title: Lung RNA-seq, EA-BN-H (200 mg/kg) replicate 2

description:
Library name: COPD_EA-H2
EA-BN-H group lung tissue collected on day 15; total RNA extracted using TRIzol; library prep TruSeq Stranded Total RNA Gold; PE sequencing.

value: LPS/CSC intranasal (days 1,6,13) + EA-BN 200 mg/kg oral (days 1–14)


title: SJALL019745_203271750073_R05C01

status: Public on Jan 13 2026

type: genomic

city: Memphis

first: Zhaoming

last: Wang

address: 262 Danny Thomas Place

country: USA

institute: St. Jude Children's Research Hospital

description:
203271750073_R05C01
blood from survivor of childhood cancer and control

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

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

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

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

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

label_protocol: Standard Illumina Protocol

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

tag: tissue

value: peripheral blood mononuclear cells

tag: age

tag: Sex

value: female

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Acute lymphoblastic leukemia

tag: average dose to whole heart, cgy

tag: race group

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: SJNBL018740_203271740052_R03C01

description:
203271740052_R03C01
blood from survivor of childhood cancer and control

value: Neuroblastoma


title: RNAseq - CN CxB rep2

type: SRA

city: Cambridge

first: Bongmin

last: Bae

state: MA

address: 16 Divinity Ave

institute: Harvard University

description:
Library name: RNAseq_CxB_2
CxB_2_genome1 and CxB_2_genome2

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Primary cortical neurons

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

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

tag: cell type

value: Primary cortical neurons

tag: genotype

value: F1 CastxBL6


title: E16 primary neuron BxC rep1

description:
Library name: CTCF_BxC_1
BxC_1_genome1 and BxC_1_genome2

library_source: other

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

molecule: other

source_name: Cortical neurons

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

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

value: Cortical neurons

value: F1 BL6xCast


title: SJALL018461_203271740052_R01C01

description:
203271740052_R01C01
blood from survivor of childhood cancer and control


title: Lung RNA-seq, COPD replicate 2

city: Jeongeup-si

first: Ba-Wool

last: Lee

state: Jeollabuk-do

address: Korea Research Institute of Bioscience and Biotechnology, center 2

country: South Korea

description:
Library name: COPD_2
COPD group lung tissue collected on day 15; total RNA extracted using TRIzol; library prep TruSeq Stranded Total RNA Gold; PE sequencing.

data_processing:
Adapter/quality trimming was performed using Trimmomatic (v0.38).
Trimmed reads were aligned to the Mus musculus reference genome (mm10) using HISAT2 (v2.1.0).
Transcript assembly and quantification were performed using StringTie (v2.1.3b) based on the reference gene model.
Expression profiles were generated as read counts and normalized values (FPKM and TPM) for each sample (StringTie output).
Differential expression analysis was performed using DESeq2 with the negative binomial Wald test (nbinomWaldTest).
Assembly: Mus musculus reference genome: mm10 (Annotation: NCBI_108).
Supplementary files format and content: Processed data files include an expression profile table produced by StringTie for mm10. The table contains transcript/gene identifiers (e.g., Transcript_ID, Gene_ID, Gene_Symbol, Gene_Description) and per-sample quantitative values including Read_Count, FPKM, and TPM.
Supplementary files format and content: Example processed file name: Expression_Profile.mm10.transcript.xlsx (StringTie expression profile output).

source_name: lung

growth_protocol: C57BL/6N male mice were obtained from Orient Bio (Republic of Korea) and maintained under specific pathogen-free conditions in accordance with the Institutional Animal Care and Use Committee (IACUC) guidelines of KRIBB (Approval No.: KRIBB-AEC-23317).

extract_protocol:
Total RNA was extracted from mouse lung tissues using TRIzol reagent according to the manufacturer’s instructions. RNA integrity/quality was assessed (e.g., Agilent TapeStation RNA ScreenTape), and only high-quality RNA was used for library construction.
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina) following the TruSeq Stranded Total RNA Reference Guide (1000000040499 v00). Sequencing was performed on an Illumina platform using paired-end reads (read length 101 bp).

treatment_protocol: Male C57BL/6N mice were divided into three groups for RNA-seq: NC, COPD, and EA-BN-H (200 mg/kg). LPS (0.5 mg/kg) and cigarette smoke condensate (CSC; 12.5 mg/kg) were intranasally instilled under light anesthesia on days 1, 6, and 13. Vehicle (2% DMSO) or EA-BN (200 mg/kg in 2% DMSO) was administered orally once daily from days 1 to 14. Lung tissues were collected on day 15.

value: lung

tag: treatment

value: LPS (0.5 mg/kg) + CSC (12.5 mg/kg) intranasal (days 1,6,13) + vehicle oral


title: SJALL017888_203259750054_R04C01

description:
203259750054_R04C01
blood from survivor of childhood cancer and control


title: SJCNS017897_203259750054_R02C01

description:
203259750054_R02C01
blood from survivor of childhood cancer and control

value: male

value: Central nervous system (CNS)


title: SJRHB018841_203271750073_R02C01

description:
203271750073_R02C01
blood from survivor of childhood cancer and control

value: Rhabdomyosarcoma


title: RNAseq - CN CxB rep1

description:
Library name: RNAseq_CxB_1
CxB_1_genome1 and CxB_1_genome2


title: E16 primary neuron BxC rep2

description:
Library name: CTCF_BxC_2
BxC_2_genome1 and BxC_2_genome2


title: CHiC - CN BxC rep2

description: Library name: CHiC_CN_BxC_2

data_processing:
Mouse genome GRCm39 was prepared using SNPsplit_genome_preparation script to mask all the CAST_EiJ single nucleotide polymorphism positions using mgp_REL2021_snps.vcf.gz from the Mouse Genomes Project. SNP-masked genome was digested at Arima restriction enzyme sequences using HiCUP_digester. Capture Hi-C fastq files were mapped using HiCUP (v0.8.0). This wrapper identified mapped paired-end reads with valid Hi-C di-tags. Allele phasing was performed inputting ‘hicup.bam’ files to SNPsplit (v0.6.0). Read pairs in ‘hicup.G1_G1.bam’ or ‘hicup.G2_G2.bam’ files were converted to ‘prejuicer’ format using HiCUP hicup2juicer script (v0.9.0) with --usemid --digest options. Using a custom script, reads were filtered for the capture regions with MAPQ score > 30 at both ends, and maternal and paternal read pair numbers were normalized by subsampling the deeper allele.
Assembly: GRCm39
Supplementary files format and content: read pair files (medium format)

growth_protocol: Mouse ESCs were grown on 0.2% gelatin coated plate in ESC media (DMEM supplemented with 10 mM HEPES, 0.11 mM β-mercaptoethanol, 1× NEAA, 2 mM L-glutamine, 15% FBS, and 1000 U/mL LIF). For drug treatment, 5 μM GSK-3484862 was added to treatment groups and volume matched DMSO was added to controls.  / Cortices from E16 embryos were carefully collected into cortical neuron plating media (Neurobasal supplemented with 2% B27, 2% FBS and 1X glutamine). Tissues were mechanically triturated into the plating media by pipetting up and down with 1000μL micropipette tips. Cell suspensions were filtered through a 40 μm cell strainer. Dissociated cells were plated onto Poly-D-lysine coated plates with plating media. Next day, media was replaced with cortical neuron maintenance media (Neurobasal supplemented with 2% B27 and 1X glutamine) and kept at 37°C with 5% CO2 until use.

extract_protocol:
Adherent cells were washed with PBS two times and scraped into 5 mL PBS. / Dissected mouse cortices (two BxC and two CxB) were snap frozen in liquid nitrogen and stored at -80 °C. Frozen tissues were pulverized using Cell crusher in liquid nitrogen.
Samples resuspended in 5 mL PBS and crosslinked in 2% formaldehyde by adding 500 μL of TC buffer and incubating at room temperature for 20 min. Reaction was quenched by adding 289 μL of strop solution I and incubating at RT for 5 min. Crosslinked tissue powder was then centrifuged at 2,000 xg at RT for 15 min and supernatant was discarded. Pellet was stored at -80 C until use. Samples were resuspended in 20 μL lysis buffer, lysed at 4 C for 30 min, conditioned using SDS solution at 62 C for 10 min, and quenched by incubating with 20 μL of stop solution II at 37 C for 15 min. Digestion of extracted chromatin was performed using Arima enzymes by incubating at 37 C 60 min, 65 C 20 min, and 25 C 10 min. Digested chromatin was subject to biotin end repair at RT for 45 min, followed by proximity ligation at RT for 15 min. Crosslinking reversal was performed using proteinase K and incubating at 55 C 30 min, 68 C overnight, and 25 C 10 min. Proximity-ligated DNA was purified using AMPure XP beads. Proximity-ligated DNA was brought to 100 μL in elution buffer and fragmented using Covaris S220 (140 W, 10% duty factor, 200 cycles per burst, 55 sec) to obtain a target fragment of 400 bp. Double sided size selection was performed using 0.6X and 0.25X AMPure XP beads. Biotin enrichment was performed using 300-400 ng of size-selected DNA and 12.5 μL T1 Streptavidin beads in 200 μL binding buffer reaction. Two washes were performed in 200 μL wash buffer at 55 C for 2 min each. Final wash was performed in 100 μL of elution buffer. Washed beads were resuspended in 50 μL of water. On beads end repair was performed by incubating end repair mix at 20 C 15 min 72 C 15 min, followed by adaptor ligation at 20 C 30 min. Samples were cleaned up by magnetizing beads and washing in 200 μL wash buffer at 55 C 2 min and in 100 μL elution buffer. Washed beads were resuspended in 34 μL of water and immediately used for library amplification using Herculase II Fusion polymerase (98 C 2 min / 10X 98 C 30 sec 60 C 30 sec 72 C 1 min / 72 C 5 min). Different index primer combinations were used for each sample. Amplified library was purified using 1X AMPure XP beads. An aliquot of 1.5 μg PCR product in 30 μL elution buffer was pre-cleared of biotin using 50 μL T1 Streptavidin beads in 230 μL reaction. Pre-cleared Hi-C library was resuspended in 14 μL water. Approximately 1 μg of Hi-C library was incubated with custom probes (Agilent Technologies) in thermocycler (95 C 5 min, 65 C 10 min / 60X 65 C 1 min 37 C 3 sec) and purified using 50 μL T1 Streptavidin beads. Vigorous washes were performed six times at 70 C 5 min each. Capture enriched library is amplified using Herculase II polymerase (98 C 2 min / 13X 98 C 30 sec 60 C 30 sec 72 C 1 min / 72 C 5min). Final library purification was performed using 1X AMPure XP beads and resuspended in 25 μL water. Samples were pooled equimolar. Sequencing was performed PE150.


title: SJHIST011273_203259600136_R07C01

description:
203259600136_R07C01
blood from survivor of childhood cancer and control

value: Histiocytosis


title: SJALL018521_203259600136_R06C01

description:
203259600136_R06C01
blood from survivor of childhood cancer and control


title: SJWLM019848_203271740052_R05C01

description:
203271740052_R05C01
blood from survivor of childhood cancer and control

value: Wilms tumor


title: SJRB019827_203271740052_R07C01

description:
203271740052_R07C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Retinoblastoma


title: SJALL017882_203259750054_R03C01

description:
203259750054_R03C01
blood from survivor of childhood cancer and control

value: cancer survivor

value: Black


title: SJNHL018785_203271740052_R02C01

description:
203271740052_R02C01
blood from survivor of childhood cancer and control

value: Non-Hodgkin lymphoma

value: White


title: SJRHB018838_203271740052_R04C01

description:
203271740052_R04C01
blood from survivor of childhood cancer and control


title: SJHL019784_203271740052_R08C01

description:
203271740052_R08C01
blood from survivor of childhood cancer and control

value: female

value: Hodgkin lymphoma


title: ATAC - 8w-old cortex CxB rep2

description:
Library name: ATAC_Cortex_CxB_2
CxB_2_genome1(BL6) and CxB_2_genome2(CAST)

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

source_name: Cortex

extract_protocol:
Dissected mouse cortices (two BxC and two CxB) were snap frozen in liquid nitrogen and stored at -80 °C.
ATAC-seq library was prepared using the ActiveMotif ATAC-seq kit. Frozen mouse brains were minced with razor blade on ice and quickly transferred to conical tubes containing cold PBS. Tissue was centrifuged at 500 xg for 5 min at 4 C. PBS was discarded, and the pellet was resuspended in 1 mL ATAC lysis buffer. Lysis was assisted by dounce homogenizer with tight fitting pestle for 30 strokes. Samples were filtered through 40 μm strainer into a new conical tubes. Nuclei were counted using trypan blue, and 100,000 nuclei were transferred to a new tube. Nuclei were centrifuged at 500 xg for 5 min at 4 C, and supernatant was discarded. Nuclei pellets were subject to tagmentation at 37 C for 30 min with gentle shaking at 800 rpm. Immediately following the tagmentation reaction, total DNA was extracted using columns. Purified DNA was PCR amplified using proper index primers. Then, the PCR reaction was purified using SPRI beads. Samples were pooled equimolar. Sequencing was performed PE150.

value: Cortex

value: F1 CastxBL6


title: SJHL017903_203259600136_R03C01

description:
203259600136_R03C01
blood from survivor of childhood cancer and control


title: RNAseq - CN CxB rep3

description:
Library name: RNAseq_CxB_3
CxB_3_genome1 and CxB_3_genome2

value: Primary cortical neurons


title: RNAseq - CN BxC rep3

description:
Library name: RNAseq_BxC_3
BxC_3_genome1 and BxC_3_genome2

value: F1 BL6xCast


title: SJALL018527_203259750054_R07C01

description:
203259750054_R07C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: SJSTS017951_203259750054_R05C01

description:
203259750054_R05C01
blood from survivor of childhood cancer and control

value: Soft tissue sarcoma


title: SJALL018525_203259750054_R06C01

description:
203259750054_R06C01
blood from survivor of childhood cancer and control


title: SJAML017891_203259600136_R02C01

description:
203259600136_R02C01
blood from survivor of childhood cancer and control

value: male

value: Acute myeloid leukemia


title: SJOS017932_203259600136_R01C01

description:
203259600136_R01C01
blood from survivor of childhood cancer and control

value: Osteosarcoma


title: ATAC - 8w-old cortex BxC rep2

description:
Library name: ATAC_Cortex_BxC_2
BxC_2_genome1(BL6) and BxC_2_genome2(CAST)


title: SJALL017885_203259750054_R01C01

description:
203259750054_R01C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells


title: SJNHL018774_203259600136_R08C01

description:
203259600136_R08C01
blood from survivor of childhood cancer and control


title: RNAseq - CN BxC rep2

description:
Library name: RNAseq_BxC_2
BxC_2_genome1 and BxC_2_genome2


title: SJMDS017914_203259600100_R05C01

description:
203259600100_R05C01
blood from survivor of childhood cancer and control

value: Myelodysplastic syndrome


title: RNAseq - CN BxC rep1

description:
Library name: RNAseq_BxC_1
BxC_1_genome1 and BxC_1_genome2


title: CHiC - 8w-old cortex CxB rep2

description: Library name: CHiC_Cortex_CxB_2


title: CHiC - CN BxC rep1

description: Library name: CHiC_CN_BxC_1


title: CHiC - 8w-old cortex BxC rep1

description: Library name: CHiC_Cortex_BxC_1


title: ATAC - 8w-old cortex BxC rep3

description:
Library name: ATAC_Cortex_BxC_3
BxC_3_genome1(BL6) and BxC_3_genome2(CAST)


title: CHiC - 8w-old cortex BxC rep2

description: Library name: CHiC_Cortex_BxC_2


title: SJALL017886_203259600136_R05C01

description:
203259600136_R05C01
blood from survivor of childhood cancer and control

value: cancer survivor


title: SJHL017906_203259600100_R04C01

description:
203259600100_R04C01
blood from survivor of childhood cancer and control


title: ATAC - 8w-old cortex CxB rep3

description:
Library name: ATAC_Cortex_CxB_3
CxB_3_genome1(BL6) and CxB_3_genome2(CAST)


title: Strep1_MIWI_testes_1n_cells_long_RNAseq_2

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description: Library name: XI-110-14

data_processing:
In vitro slicing: Reads were sorted into individual libraries based on the barcodes and the 3′ adapter sequences were clipped from the reads using cutadapt with only sequences of at least 15 nucleotides and containing adapter sequences left for further analysis (cutadapt parameters: -a AGATCGGAAGAGCACACGTCT -A GATCGTCGGACTGTAGAACTC -m 15 -e 0.2 -O 4 -q 10 --match-read-wildcards --trimmed-only -j 5). The reads were then mapped to the sequences of piRNA target RNAs (Perf.fa.gz or Bulge.fa.gz) using bowtie (with parameters: -v 0 -a --best --strata --allow-contain --threads 10). Only first reads of the sequenced read pairs were used for further analysis. Cummulative read abundances (reads per million) were created from all 15,000 target RNAs based on the start and end position of the reads relative to the 5′ end of targeting piRNA (position 0) - file  "meta_rpm_table.csv.gz". piRNA sequencing: Reads were sorted into individual libraries based on the barcodes and only first reads of the sequenced pairs were used in further analysis. The 3′ adapter sequences were clipped from the reads using cutadapt with only sequences of at least 15 nucleotides and containing adapter sequences left for further analysis (cutadapt parameters: -a AGATCGGAAGAGCACACGTCT -m 15 -e 0.2 -O 4 -q 10 --match-read-wildcards --trimmed-only -j 5). The reads were mapped to the mouse genome (GRCm39: Ensembl release 104) using STAR (parameters: --runThreadN 10 -outFilterType BySJout --limitOutSJcollapsed 50000000 --limitIObufferSize 1500000000). The reads of 25nt-32nt were considered to represent piRNAs and selected for further analysis. To compare the origin of piRNAs, the piRNAs were annotated based on ENSEMBL gene biotypes, positions of tRNAs (tRNAs table from UCSC), repeats (rmsk table from UCSC) and pachytene piRNA clusters (PMID:23523368). piRNA counts were summarized using Rsubread::featureCounts function - file "MIWI_IP_smallRNAseq.xlsx". Gene expression analysis: Reads were sorted into individual libraries based on the barcodes and mapped to the mouse genome (GRCm39: Ensembl release 104) using STAR (parameters: --runThreadN 10 -outFilterType BySJout --limitOutSJcollapsed 50000000 --limitIObufferSize 1500000000). Reads were annotated based on ENSEMBL gene biotypes, positions of tRNAs (tRNAs table from UCSC), repeats (rmsk table from UCSC) and pachytene piRNA clusters (PMID:23523368). Read counts were summarized using Rsubread::featureCounts function - file "longRNAseq_featureCounts.xlsx". To analyze the gene expression the reads were aligned to the transcriptome reference using salmon 1.3.0. Transcript counts were collapsed into gene counts and DESeq function of the DESeq2 bioconductor package was used to obtain apeglm shrunken log2 fold changes of gene expression and the adjusted p-values.
Assembly: piRNA sequencing and gene expression analysis: GRCm39 In vitro slicing: Two pools: Perfect or Bulge, each consisting of 15,000 sequences: "Perf.fa.gz", "Bulge.fa.gz"
Supplementary files format and content: In vitro slicing: The files "Perf.fa.gz" and "Bulge.fa.gz" contain 15,000 sequences of in vitro transcribed target RNAs which were used for mapping the reads. The bwt files contain the bowtie mappings to individual 15,000 piRNA target sequences in "Perf.fa.gz" or "Bulge.fa.gz".
Supplementary files format and content: In vitro slicing: The "meta_rpm_table.csv.gz" file contains the cummulative abundances (rpm) of cleaved fragments from all 15,000 target RNAs based on the start and end position of the fragment. piRNA sequencing: The file "MIWI_IP_smallRNAseq.xlsx" contains summarized counts of mapped piRNAs (rpm) to individual genomic elements (genes, repeats, pachytene clusters) obtained by Rsubread::featureCounts. Gene expression analysis: The file "longRNAseq_featureCounts.xlsx" contains summarized counts (rpm) of mapped reads to individual genomic elements (genes, repeats, pachytene clusters) obtained by Rsubread::featureCounts. The file "longRNAseq_salmon.xlsx" contains summarized counts of reads mapped to genes by salmon and normalized by DESeq2.

growth_protocol: piRNA sequencing and gene expression analysis:: We created two Strep-Miwi knock-in lines by inserting the 8-amino acid Strep II tag (WSHPQFEK) into an internal location at the N-terminus of the MIWI protein. We made two separate knock-in mouse lines (RP85 and RP86) with insertions into two separate locations at the N-terminus, which is predicted to be disordered. In vitro slicing: To design the RNA sequences targeted by MIWI bound piRNAs we searched the piRNA libraries from 10 MIWI-bound small RNA datasets (samples MD40, MD42, MD44, MD46, MD48, MD50, MD52, MD54, MD56, MD58 from GEO: GSE219200) for abundant piRNAs.  Based on 28-32 nt 5’U reads  originating from pachytene clusters we identified the unique genome sequences of 32 nt length generating most of the piRNAs.  Top 15,000 of the sequences were selected, which generated ~70% of all genome mapped reads in the datasets, and used to design the antisense RNA targets  for slicer assay. Based on these sequences, we designed the DNA pool of 15,000 individual single-stranded oligonucleotides (Twist Biosciences), each with a 5’ part having the T7 promoter, followed by a sequence antisense to the piRNAs, and a common sequence that will be used for primer-binding to PCR-amplify the library. Beside this pool containing the targets perfectly complementary to the piRNAs (perfect targets), we also designed the pool where for each sequence we introduced 2-nucleotide mismatch to the piRNA nucleotides 10 and 11 (bulged targets). The ssDNA oligo pool for each library (perfect or bulge targets) was PCR-amplified using primers binding to the T7 promoter region and the 3’ common sequence, which is separate for each library. This double-stranded DNA library was used for in vitro transcription with the T7 viral RNA polymerase to generate the pool of 15,000 target RNAs for each set (perfect or bulge targets). These RNA pools were used for in vitro slicer assays.

extract_protocol:
In vitro slicing: The samples containing the in vitro sliced RNAs were phenol-chloroform extracted and precipitated with ethanol. piRNA sequencing: To extract MIWI-bound piRNAs from adult mouse testes, eluted StrepII-MIWI was subjected to a proteinase K treatment. Briefly, two micrograms of StrepII-MIWI were digested with 10 μg of Proteinase K in Proteinase K buffer by incubation at 42°C for 20 min (with shaking at 400 rpm). The reactions were immediately phenol-chloroform extracted as standard and precipitated overnight in ethanol. After centrifugation of the samples to precipitate the piRNAs, the dry pellets were resuspended in 20 μL RNase-free water. Gene expression analysis: Around 500,000 cells from 1n (spermatids) and 4n (spermatocytes) sorted samples from testicular single cell suspensions were used as input for RNA extraction. RNA was extracted using the Allprep DNA/RNA Micro Kit (Qiagen). The extraction was carried out according to the product’s manual. Elution was performed with 15 uL DEPC water.
In vitro slicing: The precipitated RNA samples were used as input for small RNA library preparation (6 μl of the precipitated RNA following phenol-chloroform extraction), about 80 ng starting material. Libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB) and sequenced with the Illumina HiSeq 2000 platform (EMBL GeneCore facility, Heidelberg) using the P50 paired-end option. piRNA sequencing: Libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB) and sequenced with the Illumina HiSeq 2000 platform (EMBL GeneCore facility, Heidelberg) using the P50 paired-end option. Gene expression analysis: The Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit was used for the library preparation with 100 ng of total RNA as input. The libraries were sequenced on an Illumina NovaSeq 6000 sequencer for paired-end 100 reads.

treatment_protocol: In vitro slicing: Slicer assays were carried out as described (Reuter et al., 2011), but with slight modifications. After MIWI/piRNA complex isolation, as described in this study, beads were washed in Streptactin wash buffer and then in slicer buffer and used for slicer assays. Alternatively, eluted MIWI fractions were used for the assay. Beads-bound MIWI/piRNA complex or eluted MIWI/piRNA complex were incubated in slicer buffer (10 mM Tris/HCl pH 7.5, 100 mM KCl, 2 mM Mg2Cl, 40 U RiboLock) on ice for 10 min, in 1.5 ml Eppendorf tubes. RNA targets were denatured at 65°C for 5 min and then incubated on ice for 10 min. Reactions were started by the addition of the denatured RNA targets. The total volume of the slicer reactions was 20 mL for bead bound material and variant for soluble MIWI. Two micrograms of soluble MIWI were used for cold assays. The reactions were carried out at 35°C for 2 hours in a Thermoshaker (Eppendorf, Cat. No. EP5387000013) with constant changing modes of shaking (1000 rpm, 10 sec) and pause (90 sec). Reactions were then stopped by adding 300uL of a stop buffer [20 mg Proteinase K (Thermo Fisher Scientific, Cat. No. AM2542) in Proteinase K buffer] and incubated at 42 degrees in a thermoshaker for 20 minutes with shaking (400 rpm).

value: Strep1 (RP68)

tag: experiment

tag: mapped to


title: Strep2_MIWI_testes_4n_cells_long_RNAseq_3

description: Library name: XI-110-12

value: Strep2 (RP85)


title: CHiC - 8w-old cortex CxB rep1

description: Library name: CHiC_Cortex_CxB_1


title: SJALL017890_203259600136_R04C01

description:
203259600136_R04C01
blood from survivor of childhood cancer and control

value: White


title: Strep1_MIWI_testes_1n_cells_long_RNAseq_3

description: Library name: XI-110-15


title: SJNHL018765_203259600100_R08C01

description:
203259600100_R08C01
blood from survivor of childhood cancer and control

value: Non-Hodgkin lymphoma


title: SJOS018823_203259600100_R06C01

description:
203259600100_R06C01
blood from survivor of childhood cancer and control


title: ATAC - 8w-old cortex BxC rep1

description:
Library name: ATAC_Cortex_BxC_1
BxC_1_genome1(BL6) and BxC_1_genome2(CAST)


title: ATAC - 8w-old cortex CxB rep1

description:
Library name: ATAC_Cortex_CxB_1
CxB_1_genome1(BL6) and CxB_1_genome2(CAST)


title: Strep1_MIWI_testes_4n_cells_long_RNAseq_3

description: Library name: XI-110-18


title: Strep2_MIWI_testes_4n_cells_long_RNAseq_2

description: Library name: XI-110-11


title: SJRB017940_203259600021_R05C01

description:
203259600021_R05C01
blood from survivor of childhood cancer and control

value: female

value: Retinoblastoma


title: SJWLM018908_203259600021_R07C01

description:
203259600021_R07C01
blood from survivor of childhood cancer and control

value: Wilms tumor


title: Strep1_MIWI_testes_4n_cells_long_RNAseq_2

description: Library name: XI-110-17


title: Strep2_MIWI_testes_4n_cells_long_RNAseq_1

description: Library name: XI-110-10


title: SJALL017889_203259600021_R04C01

description:
203259600021_R04C01
blood from survivor of childhood cancer and control


title: Strep2_MIWI_testes_1n_cells_long_RNAseq_3

description: Library name: XI-112-9


title: SJALL017869_203259600100_R03C01

description:
203259600100_R03C01
blood from survivor of childhood cancer and control


title: SJNBL017920_203259600100_R02C01

description:
203259600100_R02C01
blood from survivor of childhood cancer and control

value: Neuroblastoma


title: SJCNS018579_203259600100_R07C01

description:
203259600100_R07C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)


title: SJGCT017901_203259600021_R01C01

description:
203259600021_R01C01
blood from survivor of childhood cancer and control

value: Germ cell tumor


title: Strep2_MIWI_testes_1n_cells_long_RNAseq_2

description: Library name: XI-112-8


title: SJOS018802_203259190165_R08C01

description:
203259190165_R08C01
blood from survivor of childhood cancer and control


title: Strep1_MIWI_testes_4n_cells_long_RNAseq_1

description: Library name: XI-110-16


title: WT_MIWI_testes_1n_cells_long_RNAseq_2

description: Library name: XI-112-2

value: WT


title: WT_MIWI_testes_1n_cells_long_RNAseq_3

description: Library name: XI-112-3


title: SJALL017883_203259190165_R04C01

description:
203259190165_R04C01
blood from survivor of childhood cancer and control

value: male

value: Acute lymphoblastic leukemia


title: WT_MIWI_testes_1n_cells_long_RNAseq_1

description: Library name: XI-112-1


title: Strep1_MIWI_testes_1n_cells_long_RNAseq_1

description: Library name: XI-110-13


title: SJEWS017900_203259600100_R01C01

description:
203259600100_R01C01
blood from survivor of childhood cancer and control

value: Ewing sarcoma family of tumors


title: MIII.MOG

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

description: Library name: GFB_51283

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Reads were mapped to the hybrid reference comprising human and mouse genomes (hg38 and mm10) with STAR  (version 2.7.10a) with default parameters, except filtering out multimapping reads (outFilterMultimapNmax=1) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”). The featureCounts  function from the Rsubread package (version 2.0.6) was used to count the number of reads (5' ends) overlapping with the exons of each mouse gene (Ensembl release 102) assuming an exon union model. Subsequent analyses were performed using the R software (version 4.3.1) and Bioconductor  3.18 packages.
Assembly: mm10
Supplementary files format and content: Counts_Table.tsv: TSV file (tab separated values) including read counts for each sample and gene (ENSEMBL ID release 102).

source_name: B cells

growth_protocol: Animals were bred and maintained in the animal facility of the Department of Biomedicine, University of Basel, Switzerland. Mice used have a transgenic B cell receptor specific for MOG.

extract_protocol:
RNA extracted with Zymo quick-RNA MicroPrep kit according to the manufactuer's instructions
Library preparation was performed starting with 5 ng of total RNA using the SMART-Seq Stranded Kit (Cat. #634444; Takara Bio) together with the SMARTer RNA Unique Dual Index Kit (Cat. #634452; Takara Bio) to generate ribosome-depleted libraries.
Library quality was assessed on a Fragment Analyzer (Advanced Analytical, Ames, IA, USA) with the High Sensitivity NGS Fragment Analysis Kit (Cat. #DNF-474), confirming excellent quality (mean concentration 121 ± 41 nmol/L; mean library size 456 ± 29 bp).
Samples were pooled to equal molarity and sequenced in paired-end 51-base mode (plus 8 bp index 1 and 8 bp index 2) on an Illumina NovaSeq 6000 using an SP flow cell.

treatment_protocol: TE671 cells stably transfected with MOG, or control non-expressing cells were cultured in 6-well plates. B cells were then added for 4 hours, or else cultured for 4 hours with 5 micromolar F(ab′)2 donkey anti-mouse IgM (catalog no: 715-006-020) (Jackson ImmunoResearch), then sorted and lysed in Lysis buffer from Zymo kit

value: Male

tag: mouse replicate

value: MIII

value: B cells

value: B cells with MOG-reacting  BCR

value: MOG


title: SJRHB017944_203259190165_R03C01

description:
203259190165_R03C01
blood from survivor of childhood cancer and control

tag: tissue

value: peripheral blood mononuclear cells

value: cancer survivor

value: Rhabdomyosarcoma

value: White


title: Strep2_MIWI_testes_1n_cells_long_RNAseq_1

description: Library name: XI-112-7

value: Strep2 (RP85)


title: SJRB018830_203259600021_R06C01

description:
203259600021_R06C01
blood from survivor of childhood cancer and control

tag: age

value: Retinoblastoma


title: SJNPCA018729_203259600021_R08C01

description:
203259600021_R08C01
blood from survivor of childhood cancer and control

tag: Sex

value: Carcinoma


title: SJALL018499_203259190163_R08C01

description:
203259190163_R08C01
blood from survivor of childhood cancer and control

value: female

tag: group


title: MI.IgM

description: Library name: GFB_51278

value: MI

value: IgM


title: SJWLM018919_203259190163_R07C01

description:
203259190163_R07C01
blood from survivor of childhood cancer and control

tag: age at cancer diagnosis

value: Wilms tumor


title: MIII.0

description: Library name: GFB_51277


title: WT_MIWI_testes_4n_cells_long_RNAseq_2

description: Library name: XI-110-5

value: WT


title: SJMEL017913_203259600021_R02C01

description:
203259600021_R02C01
blood from survivor of childhood cancer and control

tag: diagnostic group

value: Melanoma


title: MIII.IgM

description: Library name: GFB_51280

value: Male

value: MIII


title: SJRHB017945_203259190163_R03C01

description:
203259190163_R03C01
blood from survivor of childhood cancer and control

tag: average dose to whole heart, cgy


title: SJSTS018868_203259190165_R06C01

description:
203259190165_R06C01
blood from survivor of childhood cancer and control

value: Soft tissue sarcoma

tag: race group


title: WT_MIWI_testes_4n_cells_long_RNAseq_3

description: Library name: XI-110-6


title: SJNHL017925_203259190163_R01C01

description:
203259190163_R01C01
blood from survivor of childhood cancer and control

value: male

value: Non-Hodgkin lymphoma

tag: base line visit start date


title: SJWLM018920_203259190165_R07C01

description:
203259190165_R07C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: cancer survivor

tag: base line visit finish


title: MII.IgM

description: Library name: GFB_51279

value: MII

value: B cells

value: B cells with MOG-reacting  BCR


title: SJLM017912_203259190165_R05C01

description:
203259190165_R05C01
blood from survivor of childhood cancer and control

value: Liver malignancies

value: White

tag: age at death


title: WT_MIWI_testes_4n_cells_long_RNAseq_1

description: Library name: XI-110-4


title: MI.MOG

description: Library name: GFB_51281

value: MI

tag: cell type

value: MOG


title: SJALL017870_203259190163_R04C01

description:
203259190163_R04C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: MII.0

description: Library name: GFB_51276

tag: genotype


title: SJCNS018573_203259190163_R06C01

description:
203259190163_R06C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)


title: MII.MOG

description: Library name: GFB_51282

tag: treatment


title: SJHIST017902_203259190165_R01C01

description:
203259190165_R01C01
blood from survivor of childhood cancer and control

value: Histiocytosis


title: SJNBL017921_203259190163_R05C01

description:
203259190163_R05C01
blood from survivor of childhood cancer and control

value: Neuroblastoma


title: SJNBL017919_203259190165_R02C01

description:
203259190165_R02C01
blood from survivor of childhood cancer and control


title: SJEWS017899_203259190163_R02C01

description:
203259190163_R02C01
blood from survivor of childhood cancer and control

value: female

value: Ewing sarcoma family of tumors


title: CITE_GEX

city: New York City

first: Eduardo

last: Esteva

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description:
Library name: CITE_GEX
polyA RNA

data_processing:
alignment using cellranger count v6.0.1
single-cell analyses using Seurat v4.1.1
demultiplexing using HTODemux
QC filtering extracting singlets, removing cells with greater than 5 percent mitochondrial genes, removing cells with less than 200 features, and removing cells with more than 4000 features
Louvain clustering on Lymph Node Cells
Assembly: Leiden clustering on Thymus Cells
Supplementary files format and content: mm10
Supplementary files format and content: tab-separated files, matrix files, and Rds files
Library strategy: CITE-seq

molecule: polyA RNA

source_name: sdLNs and thymus

extract_protocol:
Cell suspensions were enriched for DCs by negative (sdLNs) or positive selection (thymus). Briefly, sdLN cell suspensions were stained with biotinylated antibodies against TER-119, TCR-β, CD3, NK1.1, CD19, and Ly6G (Thermo Fisher Scientific and Biolegend), and thymus cell suspensions were stained with biotinylated antibodies against CD11c. Samples were subsequently incubated with streptavidin microbeads (Miltenyi Biotec) and passed through LS columns attached to MidiMACS or QuadroMACS separators (Miltenyi Biotec) according to manufacturer protocol. Cells in the flow-through (sdLN) or eluted column-bound cells (thymus) were collected. After enrichment for DCs in the sdLNs and thymus tissue samples as described above, single cell suspensions were stained with fluorophore-conjugated antibodies as well as TotalSeqB hashtag antibodies specific against mouse CD45 and MHC-I (Biolegend) to maintain sample identity. Cell sorting was performed on FACSAria II (BD Biosciences) at the Cytometry & Cell Sorting Laboratory at NYUGSoM. 12,500 cDCs from each sample were sorted and pooled together in 50 μl PBS containing 10% FBS. cDCs = Live singlets lineage- (CD3- TCR-β- B220- CD19- NK1.1- NKp46- Siglec-F- Ly6G-) MHC-II+.
The resulting cell mixture was prepared according to the 10X Genomics protocol at the Genome Technology Center at NYUGSoM.

treatment_protocol: Skin-draining lymph nodes (sdLNs, bilateral inguinal and brachial nodes) were collected. sdLN capsules were pierced with sharp forceps, and sdLNs were digested in 1 mg/ml collagenase D (Roche) in HBSS with calcium and magnesium for 30 min at 37°C. Thymi were minced and digested in 1 mg/ml collagenase D and 20 μg/ml DNaseI in HBSS with calcium and magnesium for 30 min at 37°C. The thymocyte suspension was subjected to RBC lysis. All single cell suspensions were passed through 70 μm filters prior to downstream analysis.

value: sdLNs and thymus

value: cDC

value: Etv3+/+ and Etv3-/-

tag: library type

value: mRNA


title: SJHL018674_203259190147_R08C01

description:
203259190147_R08C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: male

value: cancer survivor

value: Hodgkin lymphoma

value: Black


title: RNA_ETV3KO_GMDC_03

description: Library name: Sample 5

data_processing:
The bulk RNA-seq analysis was performed using the Seq-N-Slide pipeline;using the rna-star and rna-star-groups-dge routes.
trimmed adapters from .fastq files using Trimmomatic (v0.36)
aligning reads to the mm10 reference genome using Star (v2.7.3a)
aligning reads to probable contaminants using fastq_screen (v0.13.0)
resulting reads are quantified using featureCounts from subread v1.6.3; differential expression is performed using DESeq2 (v1.26.0)
Assembly: mm10
Supplementary files format and content: normalized counts matrix, counts.normalized.csv.gz

source_name: GM-BMDC cultures

growth_protocol: Primary mouse bone marrow cells were plated at a density of 1x107 cells per well in 4 ml of RPMI supplemented with 10% FBS, 1% L-glutamine, 1% penicillin-streptomycin, 55 μM 2-mercaptoethanol, 20 ng/ml GM-CSF and 5 ng/ml IL-4 in 6-well plates. Cells were cultured at 37°C for 6 days. On days 2 and 3 of differentiation, 2 ml and 4 ml media respectively were replaced with fresh cytokines.

extract_protocol:
RNA was extracted from up to 6x104 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: GM-BMDC cultures were established from both Etv3+/+ and Etv3-/- mice. DCs were purified by cell sorting 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 CD11c+ CD11bint MHC-IIhi CD115-.

value: GM-BMDC cultures

value: DC


title: RNA_ETV3WT_GMDC_01

description: Library name: Sample 1


title: RNA_ETV3KO_GMDC_02

description: Library name: Sample 4


title: SJWLM018918_203259190147_R07C01

description:
203259190147_R07C01
blood from survivor of childhood cancer and control

value: Wilms tumor

value: White


title: CITE_HTO

description:
Library name: CITE_HTO
Hashtag-derived oligonucleotide (HTO)

molecule: protein

tag: hto

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

value: HTO


title: SJHL018688_203259190147_R06C01

description:
203259190147_R06C01
blood from survivor of childhood cancer and control


title: SJWLM017954_203259190147_R04C01

description:
203259190147_R04C01
blood from survivor of childhood cancer and control


title: RNA_ETV3KO_GMDC_01

description: Library name: Sample 3


title: MI.0

description: Library name: GFB_51275

value: Male

tag: mouse replicate

value: MI

value: B cells

value: B cells with MOG-reacting  BCR


title: RNA_ETV3WT_GMDC_02

description: Library name: Sample 2

tag: tissue


title: MULTI_Etv3WT_ATAC

description:
Library name: MULTI_Etv3WT_ATAC
snATAC-seq

library_source: genomic single cell

data_processing:
cellranger arc v2.0 was used to generate counts tables for both assays
Counts were QC'd using standard Signac and Seurat workflow including for ATAC: 3000 < atac peak region fragments < 20000; percent reads in peaks > 15%; percent of reads falling into blacklist regions < 10%; nucleosome signal < 4 (ratio of nucleosome-bound : nucleosome-freee fragments);TSS  > 2 (ratio of fragments falling to TSS regions : TSS-flanking regions)
RNA QC: 1000 < read counts < 25000; percent of reads mapping to mitochondrial genome < 20%
ATAC reads were normalized via TF-IDF; RNA reads normalized using SCTransform
Consensus peak set generated in ArchR(v1.0.2) and imported into Seurat as ChromatinAssay class slot
Assembly: mm10
Supplementary files format and content: list of chromatin/transcriptome counts matrices: ETV3KO_filtered_feature_bc_matrix.h5,WT_filtered_feature_bc_matrix.h5; cellular qc statistics: ETV3KO_per_barcode_metrics.csv, WT_per_barcode_metrics.csv; ATAC fragment data: ETV3KO_atac_fragments.tsv.gz, WT_atac_fragments.tsv.gz

source_name: sdLNs

extract_protocol:
Cell suspensions were enriched for DCs by negative selection. Briefly, sdLN cell suspensions were stained with biotinylated antibodies against TER-119, TCR-β, CD3, NK1.1, CD19, and Ly6G (Thermo Fisher Scientific and Biolegend), incubated with streptavidin microbeads (Miltenyi Biotec) and passed through LS columns attached to MidiMACS or QuadroMACS separators (Miltenyi Biotec) according to the manufacturer protocol. Cells in the flow-through were collected. After enrichment, ~21,000 Etv3+/+ and 54,000 Etv3-/- migratory DCs (migDCs) were sorted on FACSAria II (BD Biosciences) at the Cytometry & Cell Sorting Laboratory at NYUGSoM. migDCs = Live singlets lineage- (CD3- TCR-β- B220- CD19- NK1.1- NKp46- Siglec-F- Ly6G-) CD11c+ MHC-IIhi.
Nuclei were isolated according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (GEX) protocol (10X Genomics) using an optimized 4 minutes of lysis. Libraries were prepared according to the 10X Genomics Single Cell Multiome ATAC Kit.

treatment_protocol: Skin-draining lymph nodes (sdLNs, bilateral inguinal and brachial nodes) were collected from Etv3+/+ and Etv3-/- mice. sdLN capsules were pierced with sharp forceps, and sdLNs were digested in 1 mg/ml collagenase D (Roche) in HBSS with calcium and magnesium for 30 min at 37°C. The single cell suspension was passed through a 70 μm filter prior to downstream analysis.

value: sdLNs

value: migDC


title: MULTI_Etv3KO_ATAC

description:
Library name: MULTI_Etv3KO_ATAC
snATAC-seq


title: SJOS017935_203259190147_R05C01

description:
203259190147_R05C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: age

value: female

value: Osteosarcoma


title: MULTI_Etv3KO_GEX

description:
Library name: MULTI_Etv3KO_GEX
snRNA-seq

library_source: transcriptomic single cell

molecule: nuclear RNA


title: SJRHB017946_203259190147_R03C01

description:
203259190147_R03C01
blood from survivor of childhood cancer and control

tag: Sex

value: male

value: cancer survivor

value: Rhabdomyosarcoma


title: SJSTS017949_203259190147_R01C01

description:
203259190147_R01C01
blood from survivor of childhood cancer and control

tag: group

value: Soft tissue sarcoma

value: Black


title: RNA_Etv3KO_Treg_03

description: Library name: Sample 6

data_processing:
Sequencing results were demultiplexed and converted to fastq using bcl2fastq
FastQ files were processed using the Seq-N-Slide RNA Star Pipeline
Reads were trimmed using Trimmomatic
Aligned to mouse genome mm10 using STAR
Generated gene counts using FeatureCounts
Assembly: Differential expression using DESeq2
Supplementary files format and content: mm10
Supplementary files format and content: CSV files contain raw and normalized counts for all genes and samples

source_name: spleen

extract_protocol:
RNA was extracted from up to 1x105 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 from either Etv3+/+ Foxp3EGFP or Etv3-/- Foxp3EGFP mice were mashed between the frosted ends of glass microscope slides, passed through 70 μm Nylon mesh, and subjected to red blood cell (RBC) lysis (BioLegend). The single-cell splenocyte suspension was enriched for CD4+ T cells by negative depletion by staining splenocytes with biotinylated antibodies against TER-119, B220, CD19, NK1.1, CD11b and CD8α (Thermo Fisher Scientific and BioLegend), incubating them with streptavidin microbeads (Miltenyi Biotec) and passing them through LD 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. Treg = Live singlets CD4+ Foxp3-GFP+.

value: spleen

value: Treg

value: Etv3-/- Foxp3EGFP


title: MULTI_Etv3WT_GEX

description:
Library name: MULTI_Etv3WT_GEX
snRNA-seq


title: RNA_Etv3WT_Treg_03

description: Library name: Sample 3

value: Etv3+/+ Foxp3EGFP


title: SJALL018504_203259190123_R08C01

description:
203259190123_R08C01
blood from survivor of childhood cancer and control

tag: age at cancer diagnosis

value: Acute lymphoblastic leukemia

value: White


title: SJRHB017941_203259190123_R04C01

description:
203259190123_R04C01
blood from survivor of childhood cancer and control

tag: diagnostic group


title: RNA_Etv3KO_Treg_02

description: Library name: Sample 5


title: SJALL018544_203259190123_R07C01

description:
203259190123_R07C01
blood from survivor of childhood cancer and control

tag: average dose to whole heart, cgy


title: SJNHL017930_203259190147_R02C01

description:
203259190147_R02C01
blood from survivor of childhood cancer and control

value: Non-Hodgkin lymphoma

tag: race group


title: SJOS017933_203259190123_R05C01

description:
203259190123_R05C01
blood from survivor of childhood cancer and control

tag: base line visit start date


title: RNA_Etv3WT_Treg_02

description: Library name: Sample 2


title: SJAML007090_203259190123_R06C01

description:
203259190123_R06C01
blood from survivor of childhood cancer and control

value: Acute myeloid leukemia

tag: base line visit finish


title: SJWLM017962_203259190123_R03C01

description:
203259190123_R03C01
blood from survivor of childhood cancer and control

value: Wilms tumor

tag: age at death


title: SJSTS017950_203259190123_R02C01

description:
203259190123_R02C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells


title: RNA_Etv3WT_Treg_01

description: Library name: Sample 1

tag: cell type


title: SJWLM017956_203259190123_R01C01

description:
203259190123_R01C01
blood from survivor of childhood cancer and control

value: female


title: SJNHL018797_203259190122_R08C01

description:
203259190122_R08C01
blood from survivor of childhood cancer and control


title: 3xTg, Ramalin 3

city: Suwon

first: Dong-Gyu

last: Jo

address: 2066, Seobu-ro, Jangan-gu

institute: Sungkyunkwan University

description: Library name: Sample 6

data_processing:
FASTQ files were quality-checked using FastQC (v0.11.9) with default parameters.
Adapter sequences and low-quality bases were removed using Trimmomatic (v0.39).
Trimmed reads were aligned to the GRCm38 mouse genome using STAR (v2.7.9a).
Transcript-level quantification was performed using RSEM (v1.3.3) with GENCODE vM25 GTF annotation.
Assembly: GRCm38
Supplementary files format and content: csv file includes TPM values for each sample

extract_protocol:
Total RNA was extracted from cortex by using RNAiso Plus (Takara).
Preparation of mRNA library was conducted by Novogene Co., LTD. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Cortex


title: RNA_Etv3KO_Treg_01

description: Library name: Sample 4

tag: genotype


title: SJLM018727_203259190122_R07C01

description:
203259190122_R07C01
blood from survivor of childhood cancer and control

value: Liver malignancies


title: 3xTg, Vehicle 3

description: Library name: Sample 3


title: SJHL017908_203259190122_R05C01

description:
203259190122_R05C01
blood from survivor of childhood cancer and control

value: male

value: cancer survivor

value: Hodgkin lymphoma


title: 3xTg, Vehicle 1

description: Library name: Sample 1


title: SJHL017907_203259190122_R06C01

description:
203259190122_R06C01
blood from survivor of childhood cancer and control


title: 3xTg, Vehicle 2

description: Library name: Sample 2


title: SJWLM017960_203259190122_R02C01

description:
203259190122_R02C01
blood from survivor of childhood cancer and control


title: SJNHL017923_203259190122_R04C01

description:
203259190122_R04C01
blood from survivor of childhood cancer and control


title: 3xTg, Ramalin 1

description: Library name: Sample 4


title: SJWLM018914_203259190099_R08C01

description:
203259190099_R08C01
blood from survivor of childhood cancer and control

value: Black


title: SJWLM017957_203259190122_R01C01

description:
203259190122_R01C01
blood from survivor of childhood cancer and control


title: NaJa-F DMSO D1 1

city: Freiburg

first: Ariane

last: Lehmann

address: Breisacher Strasse 153

department: IBSM

country: Germany

institute: Medical Center Freiburg

description:
Library name: J_7
F_DMSO_D1_1

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

source_name: metastatic colorectal cancer

growth_protocol: NaJa cells were maintained in DMEM supplemented with 10 % fetal bovine serum (FBS) and 2mM Glutamin, 10mM HEPES buffer and antiobiotics

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

treatment_protocol: 0.5 µM encorafenib or corresponding amounts of DMSO were added with fresh medium to the cells at Day0 (as well as on Day2 and Day4 for the Day5 treatment time-point)

value: metastatic colorectal cancer

tag: strain

tag: cell line

value: NaJa-F

value: metastatic colorectal cancer cells

tag: time

value: Day 1

tag: treatment

value: DMSO


title: NaJa-F DMSO D1 2

description:
Library name: J_8
F_DMSO_D1_2

tag: tissue


title: NaJa-D Enco D1 2

description:
Library name: J_5
D_Enco_D1_2

value: NaJa-D

value: Encorafenib


title: SJWLM017963_203259190099_R06C01

description:
203259190099_R06C01
blood from survivor of childhood cancer and control

tag: age

value: White


title: SJALL017881_203259190099_R04C01

description:
203259190099_R04C01
blood from survivor of childhood cancer and control

tag: Sex

value: Acute lymphoblastic leukemia


title: NaJa-D Enco D1 1

description:
Library name: J_4
D_Enco_D1_1


title: SJWLM018911_203259190099_R07C01

description:
203259190099_R07C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: group

value: Wilms tumor


title: SJNHL017926_203259190122_R03C01

description:
203259190122_R03C01
blood from survivor of childhood cancer and control

tag: age at cancer diagnosis

value: Non-Hodgkin lymphoma


title: 3xTg, Ramalin 2

description: Library name: Sample 5

value: Cortex


title: SJCNS017898_203259190099_R05C01

description:
203259190099_R05C01
blood from survivor of childhood cancer and control

value: male

tag: diagnostic group

value: Central nervous system (CNS)


title: NaJa-G Enco D5 2

description:
Library name: J_35
G_Enco_D5_2

value: NaJa-G

value: Day 5


title: NaJa-D Enco D1 3

description:
Library name: J_6
D_Enco_D1_3

value: metastatic colorectal cancer


title: NaJa-G Enco D5 1

description:
Library name: J_34
G_Enco_D5_1


title: NaJa-F DMSO D1 3

description:
Library name: J_9
F_DMSO_D1_3

value: NaJa-F


title: SJNHL017928_203259190099_R02C01

description:
203259190099_R02C01
blood from survivor of childhood cancer and control

value: cancer survivor

tag: average dose to whole heart, cgy

value: Black


title: SJNHL017929_203259190099_R01C01

description:
203259190099_R01C01
blood from survivor of childhood cancer and control

tag: race group


title: NaJa-D DMSO D1 3

description:
Library name: J_3
D_DMSO_D1_3

value: metastatic colorectal cancer cells

value: Day 1

value: DMSO


title: SJALL003626_203259190055_R08C01

description:
203259190055_R08C01
blood from survivor of childhood cancer and control

value: female

value: White

tag: base line visit start date


title: NaJa-G Enco D5 3

description:
Library name: J_36
G_Enco_D5_3

value: Encorafenib


title: SJALL018515_203259190055_R07C01

description:
203259190055_R07C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Acute lymphoblastic leukemia

tag: base line visit finish


title: SJRB017938_203259190055_R03C01

description:
203259190055_R03C01
blood from survivor of childhood cancer and control

value: Retinoblastoma

tag: age at death


title: SJCA017893_203259190055_R01C01

description:
203259190055_R01C01
blood from survivor of childhood cancer and control

value: male

value: Carcinoma


title: NaJa-D Enco D5 3

description:
Library name: J_24
D_Enco_D5_3

value: NaJa-D

tag: cell type


title: SJNBL017918_203259190099_R03C01

description:
203259190099_R03C01
blood from survivor of childhood cancer and control

value: Neuroblastoma


title: NaJa-G DMSO D5 1

description:
Library name: J_31
G_DMSO_D5_1

value: metastatic colorectal cancer

value: NaJa-G

tag: genotype

value: Day 5


title: SJHL017904_203259190055_R04C01

description:
203259190055_R04C01
blood from survivor of childhood cancer and control

value: cancer survivor

value: Hodgkin lymphoma


title: NaJa-D DMSO D5 3

description:
Library name: J_21
D_DMSO_D5_3

tag: strain

value: metastatic colorectal cancer cells


title: NaJa-G DMSO D5 3

description:
Library name: J_33
G_DMSO_D5_3

tag: cell line

value: DMSO


title: NaJa-F Enco D5 1

description:
Library name: J_28
F_Enco_D5_1

value: NaJa-F

tag: time


title: SJALL003458_203259190036_R07C01

description:
203259190036_R07C01
blood from survivor of childhood cancer and control

value: White


title: NaJa-F DMSO D5 1

description:
Library name: J_25
F_DMSO_D5_1

tag: treatment


title: NaJa-F DMSO D5 3

description:
Library name: J_27
F_DMSO_D5_3

tag: tissue


title: NaJa-F Enco D5 2

description:
Library name: J_29
F_Enco_D5_2

value: Encorafenib


title: NaJa-D Enco D5 2

description:
Library name: J_23
D_Enco_D5_2


title: NaJa-D Enco D5 1

description:
Library name: J_22
D_Enco_D5_1


title: NaJa-F DMSO D5 2

description:
Library name: J_26
F_DMSO_D5_2


title: NaJa-D DMSO D5 2

description:
Library name: J_20
D_DMSO_D5_2


title: NaJa-D DMSO D1 2

description:
Library name: J_2
D_DMSO_D1_2

value: Day 1


title: SJWLM017955_203259190055_R02C01

description:
203259190055_R02C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: age

value: female

value: Wilms tumor


title: SJHL017909_203259190055_R05C01

description:
203259190055_R05C01
blood from survivor of childhood cancer and control

tag: Sex

value: Black


title: NaJa-G Enco D1 3

description:
Library name: J_18
G_Enco_D1_3


title: SJSTS017952_203259190036_R06C01

description:
203259190036_R06C01
blood from survivor of childhood cancer and control

tag: group

value: Soft tissue sarcoma


title: SJNHL017922_203259190036_R04C01

description:
203259190036_R04C01
blood from survivor of childhood cancer and control

value: male

tag: age at cancer diagnosis

value: Non-Hodgkin lymphoma


title: SJRB017939_203259190055_R06C01

description:
203259190055_R06C01
blood from survivor of childhood cancer and control

tag: diagnostic group

value: Retinoblastoma


title: NaJa-G Enco D1 1

description:
Library name: J_16
G_Enco_D1_1

value: metastatic colorectal cancer

value: NaJa-G


title: SJWLM017961_203259190036_R01C01

description:
203259190036_R01C01
blood from survivor of childhood cancer and control

value: cancer survivor

tag: average dose to whole heart, cgy


title: NaJa-G Enco D1 2

description:
Library name: J_17
G_Enco_D1_2

value: metastatic colorectal cancer cells


title: SJHL017905_203259190036_R03C01

description:
203259190036_R03C01
blood from survivor of childhood cancer and control

value: Hodgkin lymphoma

tag: race group


title: SJRB018831_203259190036_R08C01

description:
203259190036_R08C01
blood from survivor of childhood cancer and control

tag: base line visit start date


title: SJNBL017917_203259190036_R02C01

description:
203259190036_R02C01
blood from survivor of childhood cancer and control

value: Neuroblastoma

tag: base line visit finish


title: SJAML017892_203259190036_R05C01

description:
203259190036_R05C01
blood from survivor of childhood cancer and control

value: Acute myeloid leukemia

tag: age at death


title: NaJa-G DMSO D1 2

description:
Library name: J_14
G_DMSO_D1_2

tag: cell type

value: DMSO


title: NaJa-D DMSO D5 1

description:
Library name: J_19
D_DMSO_D5_1

value: NaJa-D

tag: genotype

value: Day 5


title: NaJa-F Enco D1 3

description:
Library name: J_12
F_Enco_D1_3

tag: strain

value: NaJa-F

value: Day 1

value: Encorafenib


title: NaJa-G DMSO D1 1

description:
Library name: J_13
G_DMSO_D1_1

tag: cell line


title: SJCNS041935_201503670124_R05C01

description:
201503670124_R05C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Central nervous system (CNS)

value: White


title: NaJa-F Enco D1 1

description:
Library name: J_10
F_Enco_D1_1

tag: time


title: SJCNS043123_201503670124_R06C01

description:
201503670124_R06C01
blood from survivor of childhood cancer and control

value: male

value: Black


title: SJALL041894_201503670124_R02C01

description:
201503670124_R02C01
blood from survivor of childhood cancer and control

value: female

value: Acute lymphoblastic leukemia


title: SJALL042689_201503670124_R01C01

description:
201503670124_R01C01
blood from survivor of childhood cancer and control

value: cancer survivor


title: SJSTS042766_201503670117_R08C01

description:
201503670117_R08C01
blood from survivor of childhood cancer and control

value: Soft tissue sarcoma


title: Lot 12 Nf1-/- DNp53 female transformed astrocytes, replicate 3

city: St. Louis

first: Jason

middle: Paul

last: Wong

state: MO

address: Neuroscience Research Building

department: Pediatrics

institute: Washington University in St. Louis

description:
Library name: Lot12F_Rep3
Column name in Raw_Counts.csv: Lot12F_Rep3

data_processing:
Original FASTQ files were demultiplexed using CutAdapt (2.10) to generate sample-level FASTQ files.
Reads were aligned to the mouse genome (GRCm38) using STAR (2.7.6a), and raw counts were tabulated with Subread (2.0.2).
Assembly: GRCm38
Supplementary files format and content: csv file includes raw counts for each sample

source_name: astrocyte

growth_protocol: Cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37C and 5% CO2.

extract_protocol:
Total RNA was isolated from Qiagen's Rneasy Plus Mini Kit (74136). Transcripts are annealed to primers containing a 16-nucleotide sequence unique to each sample (sample barcode), a unique molecular identifier, and a poly A 3’ end (Integrated DNA Technologies). First-strand cDNA synthesis of barcoded transcripts was performed using Maxima H Minus (Invitrogen) with a template switch oligo (TSO). Hybrid transcript:cDNA was pooled and exonuclease treated (New England Biotech, M0293), followed by subsequent cDNA amplification (KAPA HiFi HotStart).
Library construction was performed with 2 ng of amplified cDNA using the Illumina Nextera XT Protocol.

value: astrocyte

value: Female

tag: batch

value: Lot 12


title: NaJa-G DMSO D1 3

description:
Library name: J_15
G_DMSO_D1_3

tag: tissue

value: metastatic colorectal cancer

value: NaJa-G

value: metastatic colorectal cancer cells

tag: treatment

value: DMSO


title: SJCNS042704_201503670117_R05C01

description:
201503670117_R05C01
blood from survivor of childhood cancer and control

tag: age

tag: Sex


title: Lot 12 Nf1-/- DNp53 female transformed astrocytes, replicate 2

description:
Library name: Lot12F_Rep2
Column name in Raw_Counts.csv: Lot12F_Rep2


title: SJHL043130_201503670124_R07C01

description:
201503670124_R07C01
blood from survivor of childhood cancer and control

tag: group

tag: age at cancer diagnosis

value: Hodgkin lymphoma


title: Lot 12 Nf1-/- DNp53 female transformed astrocytes, replicate 1

description:
Library name: Lot12F_Rep1
Column name in Raw_Counts.csv: Lot12F_Rep1


title: NaJa-F Enco D1 2

description:
Library name: J_11
F_Enco_D1_2

value: NaJa-F

value: Day 1

value: Encorafenib


title: Lot 11 Nf1-/- DNp53 male transformed astrocytes, replicate 4

description:
Library name: Lot11M_Rep4
Column name in Raw_Counts.csv: Lot11M_Rep4

value: Male

value: Lot 11


title: SJEWS042714_201503670117_R03C01

description:
201503670117_R03C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: female

tag: diagnostic group

value: Ewing sarcoma family of tumors

tag: average dose to whole heart, cgy

value: White


title: SJGCT042716_201503670117_R02C01

description:
201503670117_R02C01
blood from survivor of childhood cancer and control

value: cancer survivor

value: Germ cell tumor

tag: race group

tag: base line visit start date


title: SJGCT041996_201503670124_R03C01

description:
201503670124_R03C01
blood from survivor of childhood cancer and control

value: Black

tag: base line visit finish

tag: age at death


title: SJCNS041929_201503670124_R04C01

description:
201503670124_R04C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)


title: Lot 12 Nf1-/- DNp53 male transformed astrocytes, replicate 1

description:
Library name: Lot12M_Rep1
Column name in Raw_Counts.csv: Lot12M_Rep1

tag: cell type

value: astrocyte

tag: genotype

value: Lot 12


title: Lot 11 Nf1-/- DNp53 female transformed astrocytes, replicate 4

description:
Library name: Lot11F_Rep4
Column name in Raw_Counts.csv: Lot11F_Rep4

value: Female


title: SJALL042696_201503670117_R04C01

description:
201503670117_R04C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: Lot 12 Nf1-/- DNp53 male transformed astrocytes, replicate 3

description:
Library name: Lot12M_Rep3
Column name in Raw_Counts.csv: Lot12M_Rep3


title: NaJa-D DMSO D1 1

description:
Library name: J_1
D_DMSO_D1_1

value: metastatic colorectal cancer

tag: strain

tag: cell line

value: NaJa-D

value: metastatic colorectal cancer cells

value: DMSO


title: SJRHB042765_201503670117_R07C01

description:
201503670117_R07C01
blood from survivor of childhood cancer and control

value: Rhabdomyosarcoma


title: Lot 11 Nf1-/- DNp53 male transformed astrocytes, replicate 1

description:
Library name: Lot11M_Rep1
Column name in Raw_Counts.csv: Lot11M_Rep1

value: Male

tag: batch

value: Lot 11


title: SJNHL042744_201503670117_R06C01

description:
201503670117_R06C01
blood from survivor of childhood cancer and control

tag: tissue

value: peripheral blood mononuclear cells

value: male

value: Non-Hodgkin lymphoma


title: Lot 12 Nf1-/- DNp53 male transformed astrocytes, replicate 2

description:
Library name: Lot12M_Rep2
Column name in Raw_Counts.csv: Lot12M_Rep2


title: SJRHB042497_201503670112_R03C01

description:
201503670112_R03C01
blood from survivor of childhood cancer and control

value: female

value: cancer survivor

value: White


title: SJALL041030_201503670112_R01C01

description:
201503670112_R01C01
blood from survivor of childhood cancer and control


title: SJOS042098_201503670112_R05C01

description:
201503670112_R05C01
blood from survivor of childhood cancer and control

value: Osteosarcoma

value: Black


title: SJNHL042086_201503670112_R04C01

description:
201503670112_R04C01
blood from survivor of childhood cancer and control


title: Lot 11 Nf1-/- DNp53 female transformed astrocytes, replicate 1

description:
Library name: Lot11F_Rep1
Column name in Raw_Counts.csv: Lot11F_Rep1

value: astrocyte

value: Female


title: Lot 11 Nf1-/- DNp53 male transformed astrocytes, replicate 2

description:
Library name: Lot11M_Rep2
Column name in Raw_Counts.csv: Lot11M_Rep2


title: Lot 11 Nf1-/- DNp53 male transformed astrocytes, replicate 3

description:
Library name: Lot11M_Rep3
Column name in Raw_Counts.csv: Lot11M_Rep3


title: Lot 8 Nf1-/- DNp53 male transformed astrocytes, replicate 4

description:
Library name: Lot8M_Rep4
Column name in Raw_Counts.csv: Lot8M_Rep4

value: Lot 8


title: SJALL042662_201503670117_R01C01

description:
201503670117_R01C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: SJCNS041942_201503670112_R07C01

description:
201503670112_R07C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)


title: Lot 8 Nf1-/- DNp53 male transformed astrocytes, replicate 3

description:
Library name: Lot8M_Rep3
Column name in Raw_Counts.csv: Lot8M_Rep3


title: SJALL042653_201503670092_R08C01

description:
201503670092_R08C01
blood from survivor of childhood cancer and control


title: SJRHB041689_201503670112_R02C01

description:
201503670112_R02C01
blood from survivor of childhood cancer and control


title: Lot 8 Nf1-/- DNp53 male transformed astrocytes, replicate 1

description:
Library name: Lot8M_Rep1
Column name in Raw_Counts.csv: Lot8M_Rep1


title: Lot 8 Nf1-/- DNp53 female transformed astrocytes, replicate 3

description:
Library name: Lot8F_Rep3
Column name in Raw_Counts.csv: Lot8F_Rep3


title: SJALL005343_201503670112_R06C01

description:
201503670112_R06C01
blood from survivor of childhood cancer and control


title: SJCNS041958_201503670092_R06C01

description:
201503670092_R06C01
blood from survivor of childhood cancer and control


title: Lot 8 Nf1-/- DNp53 female transformed astrocytes, replicate 4

description:
Library name: Lot8F_Rep4
Column name in Raw_Counts.csv: Lot8F_Rep4


title: SJCNS042496_201503670092_R03C01

description:
201503670092_R03C01
blood from survivor of childhood cancer and control


title: SJNPC042059_201503670092_R07C01

description:
201503670092_R07C01
blood from survivor of childhood cancer and control

value: Carcinoma


title: SJALL041856_201503670092_R04C01

description:
201503670092_R04C01
blood from survivor of childhood cancer and control


title: Lot 8 Nf1-/- DNp53 female transformed astrocytes, replicate 2

description:
Library name: Lot8F_Rep2
Column name in Raw_Counts.csv: Lot8F_Rep2


title: SJOS042105_201503670092_R05C01

description:
201503670092_R05C01
blood from survivor of childhood cancer and control


title: Lot 8 Nf1-/- DNp53 female transformed astrocytes, replicate 1

description:
Library name: Lot8F_Rep1
Column name in Raw_Counts.csv: Lot8F_Rep1


title: Lot 8 Nf1-/- DNp53 male transformed astrocytes, replicate 2

description:
Library name: Lot8M_Rep2
Column name in Raw_Counts.csv: Lot8M_Rep2


title: Lot 11 Nf1-/- DNp53 female transformed astrocytes, replicate 3

description:
Library name: Lot11F_Rep3
Column name in Raw_Counts.csv: Lot11F_Rep3


title: SJCNS041979_201503670075_R07C01

description:
201503670075_R07C01
blood from survivor of childhood cancer and control


title: Lot 7 Nf1-/- DNp53 male transformed astrocytes, replicate 4

description:
Library name: Lot7M_Rep4
Column name in Raw_Counts.csv: Lot7M_Rep4

value: Lot 7


title: SJALL041022_201503670092_R01C01

description:
201503670092_R01C01
blood from survivor of childhood cancer and control


title: Lot 7 Nf1-/- DNp53 female transformed astrocytes, replicate 3

description:
Library name: Lot7F_Rep3
Column name in Raw_Counts.csv: Lot7F_Rep3


title: SJALL003814_201503670075_R08C01

description:
201503670075_R08C01
blood from survivor of childhood cancer and control


title: Lot 7 Nf1-/- DNp53 male transformed astrocytes, replicate 3

description:
Library name: Lot7M_Rep3
Column name in Raw_Counts.csv: Lot7M_Rep3

value: Male


title: SJWLM019655_201503670092_R02C01

description:
201503670092_R02C01
blood from survivor of childhood cancer and control

value: Wilms tumor


title: Lot 7 Nf1-/- DNp53 male transformed astrocytes, replicate 2

description:
Library name: Lot7M_Rep2
Column name in Raw_Counts.csv: Lot7M_Rep2


title: Lot 7 Nf1-/- DNp53 female transformed astrocytes, replicate 1

description:
Library name: Lot7F_Rep1
Column name in Raw_Counts.csv: Lot7F_Rep1


title: Lot 6 Nf1-/- DNp53 male transformed astrocytes, replicate 3

description:
Library name: Lot6M_Rep3
Column name in Raw_Counts.csv: Lot6M_Rep3

value: Lot 6


title: SJNBL019440_201503670075_R02C01

description:
201503670075_R02C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Neuroblastoma


title: Lot 6 Nf1-/- DNp53 female transformed astrocytes, replicate 3

description:
Library name: Lot6F_Rep3
Column name in Raw_Counts.csv: Lot6F_Rep3


title: SJALL041851_201503670075_R04C01

description:
201503670075_R04C01
blood from survivor of childhood cancer and control

value: male


title: SJCNS041940_201503670075_R06C01

description:
201503670075_R06C01
blood from survivor of childhood cancer and control

value: cancer survivor


title: Lot 7 Nf1-/- DNp53 female transformed astrocytes, replicate 2

description:
Library name: Lot7F_Rep2
Column name in Raw_Counts.csv: Lot7F_Rep2


title: SJCNS003211_201503670075_R05C01

description:
201503670075_R05C01
blood from survivor of childhood cancer and control

value: female


title: Lot 7 Nf1-/- DNp53 male transformed astrocytes, replicate 1

description:
Library name: Lot7M_Rep1
Column name in Raw_Counts.csv: Lot7M_Rep1


title: Lot 7 Nf1-/- DNp53 female transformed astrocytes, replicate 4

description:
Library name: Lot7F_Rep4
Column name in Raw_Counts.csv: Lot7F_Rep4


title: SJCNS041002_201503670075_R01C01

description:
201503670075_R01C01
blood from survivor of childhood cancer and control

value: White


title: Lot 11 Nf1-/- DNp53 female transformed astrocytes, replicate 2

description:
Library name: Lot11F_Rep2
Column name in Raw_Counts.csv: Lot11F_Rep2

value: Lot 11


title: SJGCT042717_201503670065_R08C01

description:
201503670065_R08C01
blood from survivor of childhood cancer and control

value: Germ cell tumor

value: Black


title: Lot 6 Nf1-/- DNp53 male transformed astrocytes, replicate 1

description:
Library name: Lot6M_Rep1
Column name in Raw_Counts.csv: Lot6M_Rep1

value: astrocyte


title: SJALL041198_201503670065_R02C01

description:
201503670065_R02C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: Lot 6 Nf1-/- DNp53 male transformed astrocytes, replicate 2

description:
Library name: Lot6M_Rep2
Column name in Raw_Counts.csv: Lot6M_Rep2


title: SJRHB042761_201503670064_R08C01

description:
201503670064_R08C01
blood from survivor of childhood cancer and control

value: Rhabdomyosarcoma


title: SJALL041891_201503670065_R07C01

description:
201503670065_R07C01
blood from survivor of childhood cancer and control


title: Library A-LN, Experiment 2, HTO

description: Library name: BSSE_QGF_206983

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
STARsolo (STARsolo (version 2.7.10a)) was used to perform sample and cell demultiplexing, and alignment of reads to the mouse genome (mm39) and UMI counting on gene models from Ensembl 110. The options --outFilterType=BySJout --outFilterMultimapNmax=10 --outSAMmultNmax=1 --outFilterScoreMin=30 --soloCBmatchWLtype=1MM_multi_Nbase_pseudocounts --soloUMIfiltering=MultiGeneUMI_CR --soloUMIdedup=1MM_CR --soloType=CB_UMI_Simple –soloStrand=Reverse --soloMultiMappers EM were used.
Processing of the UMI counts matrix was performed using the Bioconductor packages DropletUtils (version  1.22.0; function emptyDrops using 5000 iterations, the option test.ambient=TRUE, a lower threshold of 100 UMIs and an FDR threshold of 0.1%), scran (version 1.30.0) and scater (version 1.30.1), following mostly the steps illustrated in the OSCA book (http://bioconductor.org/books/3.18/OSCA/).
Assembly: mm39
Supplementary files format and content: UMIsMatrix.txt.gz: TSV file (tab separated values) including UMI counts for each cell and gene (ENSEMBL ID release 110). Column headers include the library ID and cell barcode sequence separated by a dash (e.g., "BSSE_QGF_159708-AAACCTGAGCTAGGCA")
Supplementary files format and content: CellMetadata.txt.gz: TSV file (tab separated values) including metadata for cells used in the paper.

source_name: Lymph node

growth_protocol: Animals were bred and maintained in the animal facility of the Department of Biomedicine, University of Basel, Switzerland. MOG tomato mouse has a transgenic B cell receptor specific for MOG and B cells carry the fluorophore tdTomato (B6.Cg-Igh-J<tm1Aigl> x B6.129P2(C)-Cd19<tm1(cre)Cgn>/J x B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze). WT tomato mice have B cells with polyclonal B cell receptors and carry the tdTomato fluorophore (B6.Cg-Gt(ROSA)26Sor<tm14(CAG-tdTomato)Hze> x B6.129P2(C)-Cd19<tm1(cre)Cgn>/J). FluBI tomato mice have a transgenic B cell receptor specific for the Influenza HA and the B cells carry the tdTomato fluorophor (B6.Cg-Gt(ROSA)26Sor<tm14(CAG-tdTomato)Hze> x B6.129P2(C)-Cd19<tm1(cre)Cgn>/J x B6.129-Igk<FluBI> Igh<FluBI>/Hpl).

extract_protocol:
Cell suspensions from each biological sample were labeled with BioLegend hashtaging antibodies Total-seq-C before pooling and sorting on tdTomato+ cells. In each experiment a sample from each condition was used in the pool, with a total of 3 pooled libraries for experiment 1, and 2 pooled libraries for both brain and lymph node for experiment 2.
Libraries were loaded on a 10X Genomics Chromium Single Cell Controller with volumes aiming at a targeted recovery of 20'000 cells per channel, and libraries were prepared using the 5’end v2 kit.
Sequencing was performed on an Illumina NovaSeq 6000 sequencer at the Genomics Facility Basel of the ETH Zurich

treatment_protocol:
In Experiment1, 3 independent experiments (replicates) each with 2 mice per timepoint d7 and d21 (1xMOG tomato, 1xFluBI tomato), which is a total of 3 mice per condition per timepoint and therefore 12 mice in total, had been performed. All of these mice got an injection of VSV*DG in the striatum of the left hemisphere. In Experiment 2, 2 independent experiments (replicates) each with 6 mice (2x MOG tomato, 2x MOG tomato + CD40L, 2x WT tomato +CD40L), which is a total of 4 mice per condition and therefore 12 mice in total, had been performed. All of these mice got an injection of VSV*DG either alone or together with Adeno-mCD40L in the striatum of the left hemisphere (if only VSV*DG, virus had been diluted 1:1 with PBS to get same concentration as when mixed with Adeno-mCD40L).
In Experiment1, 7 or 21 days after intrastriatal injection, and in experiment 2, 28 days after intrastriatal injection, the mice were perfused with PBS and liberase buffer (26 units of liberase and 25 mg/ml of DNaseI in MEM-HEPES). In both the experiments 1 and 2, the brain (cut off the cerebellum), but the inguinal lymph-node only in experiment 2, had been isolated and crushed in separation buffer (0.5 M EDTA and 2 % heat-inactivated FCS in PBS). After the cell suspension had been incubated at 37 °C for 30 minutes, it was filtered through a 70 um cell strainer, centrifuged and the pellet resuspended in separation buffer. 10 ul of CD45 microbeads (130-052-301) per 100 ul suspension were added, incubated for 15 minutes, washed with 5 ml of same buffer and cells were isolated by positive selection using LS columns from Miltenyi.

value: Lymph node

tag: library type

value: HTO library

value: B cells

tag: experiment


title: Lot 6 Nf1-/- DNp53 female transformed astrocytes, replicate 1

description:
Library name: Lot6F_Rep1
Column name in Raw_Counts.csv: Lot6F_Rep1

tag: Sex

value: Female


title: Lot 6 Nf1-/- DNp53 female transformed astrocytes, replicate 2

description:
Library name: Lot6F_Rep2
Column name in Raw_Counts.csv: Lot6F_Rep2

value: Lot 6


title: SJSTS042127_201503670065_R05C01

description:
201503670065_R05C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

tag: age

tag: group

value: Soft tissue sarcoma


title: Library A-Brain, Experiment 2, Gene expression

description: Library name: BSSE_QGF_206980

source_name: Brain

value: Brain

value: Gene expression library


title: Library C, Experiment 1, HTO

description: Library name: BSSE_QGF_159713


title: SJCNS042482_201503670064_R03C01

description:
201503670064_R03C01
blood from survivor of childhood cancer and control

value: female

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Central nervous system (CNS)


title: SJGCT042487_201503670075_R03C01

description:
201503670075_R03C01
blood from survivor of childhood cancer and control

value: Germ cell tumor

tag: average dose to whole heart, cgy

tag: race group

value: White


title: Library B-LN, Experiment 2, HTO

description: Library name: BSSE_QGF_206985


title: SJALL041236_201503670064_R02C01

description:
201503670064_R02C01
blood from survivor of childhood cancer and control

tag: base line visit start date

tag: base line visit finish


title: Library A-Brain, Experiment 2, HTO

description: Library name: BSSE_QGF_206984

tag: cell type


title: Library B-Brain, Experiment 2, HTO

description: Library name: BSSE_QGF_206986


title: SJNBL040973_201503670065_R01C01

description:
201503670065_R01C01
blood from survivor of childhood cancer and control

value: Neuroblastoma

tag: age at death


title: Library B-Brain, Experiment 2, Gene expression

description: Library name: BSSE_QGF_206982


title: SJCNS041916_201503670064_R06C01

description:
201503670064_R06C01
blood from survivor of childhood cancer and control

value: male

value: Black


title: SJCNS041908_201503670065_R04C01

description:
201503670065_R04C01
blood from survivor of childhood cancer and control


title: SJALL004196_201503670065_R06C01

description:
201503670065_R06C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: SJCNS041963_201503670064_R05C01

description:
201503670064_R05C01
blood from survivor of childhood cancer and control


title: Library B-LN, Experiment 2, Gene expression

description: Library name: BSSE_QGF_206981

value: Lymph node


title: SJCNS042486_201503670065_R03C01

description:
201503670065_R03C01
blood from survivor of childhood cancer and control


title: SJCNS040991_201503670064_R01C01

description:
201503670064_R01C01
blood from survivor of childhood cancer and control


title: Library A-LN, Experiment 2, Gene expression

description: Library name: BSSE_QGF_206979

value: B cells


title: SJNHL042076_201503670064_R04C01

description:
201503670064_R04C01
blood from survivor of childhood cancer and control

value: Non-Hodgkin lymphoma


title: ATAC_IRF8KO_HoxB8_DC_01

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

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-.

value: DC

tag: genotype


title: SJALL042652_201503670036_R08C01

description:
201503670036_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.

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


title: Library A, Experiment 1, HTO

description: Library name: BSSE_QGF_159709

value: HTO library


title: SJHL042026_201503670064_R07C01

description:
201503670064_R07C01
blood from survivor of childhood cancer and control

value: Hodgkin lymphoma


title: SJNHL042064_201503670036_R05C01

description:
201503670036_R05C01
blood from survivor of childhood cancer and control


title: Library B, Experiment 1, Gene expression

description: Library name: BSSE_QGF_159710

value: Brain

value: Gene expression library


title: Library C, Experiment 1, Gene expression

description: Library name: BSSE_QGF_159712


title: Library A, Experiment 1, Gene expression

description: Library name: BSSE_QGF_159708


title: SJOS042096_201503670036_R04C01

description:
201503670036_R04C01
blood from survivor of childhood cancer and control

value: female

value: cancer survivor

value: Osteosarcoma


title: SJOS042100_201503670036_R06C01

description:
201503670036_R06C01
blood from survivor of childhood cancer and control

value: White


title: ATAC_IRF8KO_HoxB8_DC_02

tag: cell line


title: SJCNS041970_201503670036_R07C01

description:
201503670036_R07C01
blood from survivor of childhood cancer and control

value: Central nervous system (CNS)


title: ATAC_Control_HoxB8_pDC_01

value: pDC

value: Control


title: Library B, Experiment 1, HTO

description: Library name: BSSE_QGF_159711


title: ATAC_SpiBKO_HoxB8_pDC_01

value: Spib{delta}


title: SJCNS042472_201503670036_R03C01

description:
201503670036_R03C01
blood from survivor of childhood cancer and control

value: Black


title: SJALL041292_201503670036_R02C01

description:
201503670036_R02C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: SJNHL041039_201503670036_R01C01

description:
201503670036_R01C01
blood from survivor of childhood cancer and control

value: Non-Hodgkin lymphoma


title: ATAC_Control_HoxB8_pDC_02


title: SJALL005347_201503670004_R06C01

description:
201503670004_R06C01
blood from survivor of childhood cancer and control

value: male


title: SJALL042687_201503670004_R08C01

description:
201503670004_R08C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells


title: ATAC_IRF7KO_HoxB8_pDC_01


title: SJEWS041986_201503670004_R05C01

description:
201503670004_R05C01
blood from survivor of childhood cancer and control

value: Ewing sarcoma family of tumors


title: ATAC_IFNAR1KO_HoxB8_pDC_02


title: SJHL042004_201503670004_R07C01

description:
201503670004_R07C01
blood from survivor of childhood cancer and control

value: Hodgkin lymphoma


title: ATAC_IFNAR1KO_HoxB8_pDC_01


title: ATAC_IRF8KO_spleen_pDC_02

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: SJALL041461_201503670004_R03C01

description:
201503670004_R03C01
blood from survivor of childhood cancer and control


title: SJALL042618_201503670004_R04C01

description:
201503670004_R04C01
blood from survivor of childhood cancer and control


title: SJALL041208_201503670004_R02C01

description:
201503670004_R02C01
blood from survivor of childhood cancer and control