title: spleen scRNAseq

first: Minhyung

last: Kim

address: Elm&Carlton Streets

description:
10x Genomics
A0301 = vehicle
A0305 = low-dose of CBL0137
A0310 = high-dose of CBL0137

data_processing:
Raw sequencing data were processed using Cellranger v6.0.0 software
Filtered gene-barcode matrices were used for further analyses with Seurat single cell data analysis R package.  Each sample was demultiplexed with hashtag oligos (HTOs) using Seurat.
Cells were annotated using SingleR package with ImmGen reference database
Assembly: mm10
Supplementary files format and content: gene expression count matrix

source_name: Spleen

extract_protocol:
Minced tissue was placed into 10 mL of an enzyme solution containing 1 mg/mL collagenase type IV and 10 U/mL of DNase with shaking for 1 hour at 37 °C. Tissue was filtered through 70 μm cell strainer, flushed with 10 mL PBS, and centrifuged for 5 minutes at 380 g. After elimination of red blood cells by hypotonic lysis, leukocytes were isolated by centrifugation at 890 g for 15 minutes at 20°C through 3 mL Lymphoprep and 4 mL of cell suspension in DPBS.
Single cell libraries are generated using the 10X Genomics platform.  First, Feature Barcode conjugated molecules are bound to cell surface proteins. Cells are loaded into the Chromium Controller where they are partitioned into nanoliter-scale Gel Beads-in-emulsion with a single barcode per cell.  Reverse transcription is performed, and the resulting cDNA is amplified. The full-length amplified cDNA is used to generate libraries.

value: Spleen

value: Leukocytes

value: Hematopoietic cell

value: BALB/cAnNCrl

value: multiplexed sample:vehicle, low-dose of CBL0137, high-dose of CBL0137


title: Genomic DNA from LNCaP

status: Public on Dec 31 2023

type: genomic

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

country: USA

institute: Fred Hutchinson Cancer Cancer

hyb_protocol: Illumina Infinium MethylationEPIC standard protocol

data_processing: Methylation data were analyzed from the Illumina Human MethylationEPIC microarray platform using the minfi package in R. Samples were normalized using the subset-quantile within array normalization (SWAN) method. Probes with a detection p value of >0.01 in 50% or more of samples and probes that contained a SNP at the CpG interrogation site or at the single nucleotide extension were removed. Probes were annotated using the lluminaHumanMethylationEPICanno.ilm10b2.hg19 package.

molecule: genomic DNA

organism: Homo sapiens

source_name: Cell line

growth_protocol: PDX lines were grown as described in PMID: 28156002. Cell lines were grown under standard growth media conditions

extract_protocol: Qiagen Dneasy, Bisulfite conversion with DNA Methylation Kit (Zymo Research)

treatment_protocol: No specific treatment

tag: tissue

value: Cell line


title: 372_963049-31

type: SRA

first: Naresh

last: Doni Jayavelu

address: 1201 9th AVE

department: Systems Immunology/Bioinformatics

institute: Benaroya Research Institute at Virginia Mason

library_source: transcriptomic

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Reads were aligned by STAR v2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2), and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: raw_counts_ITN_GRASS_PBMC_samples.csv is a csv file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

molecule: total RNA

source_name: PBMC

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.

value: PBMC

tag: age

tag: Sex

value: Male

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

tag: visit number

tag: treatment

value: SCIT

tag: sts timepoint

value: PreChallenge


title: 379_957431-35

value: SLIT

value: PostChallenge


title: 364_963124-31

value: Female


title: liver scRNA-seq

city: Buffalo

institute: Roswell Park Comprehensive Cancer Center

library_source: transcriptomic single cell

organism: Mus musculus

source_name: Liver

value: Liver

tag: cell line

tag: cell type

tag: genotype


title: 363_963124-35


title: Endothelial-Biculture-non-stretched [23E-Biculture-non-stretched]

city: Waltham

first: Seyedramin

last: Pajoumshariati

state: MA

address: 35 Gatehouse Dr

institute: AstraZeneca

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hsa_GRCH38.94
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: ACBRI 128

growth_protocol: all cells after podocyte differentiation were maintained in the complete CSC medium with Rocket fuel-R supplemented with 0.5% fetal bovine serum (FBS) and antibiotics in  TGC and BGC chips in Zoe where flow applied on them in an incubator (humidified atmosphere with 5% CO2 at 37C)

extract_protocol:
Extraction protocol:TRIzol™ reagent; For RNA preparation from monocultures each cell type was lysed separately in lysis reagent (TRI Reagent, Sigma). For chip experiments GECs were extracted using TrypLE (TrypLE™, Gibco) and then lysed with TRI reagent. GMCs remained behind after this procedure and were isolated by injecting lysis reagent into the bottom channel and aspirating. For podocyte extraction, lysis reagent was injected into the top channel and aspirated. RNA extraction and RNA-seq analysis was performed by Lexogen (Lexogen, Vienna, Austria).B87
QuantSeq FWD 3’ library preparation kit following manufacturer's protocols.

treatment_protocol: three main groups are plate cultures (monocultures), TGCs (tri-culture), and BGCs (co-culture)

value: ACBRI 128

value: Primary human glomerular microvascular endothelial cells

value: WT

value: cultured in BGC

tag: time

value: Day 12


title: Endothelial-Triculture-Non stretched [10E-Triculture-non-stretched]

value: cultured in TGC


title: iPSC_3

city: Kunming

first: Weizhou

last: Wang

state: Yunnan

address: Chunrong West Road

country: China

institute: Kunming Medical University

description:
D3
FPKM.iPSC_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/ , version:cutadapt-1.9).
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/ , version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml , version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: genes_fpkm_expression.xlsx: Excel file includes FPKM values and counts for each Sample.

source_name: Induced pluripotent stem cells (iPSC)

growth_protocol: Fibroblasts were cultured in high-sugar DMEM medium containing 10% FBS and Penicillin-Streptomycin. Bone marrow MSCs and iMSC were cultured in low-sugar DMEM medium containing 10% FBS and Penicillin-Streptomycin. iPSC were cultured in DMEM/F-12 medium containing KnockOut Serum Replacement- Multi- Species, MEM Non-Essential Amino Acids Solution (100X), 2-Mercaptoethanol, LIF Recombinant Mouse Protein (10µg/ml) and Penicillin-Streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA libraries were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: iPSC are obtained from fibroblast reprogramming and iMSC are obtained from iPSC-induced differentiation.

value: Induced pluripotent stem cells (iPSC)

value: Reprogramming

value: Fibroblasts reprogrammed to iPSC by Yamanaka factor


title: 362_959055-35

value: PBMC


title: iPSC_2

description:
D2
FPKM.iPSC_2


title: Endothelial-Triculture-Non stretched [9E-Triculture-non-stretched]


title: Genomic DNA from BCaP-1

scan_protocol: Illumina Infinium MethylationEPIC standard protocol

source_name: Patient-derived xenograft

value: Patient-derived xenograft


title: 361_959055-31

value: SCIT


title: iPSC_1

description:
D1
FPKM.iPSC_1


title: 360_966701-31

value: PreChallenge


title: C57 mouse lung tissue, Control 3

city: jiangxi

first: wei

last: deng

state: China

address: 17 Yongwai Zhengjie, Donghu District, Nanchang City, Jiangxi Province, China

institute: Department of Critical Care Medicine, First Affiliated Hospital of Nanchang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The expression of  mRNA and lncRNA were normalized to FPKM
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Lung tissue

extract_protocol:
Exosomes from three sham group and three CLP groups were used to perform RNA sequencing. MiRNeasy Serum/Plasma Advanced Kit (Qiagen, cat. No. 217204) was used for the extraction and purification of total RNA from lung tissue exosomes according to the instructions of the kit.
According to the manufacturer's recommendations, SMARTer Stranded total RNA-Seq Kit V2 (Takara Bio USA, Inc.) was used for the construction of sequencing library with 4.5 ng RNA of each sample as the input material, and the index codes was then add to the attribute sequences of each sample.

value: Lung tissue


title: Patient3 biological replicate 2 [Patient3_2]

city: London

first: Manju

last: Kurian

address: Great Ormond Street Institute of Child Health, 30 Guilford Street

department: Developmental Neurosciences

country: United Kingdom

institute: University College of London

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol
Patient3_2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered for low-quality sequence, then mapped to GRCh38 whole genome using HISAT2 (v.2.1.0)
Fragments counts for genes were extracted with featureCounts (v.1.6.4) excluding duplicates, multimapping reads and chimeric fragments
Differential gene expression was analysed using edgeR (v.3.24.1), filtering low counts with 1 minimum CPM in at least 3 samples
Differential gene expression was performed comparing disease status (patients vs control) and disease-specific genotype (Patient1 vs CRISPRpatient1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text file with normalized abundance measurements for every gene and every sample (output from edgeR)

source_name: midbrain dopaminergic neurons

growth_protocol: iPSC-derived midbrain dopaminergic neurons were produced following the protocol in Lehnen et al., Stem Cell Reports (2017)

extract_protocol:
Total RNA was isolated from midbrain dopaminergic neurons using the RNeasy mini kit (Qiagen) and RNA libraries were prepared from 100 ng of total RNA using KAPA mRNA HyperPrep kit (Roche)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iPSCs-derived midbrain dopaminergic neurons

value: DNAJC6 homozygous missense variant c.801-2 A>G (Exon 7)


title: Endothelial-Biculture-non-stretched [21E-Biculture-non-stretched]


title: Patient3 biological replicate 1 [Patient3_1]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol
Patient3_1


title: Patient3 biological replicate 3 [Patient3_3]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol
Patient3_3


title: Genomic DNA from 81CR

label_protocol: Illumina Infinium MethylationEPIC standard protocol


title: Genomic DNA from 73CR


title: 359_966701-35

value: Female

value: PostChallenge


title: iMSC_3

description:
C3
FPKM.iMSC_3

source_name: Induced mesenchymal stem cells (iMSC)

value: Induced mesenchymal stem cells (iMSC)

value: iPSC were differentiated into embryoid bodies by conditioned deprivation culture and then induced with 10 ng/ml of TGF-beta1 and 5 ng/ml of bFGF recombinant protein


title: 366_970873-31


title: Patient2 biological replicate 3 [Patient2_3]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol
Patient2_3

value: DNAJC6 homozygous missense variant c.2416C>T, p.R806* (Exon 16)


title: iMSC_2

description:
C2
FPKM.iMSC_2


title: iMSC_1

description:
C1
FPKM.iMSC_1


title: Genomic DNA from 86.2CR


title: Genomic DNA from 96CR


title: 357_970807-31


title: Patient2 biological replicate 1 [Patient2_1]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol
Patient2_1


title: Fib_3

description:
B3
FPKM.Fib_3

source_name: Skin fibroblasts

value: Skin fibroblasts

value: WT

value: Isolated and cultured from mouse skin


title: Genomic DNA from 77CR


title: Fib_2

description:
B2
FPKM.Fib_2


title: Patient1 biological replicate 3 [Patient1_3]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol; Normcounts_matrix_edgeR_Patient1VSCRISPRpatient1
Patient1_3

value: DNAJC6 homozygous missense variant c.766C>T, p.R256* (Exon 6)


title: Genomic DNA from 35CR


title: Genomic DNA from 23.1CR


title: 355_958501-31


title: 354_963077-35


title: Genomic DNA from 70CR


title: Fib_1

description:
B1
FPKM.Fib_1


title: Patient1 biological replicate 2 [Patient1_2]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol; Normcounts_matrix_edgeR_Patient1VSCRISPRpatient1
Patient1_2


title: Genomic DNA from 78CR


title: 353_963077-31


title: BMSC_3

description:
A3
FPKM.BMSC_3

source_name: Bone marrow mesenchymal stem cell (BMSC)

value: Isolated and cultured from mouse femoral bone marrow cavity


title: Patient1 biological replicate 1 [Patient1_1]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol; Normcounts_matrix_edgeR_Patient1VSCRISPRpatient1
Patient1_1


title: BMSC_2

description:
A2
FPKM.BMSC_2

value: Bone marrow mesenchymal stem cell (BMSC)


title: 352_966735-35

value: PBMC

value: Placebo


title: CRISPR Patient 1 biological replicate 3 [CRISPRpatient1_3]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol; Normcounts_matrix_edgeR_Patient1VSCRISPRpatient1
CRISPRpatient1_3

value: CRISPR correction of DNAJC6 homozygous missense variant c.766C>T, p.R256* (Exon 6)


title: Patient2 biological replicate 2 [Patient2_2]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol
Patient2_2


title: BMSC_1

description:
A1
FPKM.BMSC_1


title: 350_970853-35


title: BM-WT-2AB

city: Taichung

first: Shih-Chieh

last: Hung

address: No.6, Hsueh-Shih Road., North Dist.

department: Drug Development Center, Institute of New Drug Development

country: Taiwan

institute: China Medical University

library_source: genomic

data_processing:
Cut & Tag-seq paired-end reads were trimmed adapter and the reads with quality score < 25, length < 140 bp were discarded by fastp v0.38.1.
Cut & Tag-seq reads were aligned to the UCSC mm39 genome using Bowtie2 version 2.5.0.
The mapped Cut&Tag reads were reformatted into bedgraph file format with bin size=10.
Peaks were called using UNIX command from bedgraph.
Assembly: mm39
Supplementary files format and content: bedgraph
Library strategy: CUT&RUN

source_name: bone marrow

extract_protocol:
Calculation of the cell number were performed with the TopQ Gene Probe Assay (RPP30) on real time PCR. The permeability of 10,000 cells were followed by the manufacturer's instructions from the Vazyme #TD903 Kit.
Cut & Tag libraries were prepared according to the manufacturer's instructions from the Vazyme #TD903 Kit with adapter barcode by Vazyme #TD202.

value: bone marrow

value: pool of WT and KLF1-KO cells

tag: cut and tag antibody

value: input sample prepared only with the secondary antibody added to the reaction


title: CRISPR Patient 1 biological replicate 2 [CRISPRpatient1_2]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol; Normcounts_matrix_edgeR_Patient1VSCRISPRpatient1
CRISPRpatient1_2

value: iPSCs-derived midbrain dopaminergic neurons


title: CRISPR Patient 1 biological replicate 1 [CRISPRpatient1_1]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol; Normcounts_matrix_edgeR_Patient1VSCRISPRpatient1
CRISPRpatient1_1


title: BM-WT

value: EKLF (Mybiosource, #MBS388820)


title: Control biorlogical replicate 3 [Control_3]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol
Control_3

value: Wild type


title: Genomic DNA from 147CR

value: Patient-derived xenograft


title: BM-M


title: Control biorlogical replicate 2 [Control_2]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol
Control_2


title: 348_963096-35

value: Female

value: PostChallenge


title: 351_970853-31

value: PreChallenge


title: RNA-seq 8w biol rep 3

city: Xi’an

first: Banjun

last: Ruan

address: 169 Changle West Road

institute: Air Force Medical University

data_processing:
The raw data were analyzed for quality control using the Q30 value, and then cutadapt software (v1.9.1) was used to remove the adapters and low-quality reads to obtain high-quality clean reads.
High-quality clean reads were aligned to the reference genome (GRCm38/mm10) using HISAT2 software (v2.0.4)
According to the gene level FPKM obtained by cuffdiff software, the fold change and P value were calculated to identify differentially expressed mRNAs
Assembly: mm10
Supplementary files format and content: excel file includes RPKM values for each sample

source_name: heart

extract_protocol:
Total RNA was extracted using Rneasy mini plus kit (Qiagen)
RNA libraries were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: heart

value: cardiocytes

value: mouse adult cardiocytes

value: wild type


title: Control biorlogical replicate 1 [Control_1]

description:
Raw_gene_counts_matrix
Normcounts_matrix_edgeR_patientsVScontrol
Control_1


title: 346_958502-35

value: PBMC


title: 358_970807-35

value: SCIT


title: 349_963096-31

value: Placebo


title: RNA-seq 8w biol rep 2


title: Genomic DNA from 189.4


title: Genomic DNA from 173.2


title: 345_958502-31


title: Genomic DNA from 170.3


title: MDA-MB-453_H3K27ac_input

city: ADELAIDE UNIVERSITY

first: Geraldine

last: Laven-Law

state: South Australia

address: Adelaide Health & Med Sci Bldg, Corner George St & North Terrace

country: Australia

institute: The University of Adelaide

data_processing:
Reads were trimmed for adapter sequences and poor-quality bases using the Galaxy Bioinformatics Platform (Jalili et al. 2020 Nucleic Acid Res.). Reads were aligned to human assembly GRCh37 (hg19) using Bowtie2 (Langmead & Salzberg 2012, Nature Methods).
Peaks were called with MACS2 (Zhang et al. 2008, Genome Biology) against the corresponding total chromatin input for each replicate and condition.
Consensus bed files, representing peaks present in at least two of the three replicates were generated with bedtools (Quinlan & Hall 2010 Bioinformatics). A complete RMarkdown script is available at Github.com/DRMCRL/apocrine_signature_mdamb453
Assembly: GRCh37 (hg19)
Supplementary files format and content: bigwig
Supplementary files format and content: bed

source_name: Breast cancer cell line

growth_protocol: MDA-MB-453 cells were seeded into 15 cm2 tissue culture dishes (Corning) at a density to achieve approximately 75% confluence at harvest. Cells were seeded in normal maintenance media. After overnight incubation, the culture media was removed, cells were washed in DPBS, and cells were overlaid with serum-deplete media (where 10% (v/v) FBS is replaced with 10% (v/v) dextran coated, charcoal-stripped FBS). Serum-deplete media was washed and replenished daily for two days.

extract_protocol:
Treated cells were cross-linked with 1% formaldehyde for 10 min, quenched for 5 min with 0.1 M glycine (pH 7.5), washed briefly, and scraped into ice-cold DPBS supplemented with 1x protease inhibitor cocktail (Roche). Cell pellets were resuspended in LB1 cytoplasmic lysis buffer (50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 and 0.25% Triton X-100) at 4°C for 10 min. Nuclei were washed in LB2 buffer (10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) at 4°C for 5 min, and subsequently resuspended in LB3 nuclear lysis buffer (10 mM Tris-HCl (pH 8), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodiumdeoxycholate, 0.5% N-lauroylsarcosine). Lysates were sonicated using a Bioruptor Plus (Diagenode) to produce chromatin fragments of 200-1,000 bp. Trixon X-100 was spiked into sonicated lysates to a final of 1%, lysates were cleared of debris, and 5% of the sonicated chromatin was collected for an input control. Chromatin samples were immunoprecipitated overnight at 4°C with 50 µL of Protein A Dynabeads (Invitrogen) coupled to 2-5 µg of antibody. Three independent replicate experiments were performed, representing consecutive passages of cells. DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
5 – 10 ng of ChIP DNA, along with pooled input chromatin collected from all replicates, was provided to the South Australian Genomics Centre for library preparation and sequencing. Recovered DNA was amplified using the Ultra Low Library Prep Kit (Qiagen) and libraries were sequenced on the Illumina NextSeq 500 to a depth of a minimum of approx. 20 million  75 bp single-end reads per sample.
ChIP-Seq; Illumina NextSeq 500 (High Output v2) single-end 75 bp reads.

treatment_protocol: Cells were treated for 4 hours with 10 nM DHT.

tag: chip antibody

value: DHT

tag: replicate


title: 344_966651-35

tag: tissue

tag: age


title: RNA-seq 8w biol rep 1


title: Genomic DNA from 167CR


title: RNA-seq 3d biol rep 3

value: mouse neonatal cardiocytes


title: MDA-MB-453_FOXA1_input


title: Genomic DNA from 189.3


title: Genomic DNA from 136CR


title: RNA-seq 3d biol rep 2


title: Genomic DNA from 105CR


title: 347_966735-31

tag: Sex

tag: fastq total_reads


title: MDA-MB-453_AR_input


title: Genomic DNA from 170.2


title: RNA-seq 3d biol rep 1


title: 342_970817-35

tag: percent aligned

tag: aligned counts_in_millions


title: MDA-MB-453_AP2B_input


title: Genomic DNA from 147


title: MDA-MB-453_H3K27ac


title: 341_957453-31

tag: median cv_coverage

tag: participant id


title: 340_957453-35

tag: visit number

tag: treatment


title: RNA-seq E18 biol rep 2

tag: cell line

value: mouse embryonic cardiocytes


title: 339_970817-31

tag: sts timepoint


title: RNA-seq E18 biol rep 1

tag: cell type

tag: genotype


title: MDA-MB-453_GATA3


title: MDA-MB-453_FOXA1


title: Genomic DNA from 176


title: 338_963027-35


title: Circ-seq 8w biol rep 3

data_processing:
The raw data obtained by Circle-seq were analyzed for quality control using the Q30 value, and then cutadapt software (v1.9.1) was used to remove the adapters and low-quality reads to obtain high-quality clean reads.
The clean reads were then aligned to the mouse reference genome (GRCm38/mm10) using bwa software (v0.7.12).
After the eccDNA in all samples was identified by Circle-map software (v1.1.4), Samtools (v1.9) software was used to obtain counts of soft-clip reads for breakpoints.
Differentially expressed eccDNA was screened using edgeR (v0.6.9) software for normalization and the calculation of fold change and the P value between groups.
Gene annotation of the identified eccDNA and differential eccDNA was performed by bedtools software (v2.27.1), and eccDNA was visualized through IGV software (v2.4.10).
Assembly: mm10
Supplementary files format and content: excel format
Supplementary files format and content: Number of raw junction read
Library strategy: CircRNA-sequencing

extract_protocol:
Heart samples from embryonic, neonatal and adult C57BL/6J mice were digested and then subjected to alkaline treatment and column chromatography purification.
The purified eccDNA samples were used as templates for amplification reactions by phi29 polymerase . The amplified DNA was then fragmented with the Bioruptor sonicator , and the library was prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.


title: Genomic DNA from 174.1


title: MDA-MB-453_AR


title: MDA-MB-453_GATA3_input


title: Genomic DNA from 136


title: Genomic DNA from 173.1


title: 337_963027-31


title: Genomic DNA from 170.1


title: Genomic DNA from 167


title: Circ-seq 8w biol rep 2


title: 336_966686-35


title: Genomic DNA from 105


title: PsA_SPA170130_PD-1hi_batch1

city: Boston

first: Deepak

middle: A

last: Rao

address: 60 Fenwood Road

department: Division of Rheumatology, Inflammation, and Immunity

institute: Brigham and Women's Hospital

data_processing:
Examined library qualtiy with FastQC.
Performed adapter trimming with trimmomatic.
Aligned to the GRCh38 reference genome using STAR.
Filtered lowly-expressed genes (log2 FPKM < 2).
TMM normalized read counts were generated, and data was log2 transformed, batched corrected and scaling was applied (mean=0, variation=1).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes log2TPM values for each sample.

source_name: Synovial Fluid

extract_protocol:
For each sorted subset, up to 1,500 cells were collected directly into buffer TCL (Qiagen) with 1% β-mercaptoethanol (Sigma). RNA when then isolated using RNeasy Micro Kits (Qiagen).
5µL of total RNA were placed in wells of a 96-well plate, and RNA-seq libraries were prepared at Broad Technology Labs at the Broad Institute of Harvard and MIT, using the Illumina Smart-Seq2 platform

value: Synovial Fluid

tag: disease

value: PsA

tag: donor

tag: cell population

tag: batch


title: 335_966686-31

tag: tissue

tag: age


title: PsA_SPA170130_CD38-CD127-PD-1intKLRG1+_batch1


title: MDA-MB-453_AP2B

tag: chip antibody

tag: replicate


title: RNA-seq E18 biol rep 3


title: Genomic DNA from 145.2


title: Circ-seq 3d biol rep 3


title: Circ-seq 8w biol rep 1


title: PsA_SPA170130_CD38hiCD127-PD-1int_batch1


title: 334_963040-35

tag: Sex

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions


title: Circ-seq 3d biol rep 2


title: Circ-seq 3d biol rep 1


title: PsA_SPA170130_CD38-CD127+PD-1-_batch1


title: 332_957470-31

tag: median cv_coverage

tag: participant id

tag: visit number

tag: treatment


title: PsA_SPA170130_CD38-CD127+PD-1int_batch1


title: Circ-seq E18 biol rep 3

tag: cell line

tag: cell type

tag: genotype


title: 343_966651-31

tag: sts timepoint


title: Circ-seq E18 biol rep 2


title: 330_970811-31


title: Genomic DNA from 93


title: Circ-seq E18 biol rep 1


title: 326_957463-35

value: Male


title: Genomic DNA from 141

value: Patient-derived xenograft


title: CI_P115_CD38-CD127-PD-1intKLRG1+_batch1

tag: disease

value: CI

tag: donor

tag: cell population

tag: batch


title: Genomic DNA from 81

tag: tissue


title: C57BL/6N mice, miR-29ab1-/-, 3 dpi, 4

city: Beijing

first: Yao

last: Lu

address: No. 17, Tsinghua East Rd, Haidian District, Beijing

institute: Yao Lu, a student from China Agricultural University

data_processing:
Reads were mapped to reference genome with Hisat2
Differential expression analysis was conducted using DESeq2 R
Supplementary files format and content: tab-delimited text file includes FPKM and read_count values for each Sample

source_name: small intestinal crypts

extract_protocol:
RNA was harvested using TRIzol method.
RNA libraries for RNA-seq were prepared.

tag: strain

value: small intestinal crypts

value: 3 day post irradiation


title: 325_966678-35

tag: age

tag: Sex

tag: fastq total_reads

value: PostChallenge


title: CI_P115_CD38hiCD127-PD-1int_batch1


title: C57BL/6N mice, miR-29ab1-/-, 3 dpi, 3


title: 323_957463-31

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

value: PreChallenge


title: C57BL/6N mice, miR-29ab1-/-, 3 dpi, 2

tag: treatment


title: CI_P115_CD38-CD127+PD-1-_batch1


title: Genomic DNA from 92


title: 321_963113-31

tag: participant id

tag: visit number


title: C57BL/6N mice, miR-29ab1-/-, 3 dpi, 1

tag: genotype


title: CI_P091_PD-1hi_batch2


title: 319_966710-35

tag: sts timepoint


title: Genomic DNA from 77


title: Genomic DNA from 78


title: C57BL/6N mice, WT, 3 dpi, 4

value: WT


title: CI_P091_CD38-CD127-PD-1intKLRG1+_batch2

tag: disease


title: Genomic DNA from 145.1


title: Genomic DNA from 70


title: 316_958453-31


title: C57BL/6N mice, WT, 3 dpi, 3


title: Genomic DNA from 96


title: CI_P091_CD38-CD127+PD-1-_batch2

tag: donor


title: Genomic DNA from 58


title: 312_958492-31


title: 310_963093-35


title: C57BL/6N mice, WT, 3 dpi, 1


title: CI_P115_CD38-CD127+PD-1int_batch1

tag: cell population


title: C57BL/6N mice, WT, 3 dpi, 2


title: CI_P115_PD-1hi_batch1

tag: batch


title: Genomic DNA from 176CR

label: Cy3, Cy5

tag: tissue


title: Delta16HER2_rep2 (RNAseq)

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

data_processing:
Reads are aligned by Tophat/bowtie2
Reads are counted at gene level by HTseq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count at gene level for each Sample

source_name: breast cancer tumor

growth_protocol: Delta16HER2 male mice were bred to Sirt6BAC females  to obtain Delta16HER2/SIRT6-OE females. The offspring was characterized by genotyping of tail biopsies. Delta16HER2/Sirt6wt female mice obtained from the same mating were used as controls. Starting at 8 weeks of age, both Delta16HER2/SIRT6-OE and Delta16HER2 females were weekly monitored for tumor formation by palpation. Masses greater than 1.5 mm in diameter were regarded as tumors. Tumor growth was measured by means of an electronic caliper.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following manufacture's instructions.
Libraries were prepared using TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, San Diego, CA, USA, Cat #: 20020599)

treatment_protocol: Tumors from mice were surgically removed, flash-frozen in liquid nitrogen and stored at -80 °C.

value: breast cancer tumor

value: 20 weeks


title: 307_963093-31

value: PBMC


title: Genomic DNA from EF1

source_name: Cell line

value: Cell line


title: 324_963113-35

source_name: PBMC

value: SCIT


title: Genomic DNA from 208.2


title: Genomic DNA from 86.2


title: Genomic DNA from 208.1


title: CI_P091_CD38hiCD127-PD-1int_batch2


title: 304_966655-31

value: SLIT


title: Genomic DNA from 235.2


title: RA_P090_PD-1hi_batch2

value: RA


title: Delta16HER2_rep1 (RNAseq)


title: 301_966655-35


title: 333_963040-31

value: Female


title: Delta16HER2_SIRT6-OE_rep2 (RNAseq)


title: RA_P090_CD38hiCD127-PD-1int_batch2

value: Synovial Fluid


title: Genomic DNA from 235.3


title: 297_958467-31

value: Male


title: CI_P091_CD38-CD127+PD-1int_batch2


title: Delta16HER2_rep2

data_processing:
Reads were aligned to mm10 reference genome using ‘bwa’
Unmapped reads, reads with a MAPQ smaller then 1, duplicate reads and those that mapped outside of chr 1-19 and Chr X were removed using samtools
Peak calling was performed using MACS2 using sandard paramenters and max-gap 600
Assembly: mm10
Supplementary files format and content: Text file (bed and broadPeak) containing enriched regions coordinates

growth_protocol: Delta16HER2 male mice were bred to Sirt6BAC females to obtain Delta16HER2/SIRT6-OE females. The offspring was characterized by genotyping. Delta16HER2/Sirt6 wild-type (wt) female mice obtained from the same breeding were used as controls. Starting at 8 weeks of age, both Delta16HER2/SIRT6-OE and Delta16HER2 females were weekly monitored for tumor formation by palpation. Masses greater than 1.5 mm in diameter were regarded as tumors. Tumor growth was measured by means of an electronic caliper.

extract_protocol:
20 mg of tissue were homogenized with a Dounce homogenizer in 0.5 mL of fixation solution (5 mM HEPES pH 7.5, 10 mM NaCl, 0.1 mM Na2EDTA, 0.05 mM EGTA, 1% formaldehyde) and fixed for 10 minutes at 37 °C. Cells were then lysed and subjected to chromatin extraction as previously reported (Amatori S. et al., (2018).
Libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody

value: H3K9ac (ab4441, Abcam)


title: RA_P049_PD-1hi_batch1


title: 296_966706-31

tag: age


title: Delta16HER2_rep1 (ChIPseq)


title: Genomic DNA from 35

value: Patient-derived xenograft


title: RA_P049_CD38-CD127-PD-1intKLRG1+_batch1


title: 300_958467-35

tag: Sex


title: RA_P090_CD38-CD127-PD-1intKLRG1+_batch2


title: 292_957459-35

tag: fastq total_reads


title: Delta16HER2_SIRT6-OE_rep1 (RNAseq)


title: RA_P090_CD38-CD127+PD-1-_batch2


title: Genomic DNA from 73


title: RA_P090_CD38-CD127+PD-1int_batch2


title: RA_P049_CD38-CD127+PD-1-_batch1


title: Delta16HER2_SIRT6-OE_rep2 (ChIPseq)


title: RA_P049_CD38hiCD127-PD-1int_batch1


title: 291_966706-35

tag: percent aligned


title: C57BL/6N mice, miR-29ab1-/- 4

data_processing:
Reads were mapped to reference genome with Hisat2
Differential expression analysis was conducted using DESeq2 R
Supplementary files format and content: tab-delimited text file includes count and FPKM values for each Sample

source_name: small intestinal cryptes

extract_protocol:
RNA was harvested using TRIzol method.
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit following manufacturer's protocols.

value: small intestinal cryptes


title: 298_963048-35

tag: aligned counts_in_millions


title: TF-1 WT-K rep 3

city: Durham

first: Yiran

last: Guo

state: North Carolina

address: 3 Genome Ct

institute: Duke University

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC v2.0 Kit using Illumina standard protocol.

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting.

data_processing: Data were processed and analyzed using minfi version 1.44.0

label: Cy5 and Cy3

source_name: TF-1 cell line

label_protocol: Standard labelling protocol according to the vendor’s instruction (Illumina).

growth_protocol: The TF-1 human erythroleukemic cell line was obtained from ATCC and cultivated in the RPMI 1640 base medium supplemented with 10% of FBS and 2 ng/ml of recombinant human GM-CSF.

extract_protocol: Genomic DNA was extracted using the PureLink Genomic DNA Mini Kit (Invitrogen), followed by bisulfite-conversion using the EpiTect Bisulfite Kit (Qiagen)

treatment_protocol: TF-1 cell lines with stable expression of WT or mutant DNMT3A were established with MSCV-based retrovirus followed by drug selection.

tag: gene expressed

value: DNMT3A R676K


title: TF-1 WT-TK rep 1

value: DNMT3A R676K M674T


title: 290_963056-31

tag: median cv_coverage

tag: treatment

value: PreChallenge


title: TF-1 WT-TK rep 2


title: C57BL/6N mice, miR-29ab1-/- 3


title: Delta16HER2_SIRT6-OE_rep3 (ChIPseq)


title: Genomic DNA from 49


title: Genomic DNA from 208.4


title: TF-1 WT-K rep 2


title: 293_957459-31

tag: participant id

tag: visit number


title: 289_963056-35

tag: sts timepoint

value: PostChallenge


title: Delta16HER2_SIRT6-OE_rep1 (ChIPseq)

value: breast cancer tumor

tag: genotype


title: C57BL/6N mice, miR-29ab1-/- 2


title: CI_P039C_CD38hiCD127-PD-1int_batch2

tag: disease

value: CI

tag: donor


title: 288_970796-31

value: PBMC


title: C57BL/6N mice, miR-29ab1-/- 1


title: 287_970796-35


title: C57BL/6N mice, WT 4

value: WT


title: 286_966657-31


title: CI_P039C_PD-1hi_batch2

tag: cell population

tag: batch


title: CI_P039C_CD38-CD127+PD-1int_batch2

tag: tissue


title: CI_P039C_CD38-CD127+PD-1-_batch2


title: TF-1 WT-TK rep 3


title: RA_P037_PD-1hi_batch1


title: C57BL/6N mice, WT 2


title: 285_963059-31

tag: age


title: C57BL/6N mice, WT 3


title: TF-1 WT rep 2

value: DNMT3A WT


title: C57BL/6N mice, WT 1


title: RA_P037_CD38-CD127-PD-1intKLRG1+_batch1


title: TF-1 WT-K rep 1


title: 282_966657-35

tag: Sex

value: SLIT


title: postnatal day14 keratinocyte_3

city: seoul

first: Jimin

last: Cha

address: 50-1, Yonsei-ro

country: South Korea

institute: Yonsei university

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 1.3.4d, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count, FPKM, TPM values for each sample

source_name: Skin

growth_protocol: Not applicable

extract_protocol:
Skin fresh tissue was achieved, Keratinocytes were sorted as CD45.2-(BioLegend), PI-(BioVision) by AriaIII. RNA from keratinocytes was prepared using RNeasy® Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries were generated using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina), and the samples were sequenced on a NovaSeq 6000 System User Guide Document #1000000019358 v02 (Illumina) using NovaSeq 6000 S4 Reagent Kit (Illumina).

treatment_protocol: Not applicable

value: Skin

tag: strain

value: postnatal day14

tag: cell type

value: keratinocyte


title: RA_P037_CD38hiCD127-PD-1int_batch1

value: Synovial Fluid

value: RA


title: TF-1 CK rep 3

value: DNMT3A R882C R676K


title: postnatal day14 keratinocyte_2


title: RA_P037_CD38-CD127+PD-1-_batch1


title: TF-1 CTK rep 1

value: DNMT3A R882C R676K M674T


title: 281_957448-35

value: Male

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions


title: postnatal day14 keratinocyte_1


title: RA_P037_CD38-CD127+PD-1int_batch1


title: 278_966713-31

value: Female

tag: median cv_coverage

tag: treatment

value: SCIT


title: RA_P049_CD38-CD127+PD-1int_batch1


title: RA_P012B_PD-1hi_batch2


title: postnatal day7 keratinocyte_3

value: postnatal day7


title: 277_966713-35

tag: participant id

tag: visit number

value: PostChallenge


title: TF-1 CTK rep 2

tag: gene expressed


title: RA_P012B_CD38-CD127-PD-1intKLRG1+_batch2

tag: disease


title: CI_P039C_CD38-CD127-PD-1intKLRG1+_batch2

value: CI

tag: donor


title: postnatal day7 keratinocyte_2


title: postnatal day7 keratinocyte_1


title: TF-1 WT rep 3


title: RA_P012B_CD38hiCD127-PD-1int_batch2

tag: cell population


title: 274_963050-31

value: PBMC

tag: sts timepoint

value: PreChallenge


title: postnatal day1 keratinocyte_3

tag: tissue

value: postnatal day1


title: 279_970864-35

tag: age


title: 273_963050-35

tag: Sex


title: TF-1 CK rep 1


title: 284_957448-31

value: SLIT


title: RA_P012B_CD38-CD127+PD-1int_batch2

tag: batch


title: TF-1 CTK rep 3


title: TF-1 WT rep 1

value: DNMT3A WT


title: 275_958491-31


title: postnatal day1 keratinocyte_1

value: Skin

tag: strain

tag: cell type


title: 272_970819-35

tag: fastq total_reads

tag: percent aligned

value: Placebo


title: 270_966698-35

tag: aligned counts_in_millions

tag: median cv_coverage


title: PsA_P009_PD-1hi_batch1

value: Synovial Fluid

value: PsA


title: TF-1 HTK rep 2

value: DNMT3A R882H R676K M674T


title: TF-1 R882C rep 2

value: DNMT3A R882C


title: TF-1 R882C rep 3


title: TF-1 HTK rep 3


title: 271_970819-31

tag: participant id

tag: treatment


title: RA_P012B_CD38-CD127+PD-1-_batch2

value: RA


title: Liver ORSAM18675-2

city: Bar Harbor

first: Kristen

last: O'Connell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
pcHiC data for three strains (C57BL/6J, NZO/HlLtJ, and CAST/EiJ) from, islet, liver, and adipose tissues were processed in the following way. Reads were quality trimmed with AGeNT Trim (https://www.agilent.com/en/product/next-generation-sequencing/hybridization-based-next-generation-sequencing-ngs/ngs-software/agent-232879). Trimmed reads were processed with the HiCUP pipeline [PMID: 26835000]. Following the HiCUP filter step, mapped, hicup_filter alignments were demultiplex with UMI aware AGeNT Locatit. On target ‘captured.bam’ files were then generated for demultiplex alignments with `HiCUP_Capture` a tool from the HiCUP pipeline. On target captured BAMs files were converted to Chicago format with ‘bam2chicago_V02.sh’ using the 5kb binned fragments and target baitmap as inputs (1). The resulting ‘chinput’ files were process with Chicago via the ‘runChicago.R’ script with suggested 6-base-cutter settings. Processed resulting output with ‘fitDistCurve.R’ with the flag ‘-t -5’ to obtain adjusted p-value weight settings relative to our data. The ‘chinput’ were then reprocessed with ‘runChicago.R’ with final settings from the re-weighting analysis. Due to difficulty associated with harvesting tissue, Islet and adipose samples yielded low per sample coverage. Therefore to maintain consistency across all tissues on target alignments were pooled by strain and pooled data were used in the downstream Chicago analysis.
Assembly: mm10
Supplementary files format and content: ibed : bait interactions, seqmonk.txt : bait interactions can be read by seqmonk, washU_text.txt : bait interactions can be read by the WashU browser

source_name: liver

extract_protocol:
Ligated samples underwent crosslink reversal, DNA extraction with proteinase K, and biotin removal from unligated fragments.
Promotor capture libraries were constructed via the following method. Crosslinked cells were lysed, digested with DpnII, ends filled in using biotin-14-dATP followed by overnight proximity ligation.  Ligated samples underwent crosslink reversal, DNA extraction with proteinase K, and biotin removal from unligated fragments.  DNA was fragmented to 500-600 bp, column purified, and biotinylated fragments pulled down. Biotinylated fragments were converted into Illumina compatible libraries using the SureSelect XT HS2 DNA System and a custom SureSelect probe set (design ID S3346176) (Agilent Technologies) according to the manufacture’s protocol with the following exception:  pre-capture PCR was performed as four 50 ul reactions that were recombined during clean-up. The quality and concentration of the libraries were assessed using the High Sensitivity D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.
Libraries were sequenced 150 bp paired end on an Illumina NovaSeq 6000.

value: liver

value: NZO/HILtJ

value: Whole Liver - liver

value: Male

value: 44% fat + fiber


title: TF-1 R882C rep 1

tag: gene expressed


title: TF-1 HK rep 3

value: DNMT3A R882H R676K


title: Genomic DNA from R002590-12

city: Los Angeles

first: Gangning

last: Liang

state: CA

address: 1441 Biggy street

department: Urology

institute: USC Keck school of medicine

description:
blood from Pediatric Patients with AML
SAMPLE 40

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Illumina iScan technology using standard scanner setting

data_processing: R package 'minfi' was used for data processing and background normalization

source_name: blood-R002590-Cycle2, Day 29

label_protocol: Standard Illumina Protocol

extract_protocol: Not provided

tag: disease

value: AML

value: blood


title: PsA_P009_CD38-CD127+PD-1-_batch1

tag: donor


title: PsA_P009_CD38-CD127-PD-1intKLRG1+_batch1

tag: cell population


title: 268_963120-31

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Reads were aligned by STAR v2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2), and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: raw_counts_ITN_GRASS_PBMC_samples.csv is a csv file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.

value: PBMC

value: Female

tag: visit number

tag: sts timepoint

value: PreChallenge


title: Genomic DNA from R002590-10

description:
blood from Pediatric Patients with AML
SAMPLE 39

source_name: blood-R002590-Cycle2, Day 15

tag: tissue


title: PsA_P009_CD38-CD127+PD-1int_batch1


title: postnatal day1 keratinocyte_2

value: Skin

tag: age

value: postnatal day1

value: keratinocyte


title: TF-1 HK rep 2


title: PsA_P009_CD38hiCD127-PD-1int_batch1

value: Synovial Fluid

value: PsA

tag: batch


title: 267_966698-31

tag: Sex

value: Placebo


title: Genomic DNA from R002590-6

description:
bone marrow from Pediatric Patients with AML
SAMPLE 38

source_name: bone marrow-R002590-Cycle1, Day 29

value: bone marrow


title: TF-1 HTK rep 1

value: DNMT3A R882H R676K M674T


title: TF-1 R882C rep 4

value: DNMT3A R882C


title: TF-1 HK rep 1


title: Liver ORSAM17830-2

value: liver

tag: strain

value: NZO/HILtJ

tag: cell type

value: Whole Liver - liver

value: Male

value: 10% fat + fiber


title: Genomic DNA from R002590-1

description:
bone marrow from Pediatric Patients with AML
SAMPLE 35

source_name: bone marrow-R002590-Cycle1, Day 0

value: AML


title: TF-1 R882H rep 4

value: DNMT3A R882H


title: PsA_P007_CD38-CD127+PD-1-_batch2


title: 265_958494-31

value: PBMC

value: Female

tag: fastq total_reads

tag: percent aligned

value: PreChallenge


title: Genomic DNA from R002590-7

description:
blood from Pediatric Patients with AML
SAMPLE 36

source_name: blood-R002590-Cycle1, Day 0

value: blood


title: Genomic DNA from R002295-3

description:
blood from Pediatric Patients with AML
SAMPLE 33

source_name: blood-R002295-Cycle1, Day 7


title: PsA_P007_CD38hiCD127-PD-1int_batch2

value: Synovial Fluid


title: Liver ORSAM18674-2

value: 44% fat + fiber


title: 269_963120-35

tag: aligned counts_in_millions

tag: median cv_coverage

value: Placebo

value: PostChallenge


title: Liver ORSAM17829-2

tag: treatment


title: Liver ORSAM18677-2


title: Genomic DNA from R002295-2

description:
blood from Pediatric Patients with AML
SAMPLE 32

source_name: blood-R002295-Cycle1, Day 0


title: Liver ORSAM18384-2


title: PsA_P007_CD38-CD127+PD-1int_batch2

value: PsA


title: Genomic DNA from R002295-6

description:
blood from Pediatric Patients with AML
SAMPLE 34

source_name: blood-R002295-Cycle1, Day 29


title: Liver ORSAM18379-2


title: TF-1 CK rep 2

tag: gene expressed

value: DNMT3A R882C R676K


title: 262_970848-35

tag: participant id


title: Liver ORSAM18668-2

value: liver


title: CI_P003_PD-1hi_batch2

source_name: Synovial Fluid

tag: disease

value: CI

tag: donor


title: Liver ORSAM18380-2

value: NZO/HILtJ

value: Whole Liver - liver


title: TF-1 mock-treated rep 3

value: mock


title: 260_963095-35

value: Male

tag: visit number


title: 261_970848-31

tag: sts timepoint


title: 263_966707-35

tag: tissue


title: Genomic DNA from R002284-1

description:
blood from Pediatric Patients with AML
SAMPLE 29

source_name: blood-R002284-Cycle1, Day 29

value: AML


title: TF-1 mock-treated rep 1


title: CI_P003_CD38hiCD127-PD-1int_batch2

tag: cell population


title: Liver ORSAM17827-2

value: 10% fat + fiber


title: Genomic DNA from R002284-5

description:
bone marrow from Pediatric Patients with AML
SAMPLE 30

source_name: bone marrow-R002284-Cycle1, Day 29

value: bone marrow


title: 258_958455-35

value: PBMC

tag: age


title: CI_P003_CD38-CD127+PD-1-_batch2

tag: batch


title: PsA_DiSF80_CD38hiCD127-PD-1int_batch1


title: 259_958455-31

tag: Sex

value: PreChallenge


title: Liver ORSAM18671-2

tag: strain

tag: cell type

value: Female


title: Genomic DNA from R002284-6

description:
blood from Pediatric Patients with AML
SAMPLE 28

source_name: blood-R002284-Cycle1, Day 0

value: blood


title: Liver ORSAM18670-2


title: Liver ORSAM18685-2

value: CAST/EiJ

value: 44% fat + fiber


title: Genomic DNA from R002181-6

description:
bone marrow from Pediatric Patients with AML
SAMPLE 27

source_name: bone marrow-R002181-Cycle1, Day 29


title: Genomic DNA from R002181-4

description:
blood from Pediatric Patients with AML
SAMPLE 26

source_name: blood-R002181-Cycle1, Day 29


title: 257_963095-31

source_name: PBMC

tag: fastq total_reads

tag: percent aligned

value: Placebo


title: TF-1 R882H rep 3

source_name: TF-1 cell line

value: DNMT3A R882H


title: CI_P003_CD38-CD127+PD-1int_batch2

value: Synovial Fluid


title: PsA_DiSF39_PD-1hi_batch1

value: PsA


title: 264_966707-31

tag: aligned counts_in_millions

tag: median cv_coverage


title: Liver ORSAM18389-2

source_name: liver

value: liver

tag: treatment


title: PsA_DiSF39_CD38-CD127-PD-1intKLRG1+_batch1


title: 256_963031-31

tag: participant id


title: PsA_DiSF39_CD38hiCD127-PD-1int_batch1

tag: disease


title: Liver ORSAM18388-2

value: Whole Liver - liver


title: Genomic DNA from R002181-7

description:
blood from Pediatric Patients with AML
SAMPLE 24

source_name: blood-R002181-Cycle1, Day 0


title: 254_966672-35

value: PostChallenge


title: Genomic DNA from R002181-1

description:
bone marrow from Pediatric Patients with AML
SAMPLE 23

source_name: bone marrow-R002181-Cycle1, Day 0


title: Liver ORSAM17836-2

value: Male


title: Genomic DNA from R002590-2

description:
blood from Pediatric Patients with AML
SAMPLE 37

source_name: blood-R002590-Cycle1, Day 29

value: AML


title: 255_957466-31


title: 253_966672-31


title: PsA_DiSF39_CD38-CD127+PD-1int_batch1

tag: donor


title: TF-1 mock-treated rep 2

tag: gene expressed

value: mock


title: Genomic DNA from R1046-8

description:
bone marrow from Pediatric Patients with AML
SAMPLE 22

source_name: bone marrow-R1046-Cycle1, Day 42

value: bone marrow


title: Genomic DNA from R002181-2

description:
blood from Pediatric Patients with AML
SAMPLE 25

source_name: blood-R002181-Cycle1, Day 15


title: Genomic DNA from R1046-3

description:
blood from Pediatric Patients with AML
SAMPLE 21

source_name: blood-R1046-Cycle1, Day 42


title: Liver ORSAM18690-2

value: 10% fat + fiber


title: PsA_DiSF39_CD38-CD127+PD-1-_batch1


title: Liver ORSAM18680-2


title: CI_DiSF36_CD38-CD127-PD-1intKLRG1+_batch1

value: CI


title: Liver ORSAM18387-2

value: Female


title: TF-1 R882H rep 1


title: Genomic DNA from R1046-9

description:
blood from Pediatric Patients with AML
SAMPLE 20

source_name: blood-R1046-Cycle1, Day 0

value: blood


title: Liver ORSAM17834-2

value: CAST/EiJ


title: 249_970778-31

value: PBMC

tag: visit number

value: SLIT

tag: sts timepoint

value: PreChallenge


title: 252_957466-35

tag: tissue

value: Placebo


title: Liver ORSAM18386-2

value: 44% fat + fiber


title: Genomic DNA from R1046-1

description:
bone marrow from Pediatric Patients with AML
SAMPLE 19

source_name: bone marrow-R1046-Cycle1, Day 0


title: CI_DiSF36_CD38-CD127+PD-1-_batch1

source_name: Synovial Fluid

value: Synovial Fluid

tag: cell population


title: 248_970778-35

tag: age


title: Genomic DNA from R0442-5

description:
bone marrow from Pediatric Patients with AML
SAMPLE 18

source_name: bone marrow-R0442-Cycle1, Day 29


title: Liver ORSAM17832-2

value: liver

value: Whole Liver - liver

tag: Sex


title: Genomic DNA from R002295-1

description:
bone marrow from Pediatric Patients with AML
SAMPLE 31

source_name: bone marrow-R002295-Cycle1, Day 0


title: 251_963031-35

value: Male

value: PostChallenge


title: CI_P003_CD38-CD127-PD-1intKLRG1+_batch2

tag: batch


title: Genomic DNA from R0442-2

description:
blood from Pediatric Patients with AML
SAMPLE 17

source_name: blood-R0442-Cycle1, Day 29

value: AML


title: 247_957462-31


title: CI_DiSF36_CD38-CD127+PD-1int_batch1


title: Liver ORSAM17831-2

tag: strain

tag: cell type


title: PsA_DiSF31_PD-1hi_batch1

value: PsA


title: Genomic DNA from R0442-6

description:
blood from Pediatric Patients with AML
SAMPLE 16

source_name: blood-R0442-Cycle1 Day 0


title: Liver ORSAM18683-2

value: 10% fat + fiber


title: PsA_DiSF31_CD38hiCD127-PD-1int_batch1


title: Liver ORSAM18376-2


title: 243_963057-31

tag: fastq total_reads

tag: percent aligned


title: Liver ORSAM18662-2


title: 244_963057-35

tag: aligned counts_in_millions

tag: median cv_coverage


title: Genomic DNA from R0442-1

description:
bone marrow from Pediatric Patients with AML
SAMPLE 15

source_name: bone marrow-R0442-Cycle1 Day 0

value: bone marrow


title: PsA_DiSF31_CD38-CD127+PD-1-_batch1


title: Genomic DNA from R0383-5

description:
blood from Pediatric Patients with AML
SAMPLE 14

source_name: blood-R0383-Cycle1,Day 29


title: PsA_DISF31_CD38-CD127+PD-1int_batch2


title: Genomic DNA from R0383-3

description:
blood from Pediatric Patients with AML
SAMPLE 13

source_name: blood-R0383-Cycle1 Day 15


title: Liver ORSAM18378-2

source_name: liver

tag: treatment


title: 246_957462-35

source_name: PBMC

tag: participant id


title: 241_966662-35


title: PsA_DiSF31_CD38-CD127-PD-1intKLRG1+_batch1

tag: disease

tag: donor


title: Liver ORSAM17823-2


title: CI_DISF105_PD-1hi_batch2

value: CI


title: CI_DiSF36_PD-1hi_batch1


title: 239_963073-35

tag: visit number


title: CI_DISF105_CD38hiCD127-PD-1int_batch2


title: Genomic DNA from R0383-1

description:
blood from Pediatric Patients with AML
SAMPLE 12

source_name: blood-R0383-Cycle1 Day 0

value: blood


title: Genomic DNA from R0335-1

description:
bone marrow from Pediatric Patients with AML
SAMPLE 10

source_name: bone marrow-R0335-Cycle1 Day 0


title: Genomic DNA from R0335-2

description:
blood from Pediatric Patients with AML
SAMPLE 11

source_name: blood-R0335-Cycle1 Day 0


title: Liver ORSAM17822-2


title: CI_DISF105_CD38-CD127-PD-1intKLRG1+_batch2


title: 240_966662-31

tag: sts timepoint


title: CI_DISF105_CD38-CD127+PD-1-_batch2

tag: tissue


title: 238_963073-31


title: Genomic DNA from R0265-1

description:
bone marrow from Pediatric Patients with AML
SAMPLE 9

source_name: bone marrow-R0265-Cycle1 Day 29


title: TF-1 R882H rep 2

source_name: TF-1 cell line

tag: gene expressed

value: DNMT3A R882H


title: CI_DISF105_CD38-CD127+PD-1int_batch2

tag: cell population


title: Genomic DNA from R0265-3

description:
blood from Pediatric Patients with AML
SAMPLE 8

source_name: blood-R0265-Cycle1 Day 22


title: 242_957454-31

value: PBMC

tag: age

tag: Sex


title: 236_957454-35


title: Liver ORSAM18374-2

tag: strain

value: Female


title: Liver ORSAM18373-2

tag: cell type


title: CI_DISF103_PD-1hi_batch2

tag: batch


title: Genomic DNA from R0140-4

description:
blood from Pediatric Patients with AML
SAMPLE 7

source_name: blood-R0140-Cycle1 Day 15


title: CI_DISF103_CD38hiCD127-PD-1int_batch2

source_name: Synovial Fluid


title: Genomic DNA from R0140-2

description:
blood from Pediatric Patients with AML
SAMPLE 6

source_name: blood-R0140-Cycle1 Day 0


title: Liver ORSAM17824-2


title: 235_966703-35

tag: fastq total_reads

tag: percent aligned

value: SCIT


title: Liver ORSAM1781-2


title: CI_DISF103_CD38-CD127-PD-1intKLRG1+_batch2


title: 233_966703-31

tag: aligned counts_in_millions

tag: median cv_coverage

value: PreChallenge


title: Liver ORSAM18655-2

tag: treatment

value: 44% fat + fiber


title: Liver ORSAM17820-2


title: Islet ORSAM18618-1

source_name: islet

value: islet

value: CAST/EiJ

value: Islet - islets of Langerhans


title: 230_958505-35

value: Male

tag: participant id


title: Genomic DNA from T0405-7

description:
blood from Pediatric Patients with AML
SAMPLE 4

source_name: blood-T0405-Cycle1 Day 29

tag: disease


title: CI_DISF103_CD38-CD127+PD-1-_batch2

value: Synovial Fluid

tag: donor


title: Genomic DNA from T0405-2

description:
bone marrow from Pediatric Patients with AML
SAMPLE 3

source_name: bone marrow-T0405-Cycle1 Day 29

value: AML


title: Genomic DNA from R0140-1

description:
bone marrow from Pediatric Patients with AML
SAMPLE 5

source_name: bone marrow-R0140-Cycle1 Day 0


title: Islet ORSAM18613-1


title: Genomic DNA from T0405-6

description:
blood from Pediatric Patients with AML
SAMPLE 2

source_name: blood-T0405-Cycle1 Day 0


title: 237_970808-35

tag: visit number

value: Placebo

tag: sts timepoint

value: PostChallenge


title: CI_DISF103_CD38-CD127+PD-1int_batch2

tag: tissue


title: RA_DiSF100_PD-1hi_batch1

value: RA

tag: cell population


title: 228_958505-31

tag: age


title: 232_970805-31

tag: Sex


title: RA_DiSF100_CD38-CD127-PD-1intKLRG1+_batch1


title: 226_957434-31

value: SLIT


title: Islet ORSAM18611-1

tag: strain

value: 10% fat + fiber


title: Genomic DNA from T0405-1

description:
bone marrow from Pediatric Patients with AML
SAMPLE 1

source_name: bone marrow-T0405-Cycle1 Day 0

value: bone marrow


title: Islet ORSAM18608-1

tag: cell type


title: Liver ORSAM17821-2

source_name: liver

value: liver

value: Whole Liver - liver


title: 223_963071-31

source_name: PBMC

value: PBMC

value: Female


title: RA_DiSF100_CD38-CD127+PD-1-_batch1

tag: batch


title: Islet ORSAM18605-1

value: NZO/HlLtJ


title: RA_DiSF100_CD38-CD127+PD-1int_batch1


title: Islet ORSAM18603-1

value: islet

value: 44% fat + fiber


title: RA_CYRA_CD38-CD127-PD-1intKLRG1+_batch2

value: CYRA


title: Islet ORSAM18602-1

value: Islet - islets of Langerhans

value: Male


title: RA_CYRA_CD38-CD127+PD-1-_batch2

value: Synovial Fluid


title: 219_957467-31

tag: fastq total_reads

value: SCIT

value: PreChallenge


title: Islet ORSAM18599-1


title: Islet ORSAM18598-1


title: 212_970851-31

tag: percent aligned


title: RA_CYRA_CD38-CD127+PD-1int_batch2

value: RA


title: 225_957434-35

tag: aligned counts_in_millions

value: SLIT

value: PostChallenge


title: Islet ORSAM18596-1


title: 217_963036-35

tag: median cv_coverage


title: 207_966650-31

tag: treatment


title: RA_DiSF100_CD38hiCD127-PD-1int_batch1


title: H9_S72

city: Freiburg i. Br.

first: Csaba

last: Jeney

state: Baden-Württemberg

address: Georges-Köhler-Allee 103

department: Department for Microsystems Engineering

country: Germany

institute: University of Freiburg

data_processing:
Sequencing reads were aligned to the GRCh38 cDNA reference transcriptome from Ensembl using salmon v1.3.0, kallisto v0.46.1 as well as to GRCh38.p13 genome with STAR 2.7.5c in solo mode.
Transcript abundances (TPM) and count estimates were imported with the tximeta package for salmon and tximport for kallisto and summarized to genes using the summarizeToGene() statement. STAR alignment files were counted with featureCounts v2.0.3.
Cells with an alignment efficiency below 80 % were filtered out (salmon and kallisto). Cells with less than 60 % of uniquely mapped reads were filtered out (STAR). In both cases only cells with at least 1E+5 detected reads were considered.
Pseudo-bulk differential expression analysis (MCF7 vs BT-474) was performed with DESeq2 v1.32.0.
In order to evaluate transcriptomal similarity between cells analyzed on the miniaturized Smart-seq2 platform to published data (GSE151334), the datasets were combined, batch-corrected with BBKNN and projected into a two-dimensional space with SCANPY’s (v1.8.1) built-in UMAP function.
Assembly: GRCh38 cDNA reference transcriptome from Ensembl or GRCh38.p13 genome
Supplementary files format and content: DE analysis files contain DESeq2 output including ENSEMBL identifier, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj as column names
Supplementary files format and content: Raw count files contain the raw counts of each gene detected in the cell described

molecule: polyA RNA

source_name: Epithelial cell

growth_protocol: The cell lines were cultured in a cell culture incubator under a 5 % CO2 atmosphere at 37 °C. MCF7 cells were cultured in DMEM, BT-474 cells were cultured in DMEM/F12. Cells were harvested using trypsin.

extract_protocol: cDNA synthesis was perfromed using SMART-Seq Single Cell Kit (634472, Takara BIO). Library preparation was performed using Nextera XT DNA Library Preparation Kit (FC-131-1024, Illumina). Both at 1/10 of original reaction volumes. See associated manuscript for detailed information.

value: Mammary gland

tag: cell line

value: breast cancer

value: untreated


title: H9_S168


title: Islet ORSAM18590-1


title: 206_963060-35

city: Seattle

institute: Benaroya Research Institute at Virginia Mason

value: PBMC

tag: participant id


title: H8_S64


title: 220_970871-31

value: Female


title: Islet ORSAM18583-1


title: 218_957467-35


title: 202_963035-31

value: Placebo


title: Islet ORSAM18353-1

value: islet

value: CAST/EiJ


title: H8_S160


title: 201_957432-31


title: Islet ORSAM18352-1

value: 44% fat + fiber


title: H7_S56


title: 200_966646-35


title: Islet ORSAM18351-1

value: Islet - islets of Langerhans


title: H7_S152


title: 199_963035-35

value: Male


title: Islet ORSAM18350-1


title: H6_S48


title: Islet ORSAM18348-1

value: NZO/HlLtJ


title: 198_957432-35


title: H6_S144


title: H5_S40


title: 197_970794-35


title: 195_966683-35


title: H5_S136


title: Islet ORSAM18343-1


title: H4_S32


title: 194_963092-31


title: Islet ORSAM18342-1


title: 196_970794-31


title: Islet ORSAM18344-1


title: H4_S128


title: Islet ORSAM18338-1


title: Islet ORSAM18337-1


title: H3_S24


title: 192_963092-35


title: H3_S120


title: 191_966683-31


title: H2_S16


title: 189_966675-35


title: Islet ORSAM17798-1

value: 10% fat + fiber


title: Islet ORSAM17796-1


title: H2_S112


title: 604C [Genomic DNA from umbilical cord tissue]

city: Salt

first: Abel

last: López-Bermejo

state: Girona

address: Dr. Castany s/n

department: Pediatrics

country: Spain

institute: IDIBGI

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Human DNA Methylation EPIC 850K BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: minify R-package (version 1.26.2)

source_name: Umbilical cord tissue

extract_protocol: Genomic DNA was extracted and purified from umbilical cord and placenta samples using Qiagen Puregene Kit according to standard instructions and then bisulfited with EZ DNA methylation Gold kit, according to manufacturers instructions.

value: Umbilical cord tissue

tag: pregestational obesity

value: normoweight

tag: gestational obesity

value: overweightgain

tag: offspring's sex

value: male

tag: offspring bmi 6 years of age


title: 188_966675-31

first: Naresh

last: Doni Jayavelu

address: 1201 9th AVE

tag: tissue

tag: visit number

value: SLIT

tag: sts timepoint

value: PreChallenge


title: 193_957464-31

tag: age

tag: Sex


title: Islet ORSAM17795-1

tag: strain

tag: cell type


title: H12_S96

value: Mammary gland

value: breast cancer

value: untreated


title: 317C [Genomic DNA from umbilical cord tissue]

value: obese


title: 605C [Genomic DNA from umbilical cord tissue]

value: female


title: 834C [Genomic DNA from umbilical cord tissue]


title: 187_963068-35

value: PBMC

tag: fastq total_reads

tag: percent aligned

value: PostChallenge


title: H12_S192


title: Islet ORSAM17794-1

value: islet

value: Islet - islets of Langerhans


title: Islet ORSAM17800-1

value: CAST/EiJ

value: Male


title: 186_957444-35

tag: aligned counts_in_millions

tag: median cv_coverage


title: 787C [Genomic DNA from umbilical cord tissue]

value: Umbilical cord tissue


title: Islet ORSAM17793-1

value: NZO/HlLtJ

tag: treatment

value: 10% fat + fiber


title: H11_S88

tag: cell line


title: 294C [Genomic DNA from umbilical cord tissue]

tag: pregestational obesity

value: normoweight

value: overweightgain

value: male


title: 185_963068-31

tag: participant id

value: SLIT

value: PreChallenge


title: Islet ORSAM17791-1

value: Female


title: 305C [Genomic DNA from umbilical cord tissue]

tag: gestational obesity

value: normoweightgain

tag: offspring's sex


title: 184_957444-31

tag: tissue


title: 353C [Genomic DNA from umbilical cord tissue]

tag: offspring bmi 6 years of age


title: H10_S80

value: Mammary gland

value: breast cancer

value: untreated


title: Islet ORSAM17788-1

value: islet


title: 183_966728-31

value: PBMC

tag: visit number

tag: sts timepoint


title: Islet ORSAM17787-1

value: Islet - islets of Langerhans

tag: Sex


title: H10_S176


title: 525C [Genomic DNA from umbilical cord tissue]

value: female


title: Islet ORSAM17786-1

tag: strain

value: Male


title: H11_S184

tag: cell type


title: H1_S8


title: 320C [Genomic DNA from umbilical cord tissue]

value: Umbilical cord tissue

value: obese


title: 182_970856-31

tag: age

tag: fastq total_reads


title: 181_963119-35

tag: percent aligned

tag: aligned counts_in_millions

value: PostChallenge


title: Islet ORSAM17785-1

tag: treatment

value: 10% fat + fiber


title: 396C [Genomic DNA from umbilical cord tissue]

value: normoweight

value: male


title: H1_S104

tag: cell line


title: 199C [Genomic DNA from umbilical cord tissue]

tag: pregestational obesity

value: overweightgain


title: 371C [Genomic DNA from umbilical cord tissue]


title: 317P [Genomic DNA from placenta tissue]

source_name: Placenta tissue

value: Placenta tissue


title: Islet ORSAM17784-1

value: Female


title: G9_S71

value: Mammary gland


title: 179_966728-35

tag: median cv_coverage

tag: participant id

value: SLIT


title: Islet ORSAM17783-1


title: G9_S167

value: breast cancer

value: untreated


title: 599C [Genomic DNA from umbilical cord tissue]

value: overweight

tag: gestational obesity

tag: offspring's sex


title: G8_S63

tag: tissue


title: 178_963119-31

value: PBMC

tag: visit number

value: PreChallenge


title: 795C [Genomic DNA from umbilical cord tissue]

value: normoweightgain

value: female

tag: offspring bmi 6 years of age


title: G8_S159


title: Adipose ORSAM18582-1

source_name: adipose

value: adipose

value: CAST/EiJ

value: Adipose - gonadal fat pad

tag: Sex

value: Male


title: Adipose ORSAM18577-1

tag: strain

value: 44% fat + fiber


title: 177_970856-35

tag: sts timepoint

value: PostChallenge


title: G7_S55

tag: cell type


title: 180_958678-31

tag: age

tag: fastq total_reads


title: Adipose ORSAM18575-1

value: 10% fat + fiber


title: 834P [Genomic DNA from placenta tissue]

value: Placenta tissue

value: obese

value: overweightgain


title: 294P [Genomic DNA from placenta tissue]

value: normoweight

value: male


title: Adipose ORSAM18572-1

value: Female


title: G7_S151

value: Mammary gland

value: breast cancer

value: untreated


title: 175_966734-31

value: PBMC

tag: percent aligned

tag: aligned counts_in_millions

value: SLIT

value: PreChallenge


title: 885C [Genomic DNA from umbilical cord tissue]

value: Umbilical cord tissue

value: female


title: G6_S47

tag: cell line

tag: treatment


title: Adipose ORSAM18569-1

value: adipose

value: NZO/HlLtJ

value: Adipose - gonadal fat pad

value: Male


title: 417C [Genomic DNA from umbilical cord tissue]

tag: pregestational obesity

value: normoweightgain


title: 173_970839-35

tag: median cv_coverage

tag: participant id

value: PostChallenge


title: Adipose ORSAM18567-1

value: 44% fat + fiber


title: G6_S143


title: 204C [Genomic DNA from umbilical cord tissue]

value: overweight

tag: gestational obesity

value: overweightgain

tag: offspring's sex

value: male


title: 305P [Genomic DNA from placenta tissue]

tag: tissue

value: Placenta tissue

value: normoweight


title: 171_963112-31

value: PBMC

tag: visit number


title: G5_S135

value: Mammary gland

value: breast cancer

value: untreated


title: Adipose ORSAM18563-1

tag: Sex

value: Female

value: 10% fat + fiber


title: Adipose ORSAM18566-1

value: adipose

tag: strain

value: NZO/HlLtJ


title: 170_963112-35

value: Male

value: SLIT

tag: sts timepoint


title: 174_966734-35

value: PostChallenge


title: G5_S39

tag: cell type


title: 176_958678-35

tag: age


title: 604P [Genomic DNA from placenta tissue]

tag: offspring bmi 6 years of age


title: 765C [Genomic DNA from umbilical cord tissue]

value: Umbilical cord tissue

value: female


title: G4_S31


title: G4_S127


title: 342C [Genomic DNA from umbilical cord tissue]

value: overweightgain


title: 605P [Genomic DNA from placenta tissue]

value: obese


title: 168_958685-31

tag: fastq total_reads

tag: percent aligned

value: PreChallenge


title: 199P [Genomic DNA from placenta tissue]

value: Placenta tissue

value: normoweight


title: G3_S23

value: Mammary gland

tag: cell line


title: Adipose ORSAM18547-1

value: Adipose - gonadal fat pad

tag: treatment

value: 44% fat + fiber


title: Adipose ORSAM18562-1

value: Female


title: 838C [Genomic DNA from umbilical cord tissue]

tag: pregestational obesity

value: normoweightgain

value: male


title: 396P [Genomic DNA from placenta tissue]


title: Adipose ORSAM18335-1

value: adipose

value: CAST/EiJ


title: G3_S119

value: breast cancer

value: untreated


title: 165_970779-35

value: PBMC

value: Male

tag: aligned counts_in_millions

tag: median cv_coverage

value: Placebo

value: PostChallenge


title: 885P [Genomic DNA from placenta tissue]

value: obese

tag: gestational obesity

value: overweightgain

value: female


title: G2_S111

value: Mammary gland


title: 204P [Genomic DNA from placenta tissue]

value: Placenta tissue

value: overweight

tag: offspring's sex


title: Adipose ORSAM18334-1

tag: tissue

value: Adipose - gonadal fat pad

value: 44% fat + fiber


title: G12_S95


title: Adipose ORSAM18333-1

value: Female


title: 359C [Genomic DNA from umbilical cord tissue]

value: Umbilical cord tissue

value: normoweight

value: normoweightgain

value: male


title: 164_970779-31

value: PBMC

tag: participant id

tag: visit number

value: PreChallenge


title: 166_966681-35

tag: Sex

value: Male

value: Placebo


title: G12_S191

value: breast cancer

value: untreated


title: Adipose ORSAM18560-1

value: adipose

tag: strain

value: NZO/HlLtJ


title: 172_970839-31

value: SLIT

tag: sts timepoint


title: 162_963072-31

tag: age


title: Adipose ORSAM18330-1

tag: cell type


title: 359P [Genomic DNA from placenta tissue]

value: Placenta tissue

tag: offspring bmi 6 years of age


title: Adipose ORSAM18332-1

value: CAST/EiJ

value: Adipose - gonadal fat pad


title: 838P [Genomic DNA from placenta tissue]


title: 723P [Genomic DNA from placenta tissue]


title: 11491 203081450147

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

description:
11491
hiPSCs_beta_value_matrix_normalized_batch_corrected.tsv

hyb_protocol: standard Illumina protocl

scan_protocol: standard Illumina protocl

data_processing: Raw IDAT files were processed using R package ChAMP. Probes with missing values are removed, samples with more than 10% of probes with a detection p-value of greater than 0.01, probes with a detection p-value of greater than 0.01 in at least one sample and probes for which 5% of samples have a bead count less than 3 are filtered out.  Probes targeting CpG sites that are near SNPs, belong to X/Y chromosomes, or align with multiple locations are filtered out

label: Cy3 and Cy5

source_name: hiPSCs

label_protocol: standard Illumina protocl

extract_protocol: Genomic DNA was extracted using the NucleoSpin Tissue kit (Macherey-Nagel) from two different cell pellets for each sample. A minimum of 500ng was sent to Diagenode services for DNA methylation analysis

tag: disease

tag: sentrix id

tag: sentrix position


title: 161_966681-31

tag: fastq total_reads

tag: percent aligned

tag: treatment


title: 14586 203081450147

description:
14586
hiPSCs_beta_value_matrix_normalized_batch_corrected.tsv


title: 723C [Genomic DNA from umbilical cord tissue]

tag: pregestational obesity

tag: gestational obesity


title: Adipose ORSAM18326-1

tag: tissue

value: Female

value: 44% fat + fiber


title: G11_S183

value: Mammary gland

tag: cell line


title: BAMS2 203081450147

description:
BAMS2
hiPSCs_beta_value_matrix_normalized_batch_corrected.tsv

value: BAMS (bosma arhinia microphthalmia syndrome)


title: Adipose ORSAM18325-1


title: G2_S15


title: 787P [Genomic DNA from placenta tissue]

value: obese

value: overweightgain

tag: offspring's sex

value: male


title: G10_S79


title: 159_957472-35

value: PBMC

tag: Sex

value: Male

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

tag: visit number

value: PostChallenge


title: G10_S175

tag: cell type

value: breast cancer

value: untreated


title: 320P [Genomic DNA from placenta tissue]

value: female

tag: offspring bmi 6 years of age


title: 169_958685-35

tag: age

value: SLIT

tag: sts timepoint


title: 252C [Genomic DNA from umbilical cord tissue]

value: Umbilical cord tissue

value: normoweight


title: Adipose ORSAM18324-1

value: adipose

tag: strain

value: Adipose - gonadal fat pad


title: BAMS9 203081450147

description:
BAMS9
hiPSCs_beta_value_matrix_normalized_batch_corrected.tsv

tag: disease

tag: sentrix id

tag: sentrix position


title: 353P [Genomic DNA from placenta tissue]

value: Placenta tissue

tag: pregestational obesity

tag: gestational obesity


title: BAMS1 203081450147

description:
BAMS1
hiPSCs_beta_value_matrix_normalized_batch_corrected.tsv


title: 765P [Genomic DNA from placenta tissue]

tag: tissue


title: 252P [Genomic DNA from placenta tissue]

tag: offspring's sex


title: Adipose ORSAM18322-1

tag: Sex

tag: treatment

value: 44% fat + fiber


title: Adipose ORSAM18554-1


title: 158_957472-31

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

value: PreChallenge


title: G1_S103

value: Mammary gland

tag: cell line

tag: cell type


title: 155_970814-35

tag: age

tag: participant id

tag: visit number

tag: sts timepoint


title: Adipose ORSAM18320-1

tag: strain

value: Female


title: Adipose ORSAM18319-1


title: 525P [Genomic DNA from placenta tissue]

tag: pregestational obesity

value: overweightgain

tag: offspring bmi 6 years of age


title: AG09 203081450147

description:
AG09
hiPSCs_beta_value_matrix_normalized_batch_corrected.tsv

tag: disease

value: CT

tag: sentrix id

tag: sentrix position


title: AG08C5 203081450147

description:
AG08C5
hiPSCs_beta_value_matrix_normalized_batch_corrected.tsv


title: F9_S70

tag: tissue

tag: treatment


title: 154_970814-31

value: PBMC

tag: Sex

value: Male

tag: fastq total_reads

tag: percent aligned


title: 795P [Genomic DNA from placenta tissue]

tag: gestational obesity

value: normoweightgain

tag: offspring's sex


title: F9_S166

tag: cell line

tag: cell type

value: breast cancer

value: untreated


title: BAMS1 204361730135

description:
BAMS1
Fibroblasts_beta_value_matrix_normalized_batch_corrected.tsv

source_name: Fibroblast

value: BAMS (bosma arhinia microphthalmia syndrome)


title: 153_963046-35

tag: age

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

tag: visit number

value: SLIT

value: PostChallenge


title: F8_S62


title: 152_963046-31

tag: sts timepoint


title: Adipose ORSAM17778-1

value: adipose

tag: strain

value: CAST/EiJ

value: 10% fat + fiber


title: 599P [Genomic DNA from placenta tissue]

value: Placenta tissue

tag: pregestational obesity

value: overweight

value: male

tag: offspring bmi 6 years of age


title: BAMS1 204361730131

tag: disease

tag: sentrix id

tag: sentrix position


title: G1_S7

tag: tissue

value: Mammary gland

tag: treatment


title: Adipose ORSAM17776-1

value: NZO/HlLtJ

value: Adipose - gonadal fat pad

tag: Sex


title: F8_S158

tag: cell line


title: 150_957455-35

value: PBMC

tag: fastq total_reads

tag: percent aligned


title: BAMS9 204361730135

description:
BAMS9
Fibroblasts_beta_value_matrix_normalized_batch_corrected.tsv


title: 417P [Genomic DNA from placenta tissue]

value: normoweight

tag: gestational obesity

tag: offspring's sex

value: female


title: Adipose ORSAM17775-1

tag: cell type

value: Male


title: F6_S46

value: breast cancer

value: untreated


title: 371P [Genomic DNA from placenta tissue]

value: normoweightgain


title: 11440 204361730135

description:
11440
Fibroblasts_beta_value_matrix_normalized_batch_corrected.tsv


title: 151_970784-31

tag: age

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

tag: visit number

value: SLIT

value: PreChallenge


title: 167_957452-31

value: Placebo

tag: sts timepoint


title: Adipose ORSAM17770-1

value: adipose

tag: strain

value: 10% fat + fiber


title: F7_S150


title: 149_966697-31


title: G11_S87


title: BAMS1 203081450114

tag: disease

value: BAMS (bosma arhinia microphthalmia syndrome)

tag: sentrix id

tag: sentrix position


title: 14586 204361730135

description:
14586
Fibroblasts_beta_value_matrix_normalized_batch_corrected.tsv


title: F6_S142

tag: tissue

tag: treatment


title: 342P [Genomic DNA from placenta tissue]

value: Placenta tissue

tag: pregestational obesity

value: overweightgain

value: male

tag: offspring bmi 6 years of age


title: Adipose ORSAM17773-1

value: NZO/HlLtJ

value: Adipose - gonadal fat pad

tag: Sex

value: Female


title: F5_S38

value: Mammary gland

tag: cell line


title: 11491 204361730135

description:
11491
Fibroblasts_beta_value_matrix_normalized_batch_corrected.tsv

value: PADO


title: 147_957455-31

value: PBMC

value: Male

tag: fastq total_reads

tag: percent aligned


title: 146_966697-35

tag: age

tag: aligned counts_in_millions

value: PostChallenge


title: Adipose ORSAM17769-1

tag: cell type


title: 145_963030-31

tag: median cv_coverage

tag: participant id

tag: visit number

value: SLIT


title: Adipose ORSAM17768-1

tag: strain


title: F4_S30

value: breast cancer

value: untreated


title: F5_S134


title: F4_S126


title: BAMS2 204361730131

description:
BAMS2
Fibroblasts_beta_value_matrix_normalized_batch_corrected.tsv

tag: disease

tag: sentrix id


title: 142_966674-35

tag: tissue

value: SCIT

tag: sts timepoint


title: 144_963030-35

tag: treatment


title: AG08C5 204361730135

description:
AG08C5
Fibroblasts_beta_value_matrix_normalized_batch_corrected.tsv

tag: sentrix position


title: Adipose ORSAM17766-1

value: adipose

tag: Sex

value: 10% fat + fiber


title: Adipose ORSAM17765-1


title: AG04 204361730135

description:
AG04
Fibroblasts_beta_value_matrix_normalized_batch_corrected.tsv

value: CT


title: Adipose ORSAM17767-1


title: BAMS9 204361730131

value: BAMS (bosma arhinia microphthalmia syndrome)


title: F3_S22

tag: cell line


title: MIDHiChIP_H3K27ac_WT_mESC_R4

city: La Jolla

first: Hanbin

address: 9500 Gilman Drive, NSB 5108

institute: UCSD

description:
MIDHiChIP_H3K27ac_WT_mESC_combined.hic
MIDHiChIP_H3K27ac_WT_mESC_combined.hic.mcool

data_processing:
Sequencing data of MID HiChIP was trimmed, mapped, filtered, and created HIC/COOL files in the same way as MID Hi-C data process. To assess the ChIP enrichments, we pooled all fragments below 1 MB separations to call peaks and generate tornado plots as described in ATAC-seq data analysis.
Genome_build: mm10
Supplementary files format and content: hic and mcool format
Library strategy: MID HiChIP

source_name: mESC

growth_protocol: E14TG2a mESCs were maintained in KnockOut DMEM (Thermo Fisher,10829018) medium, supplied with 15% FBS (R&D Systems, S10250H), 1mM MEM Non-Essential Amino Acids (Thermo Fisher, 11140-050), 2mM Glutamax (Thermo Fisher, 35050061), 100 U/mL Pen/Strep (Thermo Fisher, 15140122), 0.1 mM 2(β)-ME (Sigma, M-3148), and 1000 U/mL LIF (Cell Guidance Systems, GFM200) on 0.1% gelatin coated dishes at 37C with 5% CO2. Cells were passaged every two days. Medium was changed on a daily basis.

extract_protocol:
Proximal-ligated nuclei from MID Hi-C experiment were processed for ChIP following Myers Lab ChIP-seq Protocol (v011014). In brief, proximal-ligated nuclei were resuspended in RIPA buffer followed by sonication using Bioruptor. Soluble chromatin fragments are immunoprecipitated by SMC3 (abcam ab9263) or H3K27ac (ActiveMotif 39133) antibody overnight. We used 3 to 5 mg of antibody for the starting material of 5 million cells. Next day, wash the immunoprecipitated chromatin extensively. Purify the DNA for library preparation after reverse crosslinking.
Resuspend the proximal-ligated nuclei from MID HiChIP experiment in 300 uL ChIP elution buffer (1% SDS, 100 mM NaHCO3) and incubate at 65C overnight. Next day, add RnaseA and incubate at 37C for 45 min. Then, add Proteinase K and incubate at 55C for 2 hours. Purify DNA using ChIP DNA Clean & Concentrator kit from Zymo (D5205). Purified DNA can be stored in -80C till ready for library preparation. Before generating sequencing library, prepare Dynabeads MyOne Streptavidin T1 (Invitrogen, 65601) beads by washing 5 uL T1 beads twice in 600 ul Tween wash buffer (1X binding buffer, 0.05% Tween-20) at 55 C for 2 min. Reclaim the beads on magnetic stand and resuspend in 50 ul 2X binding buffer (2 M NaCl, 10 mM pH 7.5 Tris-HCl, 1 mM EDTA). The beads are ready for immobilizing biotin-labeled DNA. We used NEB fragmentase (NEB, M0348S) to fragment DNA. But sonication can be used to fulfill the same purpose. 50 ng to 500 ng DNA were treated with NEB fragmentase in 20 uL reaction volume, per manufacture instructed. Incubate the reaction at 37C for 9 to 13 min, optimized to generate 100 – 500bp fragment size. To stop the reaction, add 250 ul 2X binding buffer to the DNA fragmentation reaction and incubate at 55C for 15 min. Then, add 280 uL Zymo DNA elution buffer (Zymo Research, D3004-4-50) and 50 ul prepared T1 beads to the stopped reaction (total 600 ul). Rotate the beads and DNA mix at room temperature for 15 min. After that, reclaim the beads and wash twice in the Tween wash buffer as described above. The DNA-bound T1 beads were used for NEBNext Ultra II DNA Library Preparation (NEB, E7645S) per manufacture instruction with gentle taps during reactions to keep beads in suspension. We typically amplify 10-15 PCR cycles for library amplification. The library was then double-size selected using home-made SPRI beads to isolate fragments between 200 and 800 bp for next generation sequencing.

value: mESC

value: Mouse Embryonic Stem Cell

tag: genotype

value: WT

tag: time

tag: antibody

value: anti-H3K27ac, ActiveMotif 39133


title: 11440 204361730131


title: 148_970784-35

tag: age

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions


title: 140_970801-31

value: Female

tag: median cv_coverage

tag: participant id

tag: visit number

value: PreChallenge


title: 139_963055-35

value: PBMC


title: MIDHiChIP_H3K27ac_WT_mESC_R3

tag: cell type


title: 11491 204361730131

tag: disease

tag: sentrix id


title: MIDHiChIP_H3K27ac_WT_mESC_R2

data_processing:
Sequencing data of MID HiChIP was trimmed, mapped, filtered, and created HIC/COOL files in the same way as MID Hi-C data process. For the published HiChIP data, we processed in the same way as in situ Hi-C data process. To assess the ChIP enrichments, we pooled all fragments below 1 MB separations to call peaks and generate tornado plots as described in ATAC-seq data analysis.
Genome_build: mm10
Supplementary files format and content: hic and mcool format
Library strategy: MID HiChIP

tag: treatment


title: MIDHiChIP_H3K27ac_WT_mESC_R1


title: F12_S94

tag: tissue

value: Mammary gland


title: F2_S110


title: AG04 204361730131

tag: sentrix position


title: 137_963055-31

tag: Sex

tag: sts timepoint


title: F3_S118

tag: cell line


title: F12_S190


title: MIDHiChIP_cohesin_WT_mESC

description:
MIDHiChIP_cohesin_WT_mESC_combined.hic
MIDHiChIP_cohesin_WT_mESC_combined.hic.mcool

tag: genotype

tag: time

tag: antibody

value: anti- Smc3, abcam ab9263


title: 160_963072-35

tag: age

value: Male

tag: fastq total_reads

tag: percent aligned

value: Placebo

value: PostChallenge


title: AG08C5 204361730131


title: 135_966673-35

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

value: SCIT


title: MIDHiC_WT_mESC_R13

description:
MIDHiC_WT_mESC_combined.hic
MIDHiC_WT_mESC_combined.hic.mcool

data_processing:
Adaptors in pair-end (PE) sequencing reads were trimmed using Trimmomatic (Bolger et al., 2014). Trimmed PE reads were aligned to mm10 genome using HiC-Pro analysis pipeline (Servant et al., 2015). HiC-Pro performs ‘global’ and ‘local’ mapping. In the global mapping stage, full-length reads were first end-to-end aligned. Any unmapped reads will be split at the ligation sites (MID Hi-C ligation sites:  TTATAA, TTATNAG, CTNATNAG, CTNATAA) and the 5’ segment will be re-aligned in the local mapping stage. We denote this as one pass of iterative alignment. Instead of dumping the 3’ segment, we performed more passes of iterative alignment till no more segments of reads can be split or aligned. To obain the Hi-C valid interaction from a multi-fragment (>2) interaction read, we kept two farthest separated fragments as the representative validpair. The output validpairs were transformed to HIC (Rao et al., 2014) and COOL (Abdennur and Mirny, 2019) formats for downstream analysis. The contact maps were visualized by JUICEBOX (Durand et al., 2016b). To call HiCCUPS loops, we used the HiCCUPS subcommand in JUICER toolkit. For all other downstream analysis, we used COOLER and COOLTOOLS packages (Nora et al., 2020) to access Hi-C data stored in mcool file and analyze in python environment.
Genome_build: mm10
Supplementary files format and content: hic and mcool format
Library strategy: MID Hi-C

extract_protocol:
mESC cells were double crosslinked using formaldehyde (Fisher Scientific, 50-980-494) and DSG (ProteoChem, c1104-100mg) and aliquoted as described previously (Hsieh et al., 2020). One aliquot of fixed cells (~5 million) was washed in 1.4 mL low SDS buffer (50 mM pH 7.5 Tris-HCL, 10 mM NaCl, 0.1% SDS) with 1X Protease Inhibitor Cocktails (PICs; Roche, 11873580001). Incubate on ice for 15 min. Spin down the nuclei at 2500 rcf for 5 min at 4C. Remove supernatant and wash one more time in the low SDS buffer on ice. Then, resuspend nuclei in 1 mL digestion buffer (1X Cutsmart buffer, 1% Triton X-100, 1X PICs). Incubate at 37C for 20 min with gentle rotation. Add 250U MseI (NEB, R0525M) and 250U DdeI (NEB, R0175L) to digest nuclei at 37C for 6 hours or overnight with gentle rotation. After digestion, spin down the nuclei and resuspend in 1 mL fill-in reaction mix (1X CutSmart buffer, 1% Triton X-100, 66 uM dTTP, 66 uM dCTP, 66 uM dGTP, 66 uM dATP-Biotin (Jena Bioscience, JBS-NU-835-BIO14-L), 50 U Klenow DNA large polymerase I (NEB, M0210M), 1X PICs). Rotate at room temp for 90 min. Spin down nuclei and resuspend in 1 mL ligation mix (1X T4 DNA ligase buffer, 1% Triton X-100, 0.1 mg/mL BSA, 15 U T4 ligase (Life Technologies, 15224041), 1X PICs). Incubate at 14C overnight with gentle rotation. Next day, spin down the nuclei. The proximal ligated nuclei can be used for library preparation or proceeded to MID HiChIP.
Resuspend the proximal-ligated nuclei from MID Hi-C experiment in 300 uL ChIP elution buffer (1% SDS, 100 mM NaHCO3) and incubate at 65C overnight. Next day, add RnaseA and incubate at 37C for 45 min. Then, add Proteinase K and incubate at 55C for 2 hours. Purify DNA using Phenol:Chloroform:Isoamyl (PCI) method. Purified DNA can be stored in -80C till ready for library preparation. Before generating sequencing library, prepare Dynabeads MyOne Streptavidin T1 (Invitrogen, 65601) beads by washing 5 uL T1 beads twice in 600 ul Tween wash buffer (1X binding buffer, 0.05% Tween-20) at 55 C for 2 min. Reclaim the beads on magnetic stand and resuspend in 50 ul 2X binding buffer (2 M NaCl, 10 mM pH 7.5 Tris-HCl, 1 mM EDTA). The beads are ready for immobilizing biotin-labeled DNA. We used NEB fragmentase (NEB, M0348S) to fragment DNA. But sonication can be used to fulfill the same purpose. 50 ng to 500 ng DNA were treated with NEB fragmentase in 20 uL reaction volume, per manufacture instructed. Incubate the reaction at 37C for 9 to 13 min, optimized to generate 100 – 500bp fragment size. To stop the reaction, add 250 ul 2X binding buffer to the DNA fragmentation reaction and incubate at 55C for 15 min. Then, add 280 uL Zymo DNA elution buffer (Zymo Research, D3004-4-50) and 50 ul prepared T1 beads to the stopped reaction (total 600 ul). Rotate the beads and DNA mix at room temperature for 15 min. After that, reclaim the beads and wash twice in the Tween wash buffer as described above. The DNA-bound T1 beads were used for NEBNext Ultra II DNA Library Preparation (NEB, E7645S) per manufacture instruction with gentle taps during reactions to keep beads in suspension. We typically amplify 8-10 PCR cycles for library amplification. The library was then double-size selected using home-made SPRI beads to isolate fragments between 200 and 800 bp for next generation sequencing.

tag: cell type


title: F2_S14

value: breast cancer

value: untreated


title: 14586 204361730131

tag: disease

tag: sentrix id


title: Adipose ORSAM17780-1

tag: tissue

value: adipose

tag: strain

value: CAST/EiJ

value: Adipose - gonadal fat pad

tag: treatment

value: 10% fat + fiber


title: 11491 203081450114

tag: sentrix position


title: 138_966674-31

tag: Sex

tag: visit number

tag: sts timepoint


title: 134_966673-31


title: MIDHiC_WT_mESC_R12

tag: cell line

value: mESC

value: Mouse Embryonic Stem Cell

tag: genotype

value: WT

tag: time

tag: antibody


title: F11_S86


title: F10_S78


title: 133_970783-35

tag: age

value: Female

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions


title: BAMS9 203081450114

tag: disease

value: BAMS (bosma arhinia microphthalmia syndrome)


title: BAMS2 203081450114

tag: sentrix id


title: Adipose ORSAM17782-1

tag: tissue

tag: cell type


title: 132_970783-31

value: PBMC

tag: median cv_coverage

tag: participant id

tag: treatment

value: PreChallenge


title: F10_S174

value: Mammary gland


title: MIDHiC_WT_mESC_R10


title: 131_957437-31

tag: Sex

tag: visit number


title: MIDHiC_WT_mESC_R9

tag: cell line


title: 130_957437-35

tag: sts timepoint


title: F1_S102


title: F1_S6


title: Gene editing, RAG1 exon 2 sample3_P

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

institute: Consiglio Nazionale delle Ricerche

description:
guide1_sample3_Peaks.bed
guide2_sample3_Peaks.bed

data_processing:
Elaborate using the GUIDE-seq pipeline
Assembly: GENCODE version hg38 primary assembly v35
Supplementary files format and content: tab-delimited text files include read counts values for each Sample
Library strategy: Guide-Seq

source_name: Gene editing, RAG1 exon 2 sample3_P sample3_P

growth_protocol: Cells were cultured in RPMI 1640 medium (Corning) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Euroclone), 2mM L-glutamine (Euroclone) and 100U/I penicilin/streptomycin (Lonza)

extract_protocol:
Agencourt DNAdvance purification kit (Beckman Coulter cat. no. A48705)
Random sheraing of gDNA (500bp), end repairing/A-tailing, adapter ligation and nested PCRs

treatment_protocol: Edited cells were electroporated using SF Cell 4D-Nucleofector X Kit and Nucleofector 4D device and then cultured as descrived above

value: myelogenous leukemia cells

value: S.p. Cas9 + dsODN


title: 163_957452-35

value: Male

value: Placebo

value: PostChallenge


title: F11_S182

value: breast cancer

value: untreated


title: 127_970855-35

value: SCIT


title: MIDHiC_WT_mESC_R8

tag: genotype

tag: time


title: E9_S69


title: 157_966654-35

tag: age

value: SLIT


title: Gene editing, RAG1 exon 2 sample2_P

description:
guide1_sample2_Peaks.bed
guide2_sample2_Peaks.bed

source_name: Gene editing, RAG1 exon 2 sample2_P sample2_P

value: S.p. Cas9 + dsODN + gRNA#13


title: 126_966721-35

tag: fastq total_reads


title: Gene editing, RAG1 exon 2 sample2_N

source_name: Gene editing, RAG1 exon 2 sample2_N sample2_N


title: AG08C5 203081450114

value: CT

tag: sentrix position


title: E8_S61


title: MIDHiC_WT_mESC_R7

value: mESC

value: Mouse Embryonic Stem Cell

value: WT

tag: antibody


title: MIDHiC_WT_mESC_R11


title: 124_970855-31

value: PBMC

tag: percent aligned

tag: aligned counts_in_millions


title: MIDHiC_WT_mESC_R6


title: Gene editing, RAG1 exon 2 sample1_P

description:
guide1_sample1_Peaks.bed
guide2_sample1_Peaks.bed

source_name: Gene editing, RAG1 exon 2 sample1_P sample1_P

tag: tissue

value: S.p. Cas9 + dsODN + gRNA#11


title: MIDHiC_WT_mESC_R5

tag: cell type


title: Gene editing, RAG1 exon 2 sample3_N

source_name: Gene editing, RAG1 exon 2 sample3_N sample3_N


title: 125_966721-31

tag: median cv_coverage

value: PreChallenge


title: E8_S157

value: Mammary gland


title: E9_S165


title: MIDHiC_WT_mESC_R4


title: Gene editing, RAG1 exon 2 sample1_N

source_name: Gene editing, RAG1 exon 2 sample1_N sample1_N

value: myelogenous leukemia cells


title: E7_S53


title: MIDHiC_WT_mESC_R3


title: 122_963122-31

value: Male

tag: participant id


title: Gene editing, RAG1 intron 1 sample3_P

tag: treatment

value: unedited


title: E7_S149


title: 121_958687-31

tag: Sex


title: MIDHiC_WT_mESC_R1


title: MIDHiC_WT_mESC_R2


title: MIDHiC_Brg1FV_mESC_24h_R2

description:
ATAC_Brg1FV_mESC_24h_combined.hic
ATAC_Brg1FV_mESC_24h_combined.hic.mcool

treatment_protocol: dTAG13 24hr


title: Gene editing, RAG1 intron 1 sample2_P

value: S.p. Cas9 + dsODN + gRNA#9


title: E6_S141

value: breast cancer


title: Gene editing, RAG1 intron 1 sample2_N


title: 119_966648-35

value: Female

tag: visit number

value: Placebo

value: PostChallenge


title: MIDHiC_Brg1FV_mESC_24h_R1

tag: cell line


title: 120_958687-35

value: SCIT

tag: sts timepoint


title: E5_S37

value: untreated


title: 117_970865-31


title: MIDHiC_Brg1FV_mESC_6h_R2

description:
ATAC_Brg1FV_mESC_6h_combined.hic
ATAC_Brg1FV_mESC_6h_combined.hic.mcool

treatment_protocol: dTAG13 6hr

value: mESC

tag: genotype


title: E5_S133