release111
Supplementary files format and content: all.genes.expression.annot.txt (TPM, Count)

source_name: brain

extract_protocol:
Total RNA was extracted using TRIzol
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments. PCR library amplification is then performed, and finally, detection is carried out using the Illumina Novaseq 6000 Plus.

value: brain

value: Primary microglia

value: pparg over expression


title: SJCNS019150_201503470031_R04C01

description:
201503470031_R04C01
blood from survivor of childhood cancer and control

value: female

value: cancer survivor


title: mut3A_g8_30d

description: Library name: mRNA-seq_Sample 33

value: dCas9-DNMT3A with R882H mutation , BACH2 targeted guide RNA8 ,day30


title: dDNMT3A_BACH2_g8_30d_rep1

description: Library name: mRNA-seq_Sample 34


title: SJALL018420_201503470031_R02C01

description:
201503470031_R02C01
blood from survivor of childhood cancer and control

value: White


title: SJHL019263_201503470031_R03C01

description:
201503470031_R03C01
blood from survivor of childhood cancer and control

value: Hodgkin lymphoma


title: 3A_BACH2_g8_30d

description: Library name: mRNA-seq_Sample 31

value: dCas9_DNMT3A, BACH2 targeted guide RNA8 ,day30


title: 3A3L_BACH2_g8_30d

description: Library name: mRNA-seq_Sample 30

value: dCas9_DNMT3A_DNMT3L, BACH2 targeted guide RNA8 ,day30


title: brain, E3


title: brain, N3

value: negative control


title: brain, N2


title: CRISPRoff_BACH2_g8_30d

description: Library name: mRNA-seq_Sample 32

value: DNMT3A_DNMT3L_dCas9_BFP_KRAB(CRISPRoff), BACH2 targeted guide RNA8 ,day30


title: Non transfected cells (NT)_7d_rep2

description: Library name: mRNA-seq_Sample 28

value: Non transfected cells, day7


title: brain, E1


title: Non transfected cells (NT)_7d_rep1

description: Library name: mRNA-seq_Sample 27


title: SJHL019250_201496860120_R08C01

description:
201496860120_R08C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: male


title: SJEWS018614_201503470031_R01C01

description:
201503470031_R01C01
blood from survivor of childhood cancer and control

value: Ewing sarcoma family of tumors


title: mut3A_NTC_7d

description: Library name: mRNA-seq_Sample 26

value: epithelial-like cell

value: dCas9-DNMT3A with R882H mutation , non targeted guide RNA (NTC), day7


title: 3A3A_BACH2_g8_30d

description: Library name: mRNA-seq_Sample 29

value: dCas9_DNMT3A_DNMT3A, BACH2 targeted guide RNA8 ,day30


title: brain, N1

value: brain

value: Primary microglia


title: CRISPRoff_NTC_7d

description: Library name: mRNA-seq_Sample 25

value: DNMT3A_DNMT3L_dCas9_BFP_KRAB (CRISPRoff), non targeted guide RNA (NTC), day7


title: brain, M3

value: myelin


title: SJWLM019641_201496860120_R07C01

description:
201496860120_R07C01
blood from survivor of childhood cancer and control

value: female

value: cancer survivor

value: Wilms tumor

value: White


title: 3A_NTC_7d

description: Library name: mRNA-seq_Sample 24

value: dCas9_DNMT3A, non targeted guide RNA (NTC), day7


title: brain, M2


title: brain, M1


title: SJCNS001207_201496860120_R06C01

description:
201496860120_R06C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)


title: dDNMT3A_BACH2_g8_7d_rep1

description: Library name: mRNA-seq_Sample 20

value: dCas9_dDNMT3A, BACH2 targeted guide RNA8 ,day7


title: dDNMT3A_BACH2_g8_7d_rep2

description: Library name: mRNA-seq_Sample 21


title: 3A3A_NTC_7d

description: Library name: mRNA-seq_Sample 22

value: dCas9_DNMT3A_DNMT3A, non targeted guide RNA (NTC), day7


title: SJOS019507_201496860120_R05C01

description:
201496860120_R05C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Osteosarcoma

value: Black


title: 3A3L_BACH2_g8_7d

description: Library name: mRNA-seq_Sample 16

value: epithelial-like cell

value: dCas9_DNMT3A_DNMT3L, BACH2 targeted guide RNA8 ,day7


title: CRISPRoff_BACH2_g8_7d

description: Library name: mRNA-seq_Sample 18

value: DNMT3A_DNMT3L_dCas9_BFP_KRAB(CRISPRoff), BACH2 targeted guide RNA8 ,day7


title: mut3A_g8_7d

description: Library name: mRNA-seq_Sample 19

value: dCas9-DNMT3A with R882H mutation , BACH2 targeted guide RNA8 ,day7


title: 3A3L_NTC_7d

description: Library name: mRNA-seq_Sample 23

value: dCas9_DNMT3A_DNMT3L, non targeted guide RNA (NTC), day7


title: 3A3A_BACH2_g8_7d

description: Library name: mRNA-seq_Sample 15

value: dCas9_DNMT3A_DNMT3A, BACH2 targeted guide RNA8 ,day7


title: brain, A3

value: brain

value: Primary microglia

value: atorvastatin


title: 3A_BACH2_g8_7d

description: Library name: mRNA-seq_Sample 17

value: dCas9_DNMT3A, BACH2 targeted guide RNA8 ,day7


title: SJAML019107_201496860120_R03C01

description:
201496860120_R03C01
blood from survivor of childhood cancer and control

value: female

value: cancer survivor

value: Acute myeloid leukemia

value: White


title: Non transfected cells (NT)_3d_rep1

description: Library name: mRNA-seq_Sample 13

value: Non transfected cells, day3


title: brain, A2


title: brain, A1


title: Non transfected cells (NT)_3d_rep2

description: Library name: mRNA-seq_Sample 14


title: SJALL018510_201496860120_R02C01

description:
201496860120_R02C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Acute lymphoblastic leukemia


title: brain, C1

value: control


title: 3A_NTC_3d

description: Library name: mRNA-seq_Sample 10

value: epithelial-like cell

value: dCas9_DNMT3A, non targeted guide RNA (NTC), day3


title: CRISPRoff_NTC_3d

description: Library name: mRNA-seq_Sample 11

value: DNMT3A_DNMT3L_dCas9_BFP_KRAB (CRISPRoff), non targeted guide RNA (NTC), day3


title: 3A3A_NTC_3d

description: Library name: mRNA-seq_Sample 8

value: dCas9_DNMT3A_DNMT3A, non targeted guide RNA (NTC), day3


title: dDNMT3A_BACH2_g8_3d_rep1

description: Library name: mRNA-seq_Sample 6

value: dCas9_dDNMT3A, BACH2 targeted guide RNA8 ,day3


title: 3A3L_NTC_3d

description: Library name: mRNA-seq_Sample 9

value: dCas9_DNMT3A_DNMT3L, non targeted guide RNA (NTC), day3


title: SJALL019056_201496860120_R04C01

description:
201496860120_R04C01
blood from survivor of childhood cancer and control


title: brain, C3

value: brain

value: Primary microglia


title: 30Ddonor

city: Saint Louis

first: Daniel

last: Kreisel

state: Missouri

address: 660 S Euclid Ave

department: Surgery

institute: Washington University

data_processing:
Alignment: Cell Ranger V6, aligned to mm10 transcriptome
QC and Filtering: Seurat V4
Unsupervised Clustering: Seurat V4
Assembly: mm10
Supplementary files format and content: .rds processed data file containing all merged datasets

extract_protocol:
We performed syngeneic orthotopic murine left lung transplants from CD45.2+ C57BL/6J to CD45.1+ C57BL/6J mice with 60 minutes of cold ischemia at 4˚C then 45 minutes of warm ischemia at 28˚C. Lung grafts were collected at various time points after reperfusion including 2 hours (WT2H), 3 days (WT3D), 7 days (WT7D), and 30 days (WT30D). Additionally, we collected single cell suspensions from naïve C57BL/6J left lungs (CTRL). For each sample (CTRL, WT2H, WT3D, WT7D, WT30D), we pooled cells from two lungs and sorted recipient CD45.1+ cells, donor CD45.2+ cells, and stromal CD45.1- cells. We then performed single-cell RNA sequencing on these samples.
Chromium Single Cell 5ʹ Reagent v1.1 kit from 10X Genomics and Chromium Single Cell 3ʹ Reagent v1.1 kit from 10X Genomics

value: lung

value: B6>B6 transplant 30d reperfusion


title: mut3A_BACH2_g8_3d

description: Library name: mRNA-seq_Sample 5

value: dCas9-DNMT3A with R882H mutation , BACH2 targeted guide RNA8 ,day3


title: mut3A_NTC_3d

description: Library name: mRNA-seq_Sample 12

value: dCas9-DNMT3A with R882H mutation , non targeted guide RNA (NTC), day3


title: SJHL019329_201496860111_R07C01

description:
201496860111_R07C01
blood from survivor of childhood cancer and control

value: female

value: cancer survivor

value: Hodgkin lymphoma

value: White


title: SJHL019359_201496860111_R08C01

description:
201496860111_R08C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells


title: SJCNS001204_201496860111_R06C01

description:
201496860111_R06C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)


title: brain, C2

value: control


title: 30Dstroma


title: SJHL018668_201496860120_R01C01

description:
201496860120_R01C01
blood from survivor of childhood cancer and control

value: male


title: 3A_BACH2_g8_3d

description: Library name: mRNA-seq_Sample 3

value: epithelial-like cell

value: dCas9_DNMT3A, BACH2 targeted guide RNA8 ,day3


title: dDNMT3A_BACH2_g8_3d_rep2

description: Library name: mRNA-seq_Sample 7

value: dCas9_dDNMT3A, BACH2 targeted guide RNA8 ,day3


title: 30Drecipient


title: SJHIST019244_201496860111_R05C01

description:
201496860111_R05C01
blood from survivor of childhood cancer and control

value: Histiocytosis


title: CRISPRoff_BACH2_g8_3d

description: Library name: mRNA-seq_Sample 4

value: DNMT3A_DNMT3L_dCas9_BFP_KRAB(CRISPRoff), BACH2 targeted guide RNA8 ,day3


title: SJALL018507_201496860111_R02C01

description:
201496860111_R02C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: 7Drecipient

value: lung

value: B6>B6 transplant 7d reperfusion


title: 3A3L_BACH2_g8_3d

description: Library name: mRNA-seq_Sample 2

value: dCas9_DNMT3A_DNMT3L, BACH2 targeted guide RNA8 ,day3


title: SJALL019017_201496860100_R08C01

description:
201496860100_R08C01
blood from survivor of childhood cancer and control

value: female


title: 7Dstroma


title: Hap1_ADAR1-E912A KI_total RNA-seq_biological replicate 4

city: New York

first: Hachung

last: Chung

address: 701 W 168th St, HHSC Rm 1506

department: Microbiology & Immunology

institute: Columbia University

description:
Library name: Sample 20
Total RNA extraction
E912A_KI3_6_4_input

data_processing:
After quality control using FastQC v0.11.5, adaptor sequences and low-quality reads were trimmed from FASTQ files with fastp v0.20.1.78. Preprocessed reads were aligned to the human genome (hg38) using STAR v2.7.3a to generate BAM files. Read quantification was performed using featureCounts v1.6.4.
Assembly: hg38
Supplementary files format and content: csv files include raw count values for each sample

growth_protocol: Hap1 cells were cultured in IMDM supplemented with 10% fetal bovine serum and 1x Non-essential amino acid in 5% CO2 at 37°C.

extract_protocol:
Freshly prepared buffers included NET-2 buffer (50mM Tris-Cl, pH 7.4, 150mM NaCl, 1mM MgCl2, 0.5% NP-40), NP-40 lysis buffer (50mM Tris-Cl, pH 7.4, 150mM NaCl, 5mM EDTA, 0.5% NP-40), and high salt wash buffer (50mM Tris-Cl, pH 7.4, 1M NaCl, 1mM EDTA, 1% NP-40, 0.5% DOC, 0.1% SDS). Protein G Dynabeads (Thermo Fisher Scientific) were washed and resuspended in NET-2 buffer. J2 antibody (15ug) was added to 100uL of beads and incubated for 1 h at room temperature on a rotator. Hap1 cells (1 × 107; WT, E912A KI_clone #1, ADAR1 KO_clone #1) were lysed with 300uL of NP-40 lysis buffer supplemented with RNasin® (80mU/uL, Promega) and cOmplete protease inhibitor (Roche), then incubated on ice for 5 min. Lysates were centrifuged at 17,000g for 5 min at 4°C. RNA for total RNA-seq was extracted from 50uL of lysate using Trizol reagent. For dsRNA immunoprecipitation, 250uL of lysate was diluted with 750uL of NET-2 buffer containing 12U of RQ1 RNase-free DNase (Promega) and 10mM MgCl2. 100uL of J2-Dynabeads were added and rotated for 2h at 4°C. Beads were washed twice with high salt wash buffer and twice with NET-2 buffer, and dsRNA was extracted using Trizol reagent. For total RNA-seq library preparation, RNA was extracted with the Direct-zol RNA MiniPrep (Zymo Research) from Trizol solution dissolving total cell lysate. To remove cytoplasmic rRNAs (5S, 5.8S, 18S, and 28S), the RiboMinus™ Eukaryote Kit (Thermo Fisher Scientific) was used, while mitochondrial ribosomal RNAs (12S and 16S) were retained.  For dsRNA-seq library preparation, RNA was extracted from the Trizol solution in which the bead complexes of the above dsRNA preparations were dissolved. RNA was purified using ethanol precipitation with GlycoBlue™ Coprecipitant (Thermo Fisher Scientific). The resulting blue RNA pellets were reconstituted in nuclease-free water and spiked with ERCC RNA Spike-In Mix (Thermo Fisher Scientific).
Libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs) with multiplex oligos (New England Biolabs).


title: SJNBL006047_201496860111_R03C01

description:
201496860111_R03C01
blood from survivor of childhood cancer and control

value: cancer survivor

value: Neuroblastoma


title: Hap1_ADAR1-E912A KI_total RNA-seq_biological replicate 2

description:
Library name: Sample 18
Total RNA extraction
E912A_KI3_6_2_input


title: SJALL018952_201496860100_R07C01

description:
201496860100_R07C01
blood from survivor of childhood cancer and control

value: White


title: Hap1_ADAR1-E912A KI_total RNA-seq_biological replicate 3

description:
Library name: Sample 19
Total RNA extraction
E912A_KI3_6_3_input


title: Hap1_ADAR1 KO_total RNA-seq_biological replicate 3

description:
Library name: Sample 23
Total RNA extraction
ADAR1KO_1_a_3_input

value: ADAR1 knock-out


title: SJNHL019456_201496860111_R04C01

description:
201496860111_R04C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Non-Hodgkin lymphoma


title: 3Ddonor

value: B6>B6 transplant 3d reperfusion


title: Hap1_ADAR1 KO_total RNA-seq_biological replicate 2

description:
Library name: Sample 22
Total RNA extraction
ADAR1KO_1_a_2_input


title: Hap1_ADAR1-E912A KI_total RNA-seq_biological replicate 1

description:
Library name: Sample 17
Total RNA extraction
E912A_KI3_6_1_input


title: Hap1_ADAR1 KO_total RNA-seq_biological replicate 4

description:
Library name: Sample 24
Total RNA extraction
ADAR1KO_1_a_4_input


title: 3A3A_BACH2_g8_3d

description: Library name: mRNA-seq_Sample 1

value: epithelial-like cell

value: dCas9_DNMT3A_DNMT3A, BACH2 targeted guide RNA8 ,day3


title: 7Ddonor


title: SJALL003838_201496860111_R01C01

description:
201496860111_R01C01
blood from survivor of childhood cancer and control

value: Black


title: 3Dstroma


title: 2HRdonor

value: B6>B6 transplant 2h reperfusion


title: SJHL019271_201496860100_R05C01

description:
201496860100_R05C01
blood from survivor of childhood cancer and control

value: male

value: Hodgkin lymphoma


title: Hap1_ADAR1 KO_dsRNA-seq_biological replicate 4

description:
Library name: Sample 12
Transcripts prone to forming double-stranded RNA were enriched
ADAR1KO_1_a_4_dsRNA


title: Hap1_ADAR1 KO_total RNA-seq_biological replicate 1

description:
Library name: Sample 21
Total RNA extraction
ADAR1KO_1_a_1_input


title: SJEWS019201_201496860100_R04C01

description:
201496860100_R04C01
blood from survivor of childhood cancer and control

value: Ewing sarcoma family of tumors


title: Hap1_WT_total RNA-seq_biological replicate 3

description:
Library name: Sample 15
Total RNA extraction
WT_EV_5_3_input

value: WT


title: Hap1_WT_total RNA-seq_biological replicate 4

description:
Library name: Sample 16
Total RNA extraction
WT_EV_5_4_input


title: Hap1_ADAR1 KO_dsRNA-seq_biological replicate 3

description:
Library name: Sample 11
Transcripts prone to forming double-stranded RNA were enriched
ADAR1KO_1_a_3_dsRNA


title: Hap1_ADAR1 KO_dsRNA-seq_biological replicate 1

description:
Library name: Sample 9
Transcripts prone to forming double-stranded RNA were enriched
ADAR1KO_1_a_1_dsRNA


title: Hap1_WT_total RNA-seq_biological replicate 2

description:
Library name: Sample 14
Total RNA extraction
WT_EV_5_2_input


title: Hap1_ADAR1-E912A KI_dsRNA-seq_biological replicate 4

description:
Library name: Sample 8
Transcripts prone to forming double-stranded RNA were enriched
E912A_KI3_6_4_dsRNA


title: SJCNS019175_201496860100_R06C01

description:
201496860100_R06C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)


title: 2HRstroma

value: lung


title: Hap1_ADAR1-E912A KI_dsRNA-seq_biological replicate 2

description:
Library name: Sample 6
Transcripts prone to forming double-stranded RNA were enriched
E912A_KI3_6_2_dsRNA


title: Hap1_WT_total RNA-seq_biological replicate 1

description:
Library name: Sample 13
Total RNA extraction
WT_EV_5_1_input


title: RNA_SMC3KOf0_cDC1_02

data_processing:
Adapters were trimmed using Trimmomatic
reads were alligned using Star
reads quantified using featureCount
count normalization and differential expression performed using DEseq2
Assembly: mm10
Supplementary files format and content: counts.raw.csv.gz; raw gene x sample counts matrix

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: 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). The single-cell splenocyte suspension was enriched for DCs by negative depletion by staining splenocytes with biotinylated antibodies against TER-119, TCR-β, CD3ε, NK1.1, CD19, and Ly6G (Thermo Fisher Scientific and BioLegend), incubating them with streptavidin microbeads (Miltenyi Biotec) and passing them through LS columns attached to MidiMACS or QuadroMACS separators (Miltenyi Biotec). Cell sorting was performed on 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. cDC1 = Live singlets CD11c+ MHC-II+ XCR1+ SIRPα-, cDC2 = Live singlets CD11c+ MHC-II+ XCR1- SIRPα+.

value: spleen

value: CD11cCre/+ Smc3fl/-


title: CTRLstroma

description: CTRLs

source_name: CTRLs

value: naive


title: Hap1_ADAR1 KO_dsRNA-seq_biological replicate 2

description:
Library name: Sample 10
Transcripts prone to forming double-stranded RNA were enriched
ADAR1KO_1_a_2_dsRNA

value: ADAR1 knock-out


title: RNA_SMC3KOf0_cDC2_01


title: RNA_SMC3KOf0_cDC1_01


title: Hap1_ADAR1-E912A KI_dsRNA-seq_biological replicate 3

description:
Library name: Sample 7
Transcripts prone to forming double-stranded RNA were enriched
E912A_KI3_6_3_dsRNA


title: SJHL018680_201496860100_R02C01

description:
201496860100_R02C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: female

value: cancer survivor

value: White


title: Hap1_WT_dsRNA-seq_biological replicate 4

description:
Library name: Sample 4
Transcripts prone to forming double-stranded RNA were enriched
WT_EV_5_4_dsRNA


title: SJGICT018824_201496860100_R01C01

description:
201496860100_R01C01
blood from survivor of childhood cancer and control

value: Other malignancy


title: RNA_SMC3KOf0_cDC2_02


title: Hap1_WT_dsRNA-seq_biological replicate 3

description:
Library name: Sample 3
Transcripts prone to forming double-stranded RNA were enriched
WT_EV_5_3_dsRNA


title: SJCNS019145_201496860100_R03C01

description:
201496860100_R03C01
blood from survivor of childhood cancer and control

value: Unknown


title: Hap1_WT_dsRNA-seq_biological replicate 2

description:
Library name: Sample 2
Transcripts prone to forming double-stranded RNA were enriched
WT_EV_5_2_dsRNA


title: Hap1_WT_dsRNA-seq_biological replicate 1

description:
Library name: Sample 1
Transcripts prone to forming double-stranded RNA were enriched
WT_EV_5_1_dsRNA


title: SJCNS019123_201496860075_R08C01

description:
201496860075_R08C01
blood from survivor of childhood cancer and control


title: SJSTS019607_201496860075_R05C01

description:
201496860075_R05C01
blood from survivor of childhood cancer and control

value: Soft tissue sarcoma

value: Black


title: Input, YFP-BAF-T4A/S5A  S2 cells, Replicate2

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

description:
Library name: N-BAF_T4A/S5A_Input_r2
sequenced by 2x150 paired-end reads

data_processing:
FastQ files were aligned to the Drosophila melanogaster dm6 genome using Bowtie2 v2.2.2  with options -N 1 -k 1. Duplicated reads for generation of TDF tracks were identified and removed with sambamba v0.5.1. BigWig tracks were generated with IGVTools2. Quality control was performed using FastQC v1.7 and summarized with MultiQC.
Assembly: Dm6
Supplementary files format and content: BigWig of normalized signal vs input

organism: Drosophila melanogaster

source_name: S2 N-BAF_T4A/S5A

growth_protocol: Cultured cells used in these experiments were Schneider's Drosophila Line 2 [D. Mel. (2), SL2] (ATCC® CRL-1963™). To obtain stable cell lines, Drosophila S2 cells were grown under standard conditions (25°C in Schneider's medium (Sigma) supplemented with 10% FBS (Gibco), 100mg/ml Streptomycin and 100mg/ml Penicillin) and transfected with the indicated constructs by the calcium phosphate method as described in {Moreno-Moreno, 2006 #61}. After 48h of transfection, 0.8 mg/ml of G418 and/or 0.02 mg/ml of Blasticidine were added for selection.

extract_protocol:
S2 cells (14 × 10⁶) were crosslinked with 1.8% formaldehyde for 10 minutes at room temperature and chromatin was prepared as described in {Bujosa, 2024 #65}. Chromatin samples were sonicated using a Bioruptor Pico (Diagenode) to obtain fragments between 200–500 bp and, after sonication, lysates were adjusted to 1% Triton X-100, 0.1% sodium deoxycholate (DOC), 140mM NaCl, incubated for 10 minutes on a rotating wheel at 4°C, and chromatin was recovered by centrifugation. For each experiment, 400 μl of chromatin were used for IP, and 40 μl were retained as input. Immunoprecipitation (IP) was carried out in RIPA buffer (140mM NaCl, 10mM Tris–HCl, pH 8.0, 1mM EDTA, 1% Triton X-100, 0.01% SDS, 0.1% DOC). For endogenous BAF, lysates were pre-cleared with 30 μl of 50% (v/v) protein A–Sepharose CL-4B beads (GE Healthcare, 17-0780-01) pre-blocked with RIPA + 1% BSA and, after pre-clearing, 10 μl of aBAF antibodies were added, and samples were incubated overnight at 4°C with rotation. Then, IPs were performed by adding 40 μl of 50% (v/v) protein A–Sepharose CL-4B beads (pre-blocked with RIPA + 1% BSA) and incubating for 3 hours at 4°C on a rotating wheel. For N-BAF, C-BAF and N-BAFT4A/S5A samples, 40 μl of GFP-Trap Magnetic Agarose beads (Chromotek) were added, and samples were incubated for 3 hours at 4°C with rotation. After IP, beads from all conditions were washed five times for 5 minutes with 1 ml of RIPA buffer, once with high-salt buffer (250mM LiCl, 10mM Tris–HCl, pH 8.0, 1mM EDTA, 0.5% NP-40, 0.5% DOC), and twice with TE buffer for 5 minutes. Beads were resuspended in 40 μl of TE and RNase A (DNase-free) was added to a final concentration of 0.25 μg/ml to both IP and input samples, and samples were incubated for 30 minutes at 37°C. To purify DNA, samples were adjusted to 1% SDS, 100mM NaHCO₃, 0.2 mg/ml Proteinase K, and incubated overnight at 65°C. DNA was purified using phenol-chloroform extraction.
Libraries were generated using NEBNext Ultra II DNA Library Prep Kit (Illumina) and sequenced by 2x150 paired-end reads on a NovaSeq S4 (Illumina) at the CNAG (Barcelona).

tag: barcode

value: S2 N-BAF_T4A/S5A

value: Schneider's Drosophila Line 2 [D. Mel. (2), SL2] (ATCC CRL-1963)


title: RNA_SMC3KOff_cDC2_03

value: CD11cCre/+ Smc3fl/fl


title: Input, YFP-BAF-T4A/S5A  S2 cells, Replicate1

description:
Library name: N-BAF_T4A/S5A_Input_r1
sequenced by 2x150 paired-end reads


title: Hap1_ADAR1-E912A KI_dsRNA-seq_biological replicate 1

description:
Library name: Sample 5
Transcripts prone to forming double-stranded RNA were enriched
E912A_KI3_6_1_dsRNA


title: SJWLM019645_201496860075_R07C01

description:
201496860075_R07C01
blood from survivor of childhood cancer and control

value: Wilms tumor


title: ChIP-αGFP, YFP-BAF-T4A/S5A  S2 cells, Replicate2

description:
Library name: N-BAF_T4A/S5A_ChIP_r2
sequenced by 2x150 paired-end reads


title: SJOS019517_201496860075_R04C01

description:
201496860075_R04C01
blood from survivor of childhood cancer and control

value: male

value: Osteosarcoma


title: ChIP-αGFP, BAF-YFP S2 cells, Replicate1

description:
Library name: C-BAF_ChIP_r1
sequenced by 2x150 paired-end reads

source_name: S2 C-BAF

value: S2 C-BAF


title: RNA_SMC3KOff_cDC1_03

value: spleen


title: RNA_SMC3KOff_cDC2_02


title: Input, BAF-YFP S2 cells, Replicate2

description:
Library name: C-BAF_Input_r2
sequenced by 2x150 paired-end reads


title: ChIP-αGFP, BAF-YFP S2 cells, Replicate2

description:
Library name: C-BAF_ChIP_r2
sequenced by 2x150 paired-end reads


title: ChIP-αGFP, YFP-BAF-T4A/S5A  S2 cells, Replicate1

description:
Library name: N-BAF_T4A/S5A_ChIP_r1
sequenced by 2x150 paired-end reads


title: RNA_SMC3KOff_cDC1_02


title: ChIP-αGFP, YFP-BAF S2 cells, Replicate2

description:
Library name: N-BAF_ChIP_r2
sequenced by 2x150 paired-end reads

source_name: S2 N-BAF

value: S2 N-BAF


title: Input, BAF-YFP S2 cells, Replicate1

description:
Library name: C-BAF_Input_r1
sequenced by 2x150 paired-end reads


title: SJCNS019168_201496860075_R06C01

description:
201496860075_R06C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Central nervous system (CNS)


title: SJALL018418_201496860075_R02C01

description:
201496860075_R02C01
blood from survivor of childhood cancer and control

value: female

value: cancer survivor

value: Acute lymphoblastic leukemia


title: Input, YFP-BAF S2 cells, Replicate2

description:
Library name: N-BAF_Input_r2
sequenced by 2x150 paired-end reads


title: RNA_SMC3KOff_cDC2_01


title: ChIP-αBAF, S2 control cells, Replicate2

description:
Library name: S2_ChIP_r2
sequenced by 2x150 paired-end reads


title: Input, YFP-BAF S2 cells, Replicate1

description:
Library name: N-BAF_Input_r1
sequenced by 2x150 paired-end reads


title: SJMEL019377_201496860075_R03C01

description:
201496860075_R03C01
blood from survivor of childhood cancer and control

value: Melanoma


title: RNA_SMC3KOff_cDC1_01


title: ChIP-αBAF, S2 control cells, Replicate1

description:
Library name: S2_ChIP_r1
sequenced by 2x150 paired-end reads


title: SJCNS001218_201496860071_R08C01

description:
201496860071_R08C01
blood from survivor of childhood cancer and control

value: White


title: Input, S2 control cells, Replicate1

description:
Library name: S2_Input_r1
sequenced by 2x150 paired-end reads


title: RNA_WT_cDC1_03


title: SJNBL019428_201496860071_R07C01

description:
201496860071_R07C01
blood from survivor of childhood cancer and control

value: Neuroblastoma


title: RNA_WT_cDC2_03


title: T-MSC add DNCB mice #1

type: RNA

city: SEOUL

first: SOYOUN

last: WOO

address: 25, Magokdong-ro 2-gil, Gangseo-gu

country: South Korea

institute: Ewha Womans University, College of Medicine

description: Gene expression data from T-MSC-treated DNCB dermatitis C57BL/6 mice spleen

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

source_name: T-MSC add DNCB mice #1 spleen

label_protocol: [Clariom™ S Assay, mouse] The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Female C57BL/6J mice, 8 weeks old, were housed under specific pathogen-free (SPF) conditions at 21–23°C with 51–54% humidity, maintained on a 12-hour light/dark cycle, and provided food and water ad libitum.

extract_protocol: Trizol extraction of total RNA from spleen tissue was performed according to the manufacturer's instructions.

treatment_protocol: Vehicle control, Vehicle + T-MSCs, DNCB (138630; Sigma-Aldrich), and DNCB + T-MSCs. A 1% DNCB solution was prepared in a mixture of acetone (179124; Sigma-Aldrich, 75%) and olive oil (25%). The vehicle solution consisted of the same acetone/olive oil mixture without DNCB. Each group received 200 µL of the respective solution applied to shaved dorsal skin on days 1, 2, 3, 8, and 9. On day 2, T-MSCs (5×10^5 cells in 200 µL PBS) were administered by intravenous injection via the tail vein to the designated groups.

value: Female

tag: strain


title: ChIP-αGFP, YFP-BAF S2 cells, Replicate1

description:
Library name: N-BAF_ChIP_r1
sequenced by 2x150 paired-end reads

value: Schneider's Drosophila Line 2 [D. Mel. (2), SL2] (ATCC CRL-1963)


title: RNA_WT_cDC2_02


title: DNCB dermatitis mice #2

description: Gene expression data from DNCB dermatitis C57BL/6 mice spleen

source_name: DNCB dermatitis mice #2 spleen


title: SJALL018939_201496860071_R05C01

description:
201496860071_R05C01
blood from survivor of childhood cancer and control


title: T-MSC add DNCB mice #3

source_name: T-MSC add DNCB mice #3 spleen


title: T-MSC only #3 mice

description: Gene expression data from T-MSC-treated C57BL/6 mice spleen

source_name: T-MSC only #3 mice spleen


title: Input, S2 control cells, Replicate2

description:
Library name: S2_Input_r2
sequenced by 2x150 paired-end reads


title: DNCB dermatitis mice #3

source_name: DNCB dermatitis mice #3 spleen


title: RNA_WT_cDC2_01


title: DNCB dermatitis mice #1

source_name: DNCB dermatitis mice #1 spleen


title: RNA_WT_cDC1_01


title: SJHL019247_201496860071_R04C01

description:
201496860071_R04C01
blood from survivor of childhood cancer and control

value: Hodgkin lymphoma


title: T-MSC only #2 mice

source_name: T-MSC only #2 mice spleen


title: T-MSC only #1 mice

source_name: T-MSC only #1 mice spleen


title: SJNBL018757_201496860071_R02C01

description:
201496860071_R02C01
blood from survivor of childhood cancer and control


title: SJMEL019375_201496860071_R03C01

description:
201496860071_R03C01
blood from survivor of childhood cancer and control


title: RNA_WT_cDC1_02


title: Chronic_Tnfa-biol rep 3

city: College Station

first: Shreya

middle: A

last: Raghavan

state: Texas

address: Texas A&M University, Emerging Technologies Building 3120, 101 Bizzell St

department: Department of Biomedical Engineering

institute: Texas A&M University

description: Library name: Sample  21

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Mapped to mus musculus (GRCm38) usign STAR aligner v.2.5.2b
Assembly: GRCm38
Supplementary files format and content: Tab-deliminating text file contains raw counts for each sample

source_name: Bioengineered Colon Assembloids

growth_protocol: Bioengineered Colon constructs; comprising of immortalized Bone Marrow Derived Macrophages (iBMDMs), immortalized Murine Fetal Enteric Neurons (IM-FENs), and immortalized Colonic Smooth Muscle Cells (icSMCs); were maintained in complete DMEM, N2C and SMC media. The constructs were incubated at 37°C in a humidified incubator with 5% CO2. Formation of bioengineered colon assembloids was monitored  over 7 days.

extract_protocol:
RNA was extracted from assembloids using a RNeasy extraction kit (Qiagen, Hilden, Germany).
RNA Seq libraries were constructed by Azenta Life Sciences

treatment_protocol: Bioengineered Colonic Assembloids were subjected to inflammatory insult by exposing to PB or TNF-α for 24 hours. RNA was isolated from PB or TNF-α and control assembloids at Day 4 (acute; n=4) and Day 7 (chronic; n=3).

value: Bioengineered Colon Assembloids

tag: treatment

value: Tumor Necrosis Factor-alpha

tag: condition

value: Chronic (Day 7)


title: normal control #1 mice

description: Gene expression data from control C57BL/6 mice spleen

source_name: normal control #1 mice spleen


title: Chronic_Tnfa-biol rep 1

description: Library name: Sample  19


title: SJHIST018641_201496860075_R01C01

description:
201496860075_R01C01
blood from survivor of childhood cancer and control

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

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: male

value: Histiocytosis


title: SJSTS018862_201496860071_R01C01

description:
201496860071_R01C01
blood from survivor of childhood cancer and control

value: Soft tissue sarcoma


title: normal control #2 mice

source_name: normal control #2 mice spleen

value: spleen


title: Chronic_PB-biol rep 3

description: Library name: Sample  18

value: Pyrodostigmine Bromide


title: RNA_IRF8KO_HoxB8_03

data_processing:
Adapters were trimmed using Trimmomatic; reads were alligned using Star; reads quantified using featureCount; count normalization and differential expression performed using DEseq2.
Assembly: mm10
Supplementary files format and content: counts.raw.csv.gz; raw gene x sample counts matrix

extract_protocol:
RNA was extracted from 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: Cas9 ribonucleoproteins (RNPs) were prepared by incubating 250 pmol IRF8 sgRNA, 250 pmol CD45 sgRNA, 75 pmol S. pyogenes Cas9 Nuclease V3, and 100 pmol Alt-R Cas9 electroporation enhancer (all from IDT) together for 15 min at room-temperature. Control Cas9-RNPs were prepared containing 250 pmol non-targeting control crRNA and 250 pmol tracrRNA instead of 250 pmol IRF8 sgRNA. Hoxb8-FL cells (1x106) were resuspended in 100 μl Opti-MEM I reduced serum medium (Thermo Fisher Scientific), to which Cas9-RNPs were added. Cells were electroporated with 4D-Nucleofector X Unit (Lonza) using program CM-137. Transfected HoxB8-FL cells were passaged every other day until day 6 post transfection, at which point Hoxb8-FL progenitors were differentiated into mature DCs. Successful transfection was confirmed by loss of CD45 expression on both IRF8-deficient (Irf8Δ) and control Hoxb8-FL cell lines. Cell sorting was performed on 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. DC = Live singlets CD45-.

tag: cell line

tag: cell type

value: DC


title: RNA_Control_HoxB8_01

tag: genotype

value: Control


title: SJWLM019654_201496860027_R08C01

description:
201496860027_R08C01
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.

tag: tissue

value: peripheral blood mononuclear cells

tag: age

value: female

value: cancer survivor

value: Wilms tumor


title: SJNBL019408_201496860071_R06C01

description:
201496860071_R06C01
blood from survivor of childhood cancer and control

tag: Sex

tag: group

value: Neuroblastoma

value: White


title: Chronic_control-biol rep 2

description: Library name: Sample  14

value: control


title: SJCNS019135_201496860027_R06C01

description:
201496860027_R06C01
blood from survivor of childhood cancer and control

tag: age at cancer diagnosis

tag: diagnostic group

value: Central nervous system (CNS)


title: RNA_IRF8KO_HoxB8_01


title: Spinal cord T cell

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope v1.15.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a  to map reads to the reference genome GRCm38 (ensembl version 92 annotation). UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 (Ref) software, and used to generate expression matrix files for subsequent analysis.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: injured spinal cord

extract_protocol:
The fresh tissues were stored in the sCelLiveTMTissue Preservation Solution (Singleron) on ice after the surgery within 30 mins. The specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times, minced into small pieces, and then digested with 3 mL sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN™ Tissue Dissociation System at 37 °C for 15 min. The cell suspension was collected and filtered through a 40-micron sterile strainer. Afterwards, the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added, and the mixture[Cell: RCLB=1:2 (volume ratio)] was incubated at room temperature for 5-8 min to remove red blood cells. The mixture was then centrifuged at 300 × g 4 ℃ for 5 mins to remove supernatant and suspended softly with PBS
Single-cell suspensions at a concentration of 1×105 cells ml-1 were converted to barcoded scRNA-seq libraries according to the protocols of the Chromium Single Cell 5’Library, Gel Bead & Multiplex Kit (10x Genomics). Briefly, the cells were partitioned into Gel Beads in Emulsion in the ChromiumTM Controller instrument where cell lysis and barcoded reverse transcription of RNA occurred. TCR- enriched libraries were generated with aliquots from each of the aforementioned cDNAs using the Chromium Single Cell V(D)J Enrichment kit. All the libraries were sequenced on Illumina Novaseq 6000 with 150 bp paired end reads.

value: injured spinal cord

value: T cell


title: Acute_Tnfa-biol rep 4

description: Library name: Sample  12

value: Bioengineered Colon Assembloids

value: Tumor Necrosis Factor-alpha

value: Acute (Day 4)


title: RNA_Control_HoxB8_03


title: T-MSC add DNCB mice #2

source_name: T-MSC add DNCB mice #2 spleen

value: Female

value: spleen


title: SJALL018963_201496860027_R05C01

description:
201496860027_R05C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia

tag: average dose to whole heart, cgy

tag: race group


title: SJCNS019186_201496860027_R07C01

description:
201496860027_R07C01
blood from survivor of childhood cancer and control

value: male

tag: base line visit start date

tag: base line visit finish


title: Chronic_Tnfa-biol rep 2

description: Library name: Sample  20

value: Chronic (Day 7)


title: Acute_Tnfa-biol rep 2

description: Library name: Sample  10


title: RNA_IRF8KO_HoxB8_02

value: DC


title: Chronic_PB-biol rep 1

description: Library name: Sample  16

value: Pyrodostigmine Bromide


title: Chronic_control-biol rep 3

description: Library name: Sample  15


title: Spleen T cell

source_name: spleen


title: RNA_Control_HoxB8_02

value: Control


title: ATAC_HoxB8_pDC_CpGA_24h_02

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)

extract_protocol:
Cells were washed with PBS and immediately processed as previously described (Buenostro et al, 2015, PMC4374986).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HoxB8-FL-derived pDCs were sorted 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. pDCs = Live singlets CD11c+ MHC-II- B220+ Siglec-H+. Purified pDCs were stimulated with 1 μM CpG-A/ODN2216 (InvivoGen) for 6 hours and 24 hours or left unstimulated as a control for the same duration of time. Successful pDC activation was confirmed by flow cytometric analysis of CD69 upregulation and/or intracellular staining for IFN-α.

value: pDC

value: CpG-A (24h)


title: ATAC_HoxB8_pDC_US_24h_02

value: Unstimulated (24h)


title: Chronic_PB-biol rep 2

description: Library name: Sample  17


title: Acute_control-biol rep 4

description: Library name: Sample  4

value: control


title: Chronic_control-biol rep 1

description: Library name: Sample  13


title: Acute_control-biol rep 3

description: Library name: Sample  3


title: SJALL018934_201496850205_R08C01

description:
201496850205_R08C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: female

value: cancer survivor

value: White

tag: age at death


title: Acute_Tnfa-biol rep 3

description: Library name: Sample  11

value: Bioengineered Colon Assembloids

value: Tumor Necrosis Factor-alpha

value: Acute (Day 4)


title: Acute_control-biol rep 1

description: Library name: Sample  1


title: SJEWS019206_201496860027_R04C01

description:
201496860027_R04C01
blood from survivor of childhood cancer and control

value: Ewing sarcoma family of tumors


title: SJOS019509_201496850205_R07C01

description:
201496850205_R07C01
blood from survivor of childhood cancer and control

value: Osteosarcoma


title: normal control #3 mice

source_name: normal control #3 mice spleen

value: Female

tag: strain

value: spleen


title: ATAC_HoxB8_pDC_CpGA_6h_01

tag: treatment

value: CpG-A (6h)


title: Acute_PB-biol rep 2

description: Library name: Sample  6

value: Pyrodostigmine Bromide

tag: condition


title: Acute_PB-biol rep 3

description: Library name: Sample  7


title: ATAC_HoxB8_pDC_CpGA_6h_02

tag: cell line

value: pDC


title: WT_Gastrocnemius_3793553

city: Tarrytown

first: Michael

last: Stec

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

description:
Library name: 1088160_1_1
4133.9869.1088160.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

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

value: WT

tag: target gene

value: Cdh15 (Mus musculus)

value: muscle

tag: tissue details

value: Gastrocnemius


title: SJHL018699_201496860027_R02C01

description:
201496860027_R02C01
blood from survivor of childhood cancer and control

tag: tissue

value: peripheral blood mononuclear cells

tag: age

tag: Sex

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

value: Hodgkin lymphoma

value: White


title: SJGCT019221_201496860027_R03C01

description:
201496860027_R03C01
blood from survivor of childhood cancer and control

tag: diagnostic group

value: Germ cell tumor

tag: average dose to whole heart, cgy

tag: race group

value: Black

tag: base line visit start date

tag: base line visit finish


title: ATAC_HoxB8_pDC_US_24h_01

tag: cell line

tag: cell type

tag: treatment

value: Unstimulated (24h)


title: WT_Gastrocnemius_3805673

description:
Library name: 1088156_1_1
4133.9869.1088156.S33.W101102

tag: age unit

tag: animal id

tag: fast time

tag: genotype

tag: strain


title: ATAC_HoxB8_pDC_US_6h_01

value: Unstimulated (6h)


title: WT_Gastrocnemius_3817948

description:
Library name: 1088155_1_1
4133.9869.1088155.S33.W101102

tag: age

tag: gender

tag: target gene

tag: tissue

tag: tissue details


title: ATAC_HoxB8_pDC_CpGA_24h_01

value: pDC

value: CpG-A (24h)


title: Acute_PB-biol rep 1

description: Library name: Sample  5

value: Bioengineered Colon Assembloids

value: Pyrodostigmine Bromide

tag: condition

value: Acute (Day 4)


title: Acute_Tnfa-biol rep 1

description: Library name: Sample  9

value: Tumor Necrosis Factor-alpha


title: SJNHL019466_201496850205_R03C01

description:
201496850205_R03C01
blood from survivor of childhood cancer and control

tag: Sex

tag: group

tag: age at cancer diagnosis

tag: diagnostic group

value: Non-Hodgkin lymphoma

tag: average dose to whole heart, cgy

tag: race group

tag: age at death


title: CUTRUN_pDC_H3K27me3

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_cDC2_H3K27me3


title: Cdh15 KO_Gastrocnemius_3817943

description:
Library name: 1088152_1_1
4133.9869.1088152.S33.W101102

tag: age unit

value: days

tag: animal id

tag: fast time

value: Fasted 18h

value: M

value: Cdh15 KO

value: Cdh15 (Mus musculus)

value: muscle

value: Gastrocnemius


title: WT_Gastrocnemius_3805657

description:
Library name: 1088153_1_1
4133.9869.1088153.S33.W101102

tag: age

tag: genotype

value: WT

tag: strain


title: Cdh15 KO_Gastrocnemius_3805676

description:
Library name: 1088158_1_1
4133.9869.1088158.S33.W101102

tag: gender

tag: target gene

tag: tissue


title: SJRHB003947_201496850205_R06C01

description:
201496850205_R06C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: Sex

value: female

value: cancer survivor

value: Rhabdomyosarcoma

value: White

tag: base line visit start date

tag: base line visit finish


title: Cdh15 KO_Gastrocnemius_3805666

description:
Library name: 1088159_1_1
4133.9869.1088159.S33.W101102

tag: tissue details


title: SJNBL018752_201496860027_R01C01

description:
201496860027_R01C01
blood from survivor of childhood cancer and control

tag: group

tag: age at cancer diagnosis

tag: diagnostic group

value: Neuroblastoma

tag: average dose to whole heart, cgy

value: Black


title: Acute_control-biol rep 2

description: Library name: Sample  2

value: Bioengineered Colon Assembloids

tag: treatment

value: control

tag: condition

value: Acute (Day 4)


title: Panc-1_10% FBS_replicate _1

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.

source_name: Panc-1, 10% FBS, 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

value: 10% FBS


title: Panc-1_10% FBS_replicate _2

source_name: Panc-1, 10% FBS, replicate 2


title: Acute_PB-biol rep 4

description: Library name: Sample  8

value: Pyrodostigmine Bromide


title: SJCNS018589_201496850205_R01C01

description:
201496850205_R01C01
blood from survivor of childhood cancer and control

tag: age

value: Central nervous system (CNS)

tag: race group

tag: age at death


title: ATAC_HoxB8_pDC_US_6h_02

tag: cell type

value: pDC

value: Unstimulated (6h)


title: SJAML019105_201496850205_R04C01

description:
201496850205_R04C01
blood from survivor of childhood cancer and control

tag: tissue

value: male

value: Acute myeloid leukemia


title: SJWLM019637_201496850182_R08C01

description:
201496850182_R08C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: Sex

value: female

value: Wilms tumor


title: CUTRUN_undiff_H3K27me3

value: Undifferentiated


title: Panc-1_CAF-CM_replicate_2

source_name: Panc-1, CAF-CM, replicate 2

value: CAF-CM


title: Cdh15 KO_Gastrocnemius_3779417

description:
Library name: 1088149_1_1
4133.9869.1088149.S33.W101102

tag: age unit

value: days

tag: animal id

tag: fast time

value: Fasted 18h

tag: gender

value: M

tag: genotype

value: Cdh15 KO

tag: strain

tag: target gene

value: Cdh15 (Mus musculus)

value: muscle

value: Gastrocnemius


title: Panc-1_CAF-CM_replicate_1

source_name: Panc-1, CAF-CM, replicate 1

value: Pancreatic ductal adenocarcinoma

tag: treatment


title: SJWLM018893_201496850205_R02C01

description:
201496850205_R02C01
blood from survivor of childhood cancer and control

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

tag: average dose to whole heart, cgy

value: White

tag: base line visit start date

tag: base line visit finish


title: Cdh15 KO_Gastrocnemius_3793546

description:
Library name: 1088151_1_1
4133.9869.1088151.S33.W101102

tag: age

tag: tissue details


title: Cdh15 KO_EDL_3805666

description:
Library name: 1088147_1_1
4133.9869.1088147.S33.W101102

tag: tissue

value: EDL


title: WT_EDL_3793553

description:
Library name: 1088148_1_1
4133.9869.1088148.S33.W101102

tag: age unit

value: WT


title: CUTRUN_cDC1_H3K27Ac

value: FL-BMDC

tag: cell type


title: CUTRUN_cDC2_H3K27Ac


title: Panc-1_control medium_replicate_3

source_name: Panc-1, control medium, replicate 3

tag: tumor

tag: cell line

value: Control medium


title: SJWLM019652_201496850182_R06C01

description:
201496850182_R06C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: Sex

value: female

value: Wilms tumor

tag: race group

tag: age at death


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

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: 11075

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

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

tag: genotype

value: Mtarc1 Homozygous KO

tag: diet

value: CDAHFD


title: WT_Gastrocnemius_3793543

description:
Library name: 1088150_1_1
4133.9869.1088150.S33.W101102

value: days

tag: animal id

tag: fast time

value: Fasted 18h

tag: gender

value: M

tag: strain

tag: target gene


title: SJALL019009_201496850182_R05C01

description:
201496850182_R05C01
blood from survivor of childhood cancer and control

tag: age

tag: group

tag: age at cancer diagnosis

tag: diagnostic group

value: Acute lymphoblastic leukemia

tag: average dose to whole heart, cgy

tag: base line visit start date

tag: base line visit finish


title: WT_EDL_3805673

description:
Library name: 1088144_1_1
4133.9869.1088144.S33.W101102

tag: age unit

value: Cdh15 (Mus musculus)

tag: tissue

value: muscle

tag: tissue details


title: CUTRUN_cDC1_H3K27me3

tag: cell type


title: Panc-1_CAF-CM_replicate_3

source_name: Panc-1, CAF-CM, replicate 3

tag: tumor

value: Pancreatic ductal adenocarcinoma

tag: cell line

tag: treatment

value: CAF-CM


title: CUTRUN_undiff_H3K27Ac

value: Undifferentiated


title: SJCNS019155_201496850182_R04C01

description:
201496850182_R04C01
blood from survivor of childhood cancer and control

tag: Sex

value: male

value: cancer survivor

value: Central nervous system (CNS)

tag: race group

value: Black

tag: age at death


title: CUTRUN_pDC_H3K27Ac

value: FL-BMDC

value: pDC


title: CUTRUN_cDC2_H3K9me3


title: Mouse Liver, Mtarc1 homozygous KO CDAHFD, Sample 8

description: Library name: 11143

value: Liver

tag: genotype

value: Mtarc1 Homozygous KO

tag: diet


title: Cdh15 KO_EDL_3805676

description:
Library name: 1088146_1_1
4133.9869.1088146.S33.W101102

tag: age

value: days

tag: animal id

tag: fast time

tag: gender

value: Cdh15 KO

tag: strain

tag: target gene

value: EDL


title: SJCNS019180_201496850205_R05C01

description:
201496850205_R05C01
blood from survivor of childhood cancer and control

tag: tissue

value: peripheral blood mononuclear cells

value: female

tag: group

tag: age at cancer diagnosis

tag: diagnostic group

tag: average dose to whole heart, cgy

value: White

tag: base line visit start date

tag: base line visit finish


title: SJALL018948_201496850182_R07C01

description:
201496850182_R07C01
blood from survivor of childhood cancer and control

tag: Sex

value: Acute lymphoblastic leukemia

tag: race group


title: Panc-1_control medium_replicate_2

source_name: Panc-1, control medium, replicate 2

tag: tumor

value: Pancreatic ductal adenocarcinoma

tag: cell line

tag: treatment

value: Control medium


title: CUTRUN_pDC_H3K9me3

tag: cell type