title: PTRG7_S7

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample253

value: saliva

value: Infected-Vax

value: Male

value: White or Caucasian


title: PTRG8_S15

status: Public on Sep 19 2023

type: SRA

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

country: USA

institute: SUNY Upstate Medical Univ

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample254

library_source: transcriptomic

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt 1.2.1
Trimmed sequence reads were quantified to hg38 Ensembl transcripts release 105 using Salmon, using minimum assigned fragments of 10, minimum score fraction of 0.65, match value 2, mismatch value -4, gap opening value 6 and gap extension value of 2
Quantified features were filtered to eliminate those with less than 1 count in 80% or more of the samples
Normalization performed on filtered features using TPM followed by quantile and log2 transformation
Assembly: Homo sapiens hg38
Supplementary files format and content: Tab-separated values matrix file containing raw Salmon feature counts
Supplementary files format and content: Tab-separated matrix file containing filtered and normalized feature abundances

molecule: total RNA

organism: Homo sapiens

source_name: saliva

extract_protocol:
RNA was purified from saliva swabs used for clinical PCR COVID-19 testing, using Zymo Quick-RNA Viral 96 Kit or the KingFisher MagMAX Viral/Pathogen Nucleic Acid Isolation Kit
RNA-seq libraries were synthesized using TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina) according to manufacturer protocol

tag: tissue

tag: group

tag: Sex

tag: race

tag: ethnicity

value: Not Hispanic

tag: age


title: PTRG6_S15

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample252

value: Infected-Unvax

value: Black or African American

value: Hispanic


title: PTRG5_S7

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample251

value: Female


title: hESCs_NIPBL_Rep2

city: XIAMEN

first: XIAOWEN

last: LYU

state: FUJIAN

address: No.4221, Xiang'an South Road, Xiang'an District

country: China

institute: XIAMEN UNIVERSITY

description:
processed file: H9_NIPBL.normbyinput.qnorm_100bp.bw
processed file: H9_NIPBL_CPmnt.p0.00001_peaks.narrowPeak

library_source: genomic

data_processing:
ChIP-seq and CUT&Tag data processing: All reads were mapped to unique genomic regions using Bowtie2 and the hg38 human genome. PCR duplicates were removed manually. Bedtools genome Coverage function was used to derive bedgraph files for further analysis. To compare changes in ChIP-Seq signals, libraries were normalized by random picking to obtain the same numbers of reads. Normalized reads were used to derive bedgraph files for comparison in IGV. MACS2 was used to call peaks using default parameters with IgG ChIP-Seq data as control. Differential peaks were found using the edgeR (Robinson et al., 2010) R package at p<0.05, changes over 20% up/down.
Analysis of ATAC-seq data: ATAC-Seq data was processed by our in-house pipeline. First, paired end reads were aligned to the hg38 human reference genome using Bowtie2 with default parameters except -X 2000 -m 1. PCR     duplicates     were     removed using     Picard     Tools (http://picard.sourceforge.net;https://broadinstitute.github.io/picard/).  To adjust for fragment sizes, reads mapped to + strands and -strands were offset by +4 bp and -5 bp respectively. For all ATAC-seq datasets, sub-nucleosome and mono-nucleosome reads were separated based on fragment sizes: THSSs (transposases hypersensitive sites, bound by TFs, <115bp) and mono-nucleosomes (180~247bp). To obtain the exact positioning of nucleosomes, DANPOS (Chen et al., 2013) was used to derive the nucleosomal signals genome wide by dpos function using 180~247 bp fragments as input and 115 bp fragments as background using -p 1 -a 1 -jd 20 -u 0 -m 1. Reads were normalized between samples before running DANPOS. THSSs bedgraphs were made using the bedtools genomeCoverage function.   MACS2 was used to call peaks for subnucleosomal reads, which were bound by transcription factors.   To analyze the footprints of TFs in ATAC-seq data, motifs on a set of peaks or loop anchors were used as anchors for running dnase_average_profile.py scripts of the Wellington program in ATAC-seq mode. To compare between Ctrl and HS samples, read-normalized ATAC-seq THSSs (<115 bp) fragments were used as input to obtain the footprint average profiles. The footprint p values of all motifs on a set of peaks or anchors were derived using the wellington_footprints.py scripts of the Wellington program in ATAC-seq mode on read-normalized ATAC-seq THSSs (<115 bp) fragments.
RNA-seq data processing: RNA-seq raw reads were aligned using HISAT2 v2.2.0 to the hg38 human genome with default parameters. Transcripts per million (TPM) counts for all annotated human genes and transcripts were calculated by StringTie v2.1.6. Differentially expressed genes were identified using the R package “edgeR” with a cut-off p value ≤0.05 and fold change over 20% up/down.
Assembly: hg38
Supplementary files format and content: .bw; bigwig files including processed signals of RNA-Seq, ATAC-Seq, CUT&Tag and ChIP-Seq data
Supplementary files format and content: .genenamesorted; txt files including TPM counts for all genes calculated from RNA-Seq data

molecule: genomic DNA

source_name: H9 hESCs

extract_protocol:
For ChIP-seq, H9 cells and their in vitro differentiated organoids were collected, fixed with 1% formaldehyde and homogenized to prepare for the ChIP-Seq libraries. After cell lysis, whole nuclear lysates were sonicated to shear the chromatin into fragments with an average size of around 200-500 bp in length. Chromatin was precleared with Protein A or G Dynabeads at 4°C for 2 hours and precipitated with antibody overnight at 4°C. Immunoprecipitated chromatin was tagmented with Tn5 transposes mixture on beads and then eluted, reverse crosslinked and purified by standard methods, followed by PCR amplification. For ATAC-seq, H9 cells and their in vitro differentiated organoids were collected for performing the OMNI-ATAC protocol. For OMNI-ATAC, organoids were homogenized with electric homogenizer for 10 seconds into small clusters of cells to perform standard OMNI-ATAC protocol. Briefly, cells were washed with PBS and nuclear membrane was disrupted by soaking in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) on ice, nuclei was washed once in cold lysis buffer without NP40 or digitonin, and then incubated in Tn5 transposes mixture (25 ul 2x TD buffer, 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) at 37°C for 20 min with occasional shaking. After the reaction is over, DNA was directly extracted by Minelute Kit (Qiagen). Purified tagmented DNA were used to make Illumina Nextera libraries. For RNA-Seq, total RNA was isolated from H9 cells and their in vitro differentiated organoids using Trizol reagent (Invitrogen) and ribosomal RNA was removed using the Ribo Minus Transcriptome isolation kit (Invitrogen, K1550). Strand-specific RNA library prepared by TruSeq Stranded mRNA Library Prep Kit was amplified with barcoded primers for Illumina sequencing. For CUT&Tag, H9 cells and their in vitro differentiated organoids were harvested, gently homogenized with pestle A for standard library preparation. Briefly, cells were washed twice in 1.5 mL Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 × Protease inhibitor cocktail, EDTA free), immobilized to concanavalin A coated magnetic beads (Bangs Laboratories), and then resuspended in 50 μL Dig-wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 × Protease inhibitor cocktail, 0.05% Digitonin) containing 2 mM EDTA. After sequential incubation in the primary antibody of CHD4 (abcam, #ab72418, diluted 1:50 in 50 μL of Dig-Wash buffer) , the appropriate secondary antibody (diluted 1:100 in 100 μL of Dig-Wash buffer) and a 1:200 dilution of pAG-Tn5 (gift from Henikoff Lab) in Dig-300 Buffer (0.05% digitonin, 20 mM HEPES, pH7.5, 300 mM NaCl, 0.5 mM Spermidine, 1 × Protease inhibitor cocktail) , bead-bound cells were resuspended in 50μL tagmentation buffer (10 mM MgCl2 in Dig-wash Buffer) to tagment genomic DNA. The tagmented DNA was cleaned up by 1.5 × Ampure XP beads (Beckman Counter), amplified with Illumina Nextera barcoded primers, purified by 1.1 × Ampure XP beads for Illumina sequencing.
Truseq libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding adenosine to the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligated at room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix. Nextera libraries were amplified with Nextera barcoded primers using the KAPA SYBR FAST qPCR Master Mix. Illumina libraries were sequenced paired-end at 50 bp length on Illumina Hiseq2500  v4 or NovaSeq  6000  instruments.

tag: developmental stage

value: undifferentiated hESCs

tag: cell line

value: H9 hESCs

tag: cell type

value: H9 human embryonic stem cells

tag: genotype

value: WT

tag: treatment

value: undifferentiated state


title: PTRG3_S15

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample250


title: hESCs_NIPBL_Rep1


title: DE_NIPBL_Rep2

description:
processed file: DE_NIPBL.normbyinput.qnorm_100bp.bw
processed file: DE_NIPBL_CPmnt.p0.00001_peaks.narrowPeak

value: DE stage

value: in vitro differentiated DE cells

value: Pancreatic differentiation


title: hESCs_CTCF_Rep2

description:
processed file: H9_CTCF.normbyinput.qnorm_100bp.bw
processed file: H9-CTCF-CPmnt-Rep2_ChIP.p0.00001_peaks.narrowPeak


title: PTRG2_S7

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample249

value: saliva


title: SC-β_NIPBL_Rep2

description:
processed file: BETA_NIPBL.normbyinput.qnorm_100bp.bw
processed file: BETA_NIPBL_CPmnt.p0.00001_peaks.narrowPeak

value: SC-beta stage

value: in vitro differentiated beta cells


title: PTRG11_S15

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample247

value: Control-Vax

value: White or Caucasian


title: PTRG10_S11

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample246

value: Male

value: Not Hispanic


title: PTRG1_S7

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample248

value: Infected-Unvax

value: Asian


title: PP_H3K9me3_Rep1

description:
processed file: PP_H3K9me3.normbyinput.qnorm_100bp.bw
processed file: PP_H3K9me3_ChIPmentation_peaks.broadPeak

value: PP stage

value: in vitro differentiated PP cells


title: SC-β_NIPBL_Rep1

value: H9 hESCs


title: PGT_H3K9me3_Rep1

description:
processed file: PGT_H3K9me3.normbyinput.qnorm_100bp.bw
processed file: PGT_H3K9me3_ChIPmentation_peaks.broadPeak

value: PGT stage

value: in vitro differentiated PGT cells

value: WT


title: PH_H3K9me3_Rep1

description:
processed file: PH_H3K9me3.normbyinput.qnorm_100bp.bw
processed file: PH_H3K9me3_ChIPmentation_peaks.broadPeak

value: PH stage

value: in vitro differentiated PH cells


title: PTRF9_S6

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample245

value: saliva

value: Infected-Vax


title: DE_H3K9me3_Rep1

description:
processed file: DE_H3K9me3.normbyinput.qnorm_100bp.bw
processed file: DE_H3K9me3_ChIPmentation_peaks.broadPeak

value: DE stage

value: in vitro differentiated DE cells

value: Pancreatic differentiation


title: PGT_NIPBL

description:
processed file: PGT_NIPBL.normbyinput.qnorm_100bp.bw
processed file: PGT_NIPBL_CPmnt.p0.00001_peaks.narrowPeak


title: SC-β_H3K9me3_Rep1

description:
processed file: BETA_H3K9me3.normbyinput.qnorm_100bp.bw
processed file: BETA_H3K9me3_ChIPmentation_peaks.broadPeak

value: SC-beta stage

value: in vitro differentiated beta cells


title: PH_H3K9me3_Rep2


title: PGT_H3K9me3_Rep2


title: PTRF7_S6

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample243

value: Male

value: White or Caucasian

value: Not Hispanic


title: hESCs_H3K9me3_Rep2

description:
processed file: H9_H3K9me3.normbyinput.qnorm_100bp.bw
processed file: H9_H3K9me3_ChIPmentation_peaks.broadPeak

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: PTRF6_S14

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample242

value: Infected-Unvax

value: Black or African American


title: DE_H3K9me3_Rep2

value: H9 hESCs

value: WT


title: DE_NIPBL_Rep1

description:
processed file: DE_NIPBL.normbyinput.qnorm_100bp.bw
processed file: DE_NIPBL_CPmnt.p0.00001_peaks.narrowPeak


title: SC-β_H3K9me3_Rep2


title: PH_H3K9me2_Rep2

description:
processed file: PH_H3K9me2.normbyinput.qnorm_100bp.bw
processed file: PH_H3K9me2_CPmnt.p0.00001_peaks.narrowPeak

value: PH stage

value: in vitro differentiated PH cells


title: PTRF5_S6

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample241

value: saliva

value: Female

value: Asian


title: hESCs_H3K9me2_Rep1

description:
processed file: H9_H3K9me2.normbyinput.qnorm_100bp.bw
processed file: H9_H3K9me2_CPmnt.p0.00001_peaks.narrowPeak


title: hESCs_H3K9me2_Rep2


title: DE_H3K9me2_Rep2

description:
processed file: DE_H3K9me2.normbyinput.qnorm_100bp.bw
processed file: DE_H3K9me2_CPmnt.p0.00001_peaks.narrowPeak

value: DE stage

value: in vitro differentiated DE cells

value: Pancreatic differentiation


title: PTRF4_S6

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample240

value: Male

value: White or Caucasian


title: hESCs_H3K9me3_Rep1

value: undifferentiated hESCs


title: PP_H3K9me3_Rep2

value: PP stage

value: in vitro differentiated PP cells


title: SC-β_H3K9me2_Rep2

description:
processed file: BETA_H3K9me2.normbyinput.qnorm_100bp.bw
processed file: BETA_H3K9me2_CPmnt.p0.00001_peaks.narrowPeak

value: SC-beta stage

value: in vitro differentiated beta cells


title: DE_H3K9me2_Rep1

value: H9 hESCs


title: SC-β_H3K9me2_Rep1

value: WT


title: PP_FOXA2_Rep2

description:
processed file: PP_FOXA2.normbyinput.qnorm_100bp.bw
processed file: PP_FOXA2_CPmnt.p0.00001_peaks.narrowPeak


title: PTRF8_S14

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample244

value: Infected-Vax

value: Not Hispanic


title: PTRF3_S14

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample239

value: saliva

value: Infected-Unvax


title: PTRF2_S6

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample238

value: Asian


title: PTRF1_S6

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample237

value: Female

value: Black or African American

value: Hispanic


title: SCC7240

city: Palo Alto

first: Andrew

last: Gentles

state: CA

address: 1265 Welch Rd

institute: Stanford University

description: Bulk RNAseq

data_processing:
FASTQ files were trimmed using Trim Galore v.0.6.5, a wrapper tool around Cutadapt and FastQC was used for quality control.
The gene expression quantification was done using Kallisto v.0.46.0 with GENCODE reference genome v.34
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: Head and neck squamous cell carcinoma

extract_protocol:
RNA was extracted from sorted cells using Qiagen RNeasy Plus Mini (Qiagen, Germantown, MD) columns according to the manufacturer’s handbook.
Stanford PAN, protein and nucleic acid facility performed the library preparations and Stanford center for genomics facility performed the sequencing.

value: Head and neck squamous cell carcinoma


title: PH_FOXA2_Rep1

description:
processed file: PH_FOXA2.normbyinput.qnorm_100bp.bw
processed file: PH_FOXA2_CPmnt.p0.00001_peaks.narrowPeak

value: PH stage

value: in vitro differentiated PH cells

value: Pancreatic differentiation


title: PGT_FOXA2_Rep2

description:
processed file: PGT_FOXA2.normbyinput.qnorm_100bp.bw
processed file: PGT_FOXA2_CPmnt.p0.00001_peaks.narrowPeak

value: PGT stage

value: in vitro differentiated PGT cells


title: PTRF11_S14

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample236

value: Control-Unvax

value: White or Caucasian


title: PH_H3K9me2_Rep1

value: H9 hESCs

value: WT


title: SCC7238

description: Bulk RNAseq


title: PH_FOXA2_Rep2


title: PP_FOXA2_Rep1

value: PP stage

value: in vitro differentiated PP cells


title: SCC7228-T

description: Tumor sorted


title: PTRF10_S10

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample235

value: saliva

value: Male


title: DE_FOXA2_Rep1

description:
processed file: DE_FOXA2.normbyinput.qnorm_100bp.bw
processed file: DE_FOXA2_CPmnt.p0.00001_peaks.narrowPeak

value: DE stage

value: in vitro differentiated DE cells


title: SC-β_FOXA2_Rep2

description:
processed file: BETA_FOXA2.normbyinput.qnorm_100bp.bw
processed file: BETA_FOXA2_CPmnt.p0.00001_peaks.narrowPeak

value: SC-beta stage

value: in vitro differentiated beta cells


title: SCC7228-L

description: Immune sorted

value: Head and neck squamous cell carcinoma


title: DE_FOXA2_Rep2


title: PTRE9_S5

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample234

value: Infected-Vax

value: Female

value: Unknown/Other

value: Not Hispanic


title: SC-β_FOXA2_Rep1

value: Pancreatic differentiation


title: SCC7228-F_enz

description: Fibroblast sorted enzymatic


title: DE_CTCF_Rep1

description:
processed file: DE_CTCF.normbyinput.qnorm_100bp.bw
processed file: DE-CTCF-CPmnt-Rep2_ChIP.p0.00001_peaks.narrowPeak


title: PTRE8_S13

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample233

value: White or Caucasian


title: PGT_CTCF_Rep1

description:
processed file: PGT_CTCF.normbyinput.qnorm_100bp.bw
processed file: PGT-CTCF-CPmnt-Rep2_ChIP.p0.00001_peaks.narrowPeak

value: PGT stage

value: H9 hESCs

value: in vitro differentiated PGT cells


title: PTRE7_S5

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample232


title: hESCs_CTCF_Rep1

description:
processed file: H9_CTCF.normbyinput.qnorm_100bp.bw
processed file: H9-CTCF-CPmnt-Rep2_ChIP.p0.00001_peaks.narrowPeak

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: WT

value: undifferentiated state


title: SCC7228-F

description: Fibroblast sorted


title: SCC7228-E_enz

description: Endothelial sorted enzymatic


title: PTRE6_S13

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample231

value: saliva

value: Infected-Unvax

value: Male


title: SC-β_CTCF_Rep1

description:
processed file: BETA_CTCF.normbyinput.qnorm_100bp.bw
processed file: BETA-CTCF-CPmnt-Rep2_ChIP.p0.00001_peaks.narrowPeak

value: SC-beta stage

value: in vitro differentiated beta cells


title: PP_CTCF_Rep1

description:
processed file: PP_CTCF.normbyinput.qnorm_100bp.bw
processed file: PP-CTCF-CPmnt-Rep2_ChIP.p0.00001_peaks.narrowPeak

value: PP stage

value: in vitro differentiated PP cells


title: SCC7228-E

description: Endothelial sorted

value: Head and neck squamous cell carcinoma


title: PGT_FOXA2_Rep1

value: Pancreatic differentiation


title: PH_CTCF_Rep1

description:
processed file: PH_CTCF.normbyinput.qnorm_100bp.bw
processed file: PH-CTCF-CPmnt-Rep2_ChIP.p0.00001_peaks.narrowPeak

value: PH stage

value: in vitro differentiated PH cells


title: PH_cJun_Rep2

description:
processed file: PH_cJun.normbyinput.qnorm_100bp.bw
processed file: PH_cJun_CPmnt.p0.001_peaks.narrowPeak

value: H9 hESCs


title: PTRE5_S5

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample230

value: Female

value: White or Caucasian

value: Unknown/Other


title: PTRE4_S5

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample229

value: Not Hispanic


title: SCC7228

description: Bulk RNAseq


title: hESCs_cJun

description:
processed file: H9_cJun.normbyinput.qnorm_100bp.bw
processed file: H9_cJun_CPmnt.p0.001_peaks.narrowPeak

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: WT


title: DE_cJun_Rep2

description:
processed file: DE_cJun.normbyinput.qnorm_100bp.bw
processed file: DE_cJun_CPmnt.p0.001_peaks.narrowPeak

value: DE stage

value: in vitro differentiated DE cells


title: PH_cJun_Rep1


title: DE_cJun_Rep1


title: SCC7222b-T_me

description: Tumor sorted mechanical and enzymatic


title: PTRE3_S13

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample228

value: saliva

value: Infected-Unvax

value: Black or African American


title: PTRE2_S5

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample227

value: Male


title: PH_Input

description: processed file: PH_ChIPmentation_Input.scaletoCTCF.RPM.bw

value: Pancreatic differentiation


title: PP_Input

description: processed file: PP_ChIPmentation_Input.scaletoCTCF.RPM.bw

value: PP stage

value: in vitro differentiated PP cells


title: SC-β_cJun

description:
processed file: BETA_cJun.normbyinput.qnorm_100bp.bw
processed file: BETA_cJun_CPmnt.p0.001_peaks.narrowPeak

value: SC-beta stage

value: H9 hESCs

value: in vitro differentiated beta cells


title: SCC7222b-T_m

description: Tumor sorted mechanical

value: Head and neck squamous cell carcinoma


title: PGT_Input

description: processed file: PGT_ChIPmentation_Input.scaletoCTCF.RPM.bw

value: PGT stage

value: in vitro differentiated PGT cells


title: PTRE1_S5

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample226

value: Female

value: Not Hispanic


title: hESCs_Input

description: processed file: H9_ChIPmentation_Input.scaletoCTCF.RPM.bw

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: WT

value: undifferentiated state


title: SCC7214B-T_mne

description: Tumor sorted mechanical and enzymatic


title: PTRE11_S13

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample225

value: saliva

value: Control-Unvax

value: White or Caucasian


title: DE_Input

description: processed file: DE_ChIPmentation_Input.scaletoCTCF.RPM.bw

value: DE stage

value: in vitro differentiated DE cells

value: Pancreatic differentiation


title: SC-β_Input

description: processed file: BETA_ChIPmentation_Input.scaletoCTCF.RPM.bw

value: SC-beta stage

value: H9 hESCs


title: SCC7214B-L_mne

description: Immune sorted mechanical and enzymatic

value: Head and neck squamous cell carcinoma


title: SCC7214B-L_mn

description: Immune sorted mechanical


title: PP_CHD4_Rep2

description:
processed file: PP_Chd4_live_Cuttag.normbyinput.qnorm_100bp.bw
processed file: PP_Chd4_live_Cuttag.p0.00001_peaks.narrowPeak

data_processing:
ChIP-seq and CUT&Tag data processing: All reads were mapped to unique genomic regions using Bowtie2 and the hg38 human genome. PCR duplicates were removed manually. Bedtools genome Coverage function was used to derive bedgraph files for further analysis. To compare changes in ChIP-Seq signals, libraries were normalized by random picking to obtain the same numbers of reads. Normalized reads were used to derive bedgraph files for comparison in IGV. MACS2 was used to call peaks using default parameters with IgG ChIP-Seq data as control. Differential peaks were found using the edgeR (Robinson et al., 2010) R package at p<0.05, changes over 20% up/down.
Analysis of ATAC-seq data: ATAC-Seq data was processed by our in-house pipeline. First, paired end reads were aligned to the hg38 human reference genome using Bowtie2 with default parameters except -X 2000 -m 1. PCR     duplicates     were     removed using     Picard     Tools (http://picard.sourceforge.net;https://broadinstitute.github.io/picard/).  To adjust for fragment sizes, reads mapped to + strands and -strands were offset by +4 bp and -5 bp respectively. For all ATAC-seq datasets, sub-nucleosome and mono-nucleosome reads were separated based on fragment sizes: THSSs (transposases hypersensitive sites, bound by TFs, <115bp) and mono-nucleosomes (180~247bp). To obtain the exact positioning of nucleosomes, DANPOS (Chen et al., 2013) was used to derive the nucleosomal signals genome wide by dpos function using 180~247 bp fragments as input and 115 bp fragments as background using -p 1 -a 1 -jd 20 -u 0 -m 1. Reads were normalized between samples before running DANPOS. THSSs bedgraphs were made using the bedtools genomeCoverage function.   MACS2 was used to call peaks for subnucleosomal reads, which were bound by transcription factors.   To analyze the footprints of TFs in ATAC-seq data, motifs on a set of peaks or loop anchors were used as anchors for running dnase_average_profile.py scripts of the Wellington program in ATAC-seq mode. To compare between Ctrl and HS samples, read-normalized ATAC-seq THSSs (<115 bp) fragments were used as input to obtain the footprint average profiles. The footprint p values of all motifs on a set of peaks or anchors were derived using the wellington_footprints.py scripts of the Wellington program in ATAC-seq mode on read-normalized ATAC-seq THSSs (<115 bp) fragments.
RNA-seq data processing: RNA-seq raw reads were aligned using HISAT2 v2.2.0 to the hg38 human genome with default parameters. Transcripts per million (TPM) counts for all annotated human genes and transcripts were calculated by StringTie v2.1.6. Differentially expressed genes were identified using the R package “edgeR” with a cut-off p value ≤0.05 and fold change over 20% up/down.
Assembly: hg38
Supplementary files format and content: .bw; bigwig files including processed signals of RNA-Seq, ATAC-Seq, CUT&Tag and ChIP-Seq data
Supplementary files format and content: .genenamesorted; txt files including TPM counts for all genes calculated from RNA-Seq data
Library strategy: CUT&TAG

value: PP stage

value: in vitro differentiated PP cells


title: PTRE10_S9

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample224

value: Male

value: Black or African American

value: Hispanic


title: PP_CHD4_Rep1


title: PH_CHD4_Rep2

description:
processed file: PH_Chd4_live_Cuttag.normbyinput.qnorm_100bp.bw
processed file: PH_Chd4_live_Cuttag.p0.00001_peaks.narrowPeak

value: PH stage

value: in vitro differentiated PH cells


title: PH_CHD4_Rep1

value: WT


title: SCC7214B-F_mne

description: Fibroblast sorted mechanical and enzymatic


title: PGT_CHD4_Rep1

description:
processed file: PGT_Chd4_live_Cuttag.normbyinput.qnorm_100bp.bw
processed file: PGT_Chd4_live_Cuttag.p0.00001_peaks.narrowPeak

value: PGT stage

value: in vitro differentiated PGT cells


title: SCC7214B-E_mne

description: Endothelial sorted mechanical and enzymatic


title: PGT_CHD4_Rep2


title: hESCs_CHD4_Rep2

description:
processed file: H9_Chd4_live_Cuttag.normbyinput.qnorm_100bp.bw
processed file: H9_Chd4_live_Cuttag.p0.00001_peaks.narrowPeak

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: hESCs_CHD4_Rep1


title: SCC7222b-L_me

description: Immune sorted mechanical and enzymatic


title: SC-β_CHD4_Rep2

description:
processed file: BETA_Chd4_live_Cuttag.normbyinput.qnorm_100bp.bw
processed file: BETA_Chd4_live_Cuttag.p0.00001_peaks.narrowPeak

value: in vitro differentiated beta cells

value: Pancreatic differentiation


title: SCC7207-T-e

description: Tumor sorted enzymatic


title: DE_CHD4_Rep2

description:
processed file: DE_Chd4_live_Cuttag.normbyinput.qnorm_100bp.bw
processed file: DE_Chd4_live_Cuttag.p0.00001_peaks.narrowPeak

value: DE stage

value: H9 hESCs

value: in vitro differentiated DE cells


title: DE_CHD4_Rep1


title: PP_ATACSeq_Rep2

description:
processed file: PP_ATACRep5.normbyinput.qnorm_100bp.bw
processed file: PP_ALL.ATAC.bowtie2.NFR115.p0.001_peaks.narrowPeak

value: PP stage

value: in vitro differentiated PP cells


title: SCC7207-L-m

description: Immune sorted mechanical

value: Head and neck squamous cell carcinoma


title: PTRD4_S4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample218

value: saliva

value: Infected-Unvax

value: Male

value: White or Caucasian

value: Not Hispanic


title: PTRD5_S4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample219

value: Female


title: SC-β_CHD4_Rep1

value: SC-beta stage

value: WT


title: SCC7207-L-e

description: Immune sorted enzymatic


title: PP_ATACSeq_Rep1


title: SCC7207-E-e

description: Endothelial sorted enzymatic


title: PTRD9_S4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample223

value: Infected-Vax


title: PGT_ATACSeq_Rep2

description:
processed file: PGT_ATACRep5.normbyinput.qnorm_100bp.bw
processed file: PGT_ALL.ATAC.bowtie2.NFR115.p0.001_peaks.narrowPeak

value: PGT stage

value: in vitro differentiated PGT cells


title: PTRD3_S12

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample217


title: SCC7205-T-Col

description: Tumor sorted enzymatic


title: PTRD2_S4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample216

value: Black or African American


title: DE_ATACSeq_Rep2

description:
processed file: DE_ATACRep5.normbyinput.qnorm_100bp.bw
processed file: DE_ALL.ATAC.bowtie2.NFR115.p0.001_peaks.narrowPeak

value: DE stage

value: H9 hESCs

value: Pancreatic differentiation


title: PTRD8_S12

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample222


title: DE_ATACSeq_Rep1

value: in vitro differentiated DE cells


title: PTRD7_S4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample221


title: SCC7205-T

description: Tumor sorted

value: Head and neck squamous cell carcinoma


title: SC-β_ATACSeq_Rep2

description:
processed file: BETA_ATACRep5.normbyinput.qnorm_100bp.bw
processed file: BETA_ALL.ATAC.bowtie2.NFR115.p0.001_peaks.narrowPeak

value: in vitro differentiated beta cells


title: SC-β_ATACSeq_Rep1


title: PTRD6_S12

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample220

value: saliva

value: Infected-Unvax


title: SCC7205-L-Col

description: Immune sorted enzymatic


title: PTRD12_S16

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample214

value: Control-Unvax

value: White or Caucasian


title: PTRD11_S12

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample213

value: Male

value: Not Hispanic


title: SCC7205-L

description: Immune sorted


title: SCC7205-F

description: Fibroblast sorted


title: primary CLL cells, 100µm DI pre-treatment O.N., 2.5 μg/ml CpG ODN2006 stimulation, 4h [05_DI_CPG4H]

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

data_processing:
COSR Center (Center for Omics Science, Ospedale San Raffaele) custom pipeline.
Quality checks have been done on raw data using FastQC and MultiQC.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic.
Trimmed sequence reads were mapped to hg38 using STAR.
Read count extraction has been made using Rsubread library, featureCounts function.
Assembly: hg38
Supplementary files format and content: counts_1625_GEO.txt: Tab-delimited text file contains raw counts data for all the samples.

source_name: CLL (Chronic Lymphocytic Leukemia) patient-derived primary leukemic B-cells

growth_protocol: 3*10^6 cells/ml of RPMI+10%FBS.

extract_protocol:
RNA was extracted using ReliaPrep™ RNA Miniprep Systems (Promega, Madison, WI, USA) following manufacturer protocol.
RNA libraries for RNA-seq were prepared using Illumina mRNA Stranded TruSeq Library Prep Kit following manufacturer's protocols.

tag: diagnosis

value: Chronic Lymphocytic Leukemia (CLL)

value: Primary leukemic B-cells

value: 100um electrophilic compound Dimethyl itaconate and TLR9 stimulation with 2.5ug/ml CpG-ODN2006

tag: time

tag: patient


title: PTRD10_S12

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample212

value: Infected-Vax

value: Female


title: primary CLL cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h [06_CPG4H]

value: TLR9 stimulation with 2.5ug/ml CpG-ODN2006


title: primary CLL cells, 100µm DI treatment, 20h [05_DI]

value: 100um electrophilic compound Dimethyl itaconate


title: primary CLL cells, untreated and unstimulated [06_CTRL]

value: untreated and unstimulated

value: ctrl


title: SCC7205-E

description: Endothelial sorted

value: Head and neck squamous cell carcinoma


title: primary CLL cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h [05_CPG4H]


title: PTRCH2_S16

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample211


title: SCC7202-T

description: Tumor sorted


title: SCC7202-L

description: Immune sorted


title: PTRCH1_S8

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample210

value: Control-Vax


title: primary CLL cells, 100µm DI treatment, 20h [04_DI]


title: PGT_ATACSeq_Rep1

value: PGT stage

value: H9 hESCs

value: in vitro differentiated PGT cells

value: WT

value: Pancreatic differentiation


title: primary CLL cells, untreated and unstimulated [04_CTRL]


title: SCC7202

description: Bulk RNAseq


title: PTRD1_S4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample215

value: saliva

value: Infected-Unvax

value: Black or African American

value: Not Hispanic


title: primary CLL cells, 100µm DI treatment, 20h [03_DI]

value: Chronic Lymphocytic Leukemia (CLL)

value: Primary leukemic B-cells


title: primary CLL cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h [04_CPG4H]

value: TLR9 stimulation with 2.5ug/ml CpG-ODN2006


title: primary CLL cells, 100µm DI pre-treatment O.N., 2.5 μg/ml CpG ODN2006 stimulation, 4h [03_DI_CPG4H]

value: 100um electrophilic compound Dimethyl itaconate and TLR9 stimulation with 2.5ug/ml CpG-ODN2006


title: primary CLL cells, 100µm DI treatment, 20h [06_DI]

value: 100um electrophilic compound Dimethyl itaconate


title: primary CLL cells, 100µm DI pre-treatment O.N., 2.5 μg/ml CpG ODN2006 stimulation, 4h [04_DI_CPG4H]


title: primary CLL cells, 100µm DI pre-treatment O.N., 2.5 μg/ml CpG ODN2006 stimulation, 4h [06_DI_CPG4H]


title: primary CLL cells, untreated and unstimulated [03_CTRL]

value: untreated and unstimulated

value: ctrl


title: primary CLL cells, untreated and unstimulated [05_CTRL]


title: primary CLL cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h [03_CPG4H]


title: primary CLL cells, 100µm DI treatment, 20h [02_DI]


title: PTRCF1_S6

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample206

value: Control-Vax

value: Female

value: White or Caucasian


title: L36_leChRO_sip63_Rep2

city: Stuttgart

first: Cristiana

last: Lungu

state: BW

address: Allmandring 31

department: Institute of Cell Biology and Immunology

country: Germany

institute: University of Stuttgart

description:
L36_leChRO_siP63_plus.bw
L36_leChRO_siP63_minus.bw

data_processing:
Chro-Seq analysis was performed using the pipeline developed by Charles G. Danko’s Lab as previously described (DOI: 10.1038/s41588-018-0244-3). The obtained Chro-Seq bam files for “minus” and “plus” strand were merged and normalized to counts per million (CPM) using Deeptools bamCoverage function.
Assembly: hg19
Supplementary files format and content: bigwig files
Library strategy: leChRO-seq

molecule: nuclear RNA

growth_protocol: L3.6pl cells were cultured in phenol-free minimum essential medium (MEM) supplemented with 10% FBS, 1% penicillin/streptomycin, and 1% glutamine.

extract_protocol:
leChRO-seq was performed as previously described (DOI: 10.1038/s41588-018-0244-3). Extracted chromatin from cultured cells or homogenized PDX tissue samples was subjected to sonication. Chromatin run-on reaction was performed with biotin-11-UTP (Perkin Elmer) containing master mix at 37⁰C for 5 min.  After subsequent RNA isolation, biotin RNA enrichment was performed using the streptavidin magnetic beads (NEB).
RNA was ligated with 3’ RNA Adaptor using the T4 RNA ligase I (NEB).  After 2nd biotin enrichment, RNA was de-capped using RppH (NEB) and 5’-repaied using PNK (NEB) enzymes. After 5’ RNA adaptor ligation, another round of biotin enrichment and RNA isolation was performed.Extracted RNA was reverse transcribed using SuperScript III RT enzyme (Invitrogen). The resultant DNA was PCR amplified using Phusion DNA Polymerase (NEB) with corresponding indexing primers.

treatment_protocol: Transfection of siRNAs was achieved using Lipofectamine RNAiMAX (Invitrogen) according to manufacturer’s instructions. Control non-targeting siRNA #5 (NT5) (siGENOME, #D-001210-05-20) and TP63 siRNA pool (siGENOME; #M-003330-01-0005 SMARTpool) were purchased from Dharmacon, ThermoScientific.

value: Pancreatic cancer cell line

value: P63 knockdown


title: L36_leChRO_sip63_Rep1


title: primary CLL cells, 100µm DI pre-treatment O.N., 2.5 μg/ml CpG ODN2006 stimulation, 4h [02_DI_CPG4H]


title: primary CLL cells, untreated and unstimulated [02_CTRL]


title: L36_leChRO_NT5_Rep2

description:
L36_leChRO_NT5_plus.bw
L36_leChRO_NT5_minus.bw

value: WT


title: primary CLL cells, 100µm DI treatment, 20h [01_DI]


title: PTRCG2_S15

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample209

value: saliva


title: primary CLL cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h [02_CPG4H]


title: PTRCE2_S13

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample205


title: primary CLL cells, 100µm DI pre-treatment O.N., 2.5 μg/ml CpG ODN2006 stimulation, 4h [01_DI_CPG4H]


title: PTRCG1_S7

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample208

value: Control-Unvax

value: Unknown/Other


title: PTRCD2_S12

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample203

value: Male

value: Not Hispanic


title: primary CLL cells, untreated and unstimulated [01_CTRL]

value: Chronic Lymphocytic Leukemia (CLL)

value: Primary leukemic B-cells


title: GöPDX4_leChRO

description:
GPDX4_leChRO_plus.bw
GPDX4_leChRO_minus.bw

source_name: PDX

value: PDX


title: PTRCE1_S5

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample204


title: L36_sip63_Rep3

data_processing:
Fastq files were mapped to the human reference genome assembly hg19 using RNA STAR gapped-read mapper.
The read counting was performed via HTSeq
The count files were subjected to differential analysis using the DESeq2 Package on R  3.6.0
Assembly: hg19
Supplementary files format and content: Normalized count matrix from PDX obtained using DeSeq2 package
Supplementary files format and content: DeSeq2 results table for comparisons of JQ1 vs DMSO, or P63 knockdown vs control conditions.

extract_protocol:
Total RNA from L3.6pl cells as well as from homogenized PDX tissue was isolated using QIAzol® reagent (Qiagen).
mRNA-seq libraries were prepared using the TruSeq RNA Library Prep V2 (Illumina) kit.

treatment_protocol: Transfection of siRNAs was achieved using Lipofectamine RNAiMAX (Invitrogen) according to manufacturer’s instructions. Control non-targeting siRNA #5 (NT5) (siGENOME, #D-001210-05-20) and TP63 siRNA pool (siGENOME; #M-003330-01-0005 SMARTpool) were purchased from Dharmacon, ThermoScientific. For JQ1 experiments, cells were treated for 24 h with 500 nM JQ1 (dissolved in DMSO) or an equivalent volume of DMSO.

value: Pancreatic adenosquamous carcinoma cell line

value: P63 siRNA


title: primary CLL cells, 2.5 μg/ml CpG-ODN2006 stimulation, 4h [01_CPG4H]

value: TLR9 stimulation with 2.5ug/ml CpG-ODN2006


title: L36_sip63_Rep2


title: PTRCD1_S4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample202

value: Control-Vax


title: PGT_H3K4me1_DSG_MiCP_Rep1

description: Mi-ChIP

data_processing:
Paired-end reads from Hi-ChIP and Mi-ChIP experiments were aligned to the human hg38 reference genome using HiC-Pro v2.10.0. After PCR duplicates and low-quality reads were removed, high-quality reads were assigned to DpnII restriction fragments, filtered for valid interaction PETs, and used to generate binned contact matrix hic files. For visualization and further analysis of Hi-ChIP and Mi-ChIP contact maps, Vanilla coverage square root (VCsqrt) normalized signal for the interaction matrices were derived using the Juicebox tools dump command. FitHiChIP (https://ay-lab.github.io/FitHiChIP/) was used for two analyses, 1) to generate singleton reads resembling ChIP-Seq data for finding genomic targets of specific proteins; 2) to call significant interactions with default parameters with FDR cutoff at 0.05 for finding long-range contacts associated with specific proteins.
Assembly: hg38
Supplementary files format and content: .hic; matrix showing long-range contacts in Hi-C data, visible in Juicebox browser
Supplementary files format and content: .bw; bigwig files exhibiting singleton reads of Hi-ChIP or Mi-ChIP data

extract_protocol:
For Hi-ChIP, H9 cells and their in vitro differentiated organoids were collected, fixed with 1% formaldehyde for 10 min at room temperature and quenched with glycine, washed with PBS and stored frozen at -80°C. For library preparation, fixed organoids were gently homogenized in Hi-C lysis buffer with pestle A to release nuclei. To derive the proximity ligation products of chromatin, DpnII digestion, biotin-dCTP fill in and re-ligation were applied to released nuclei sequentially. After ligation, chromatin was sheared by sonication into 200-500 bp fragments and precleared with Protein A and G Dynal beads at 4°C for 2 hours, then precipitated using Protein A or G dynal beads pre-incubated with proper antibodies overnight to enrich for ligation products bound by specific proteins. Tagmentation of immunoprecipitated chromatin by Tn5 transposes mixture was perform on beads to fragment and add sequencing adapters to ligation products. After elution, reverse crosslink and ethanol precipitation, a second pull down by streptavidin beads was performed to enrich for biotin-labeled ligation products. On bead PCR amplification was performed to derive libraries for Illumina sequencing. For Mi-ChIP, H9 cells and their in vitro differentiated organoids were collected, fixed with 3 mM DSG for 40 min and 1% formaldehyde for 10 min at RT sequentially, quenched with 0.2 M glycine for 5 min at RT, washed with PBS and stored frozen at -80°C. For library preparation, fixed organoids were gently homogenized in MB#1 (10 mM Tris-HCl, pH 7.5, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 0.2% NP-40, 1x Roche cOmplete EDTA-free) with pestle A to release nuclei. Chromatin was fragmented with MNase for 10 min at 37°C and digestion was stopped with 5 mM EGTA at 65°C for 10 min. The chromatin was resuspended in 1x NEBuffer 2.1 (NEB, #B7202S)and dephosphorylated by addition of 5 μl rSAP (NEB, #M0203) at 37°C for 45 min. 5′ overhangs were generated with this pre-mix (50 mM NaCl, 10 mM Tris, 10mM MgCl2, 100 μg/ml BSA, 2 mM ATP, 3 mM DTT 8 μl Large Klenow Fragment (NEB, #M0210L) and 2 μl T4 PNK (NEB, #M0201L))at 37°C for 15 min. The DNA overhangs were filled with biotinylated nucleotides by addition of 100 μl pre-mix (25 μl 0.4 mM Biotin-dATP (Invitrogen, #19524016), 25 μl 0.4 mM Biotin-dCTP (Invitrogen, #19518018), 2 μl 10 mM dGTP and 10 mM dTTP (stock solutions: NEB, #N0446), 10 μl 10x T4 DNA Ligase Reaction Buffer (NEB #B0202S), 0.5 μl 200x BSA (NEB, #B9000S), 38.5 μl H2O) and incubation at 25°C for 45 min.  The reaction was stopped by addition of 12 μl 0.5 M EDTA (Invitrogen, #15575038) at 65°C for 20 min. After proximity ligation and removal of unligated ends, chromatin was sheared by sonication into 200-500 bp fragments and precleared with Protein A and G Dynal beads at 4°C for 2 hours, then precipitated using Protein A or G dynal beads pre-incubated with proper antibodies overnight to enrich for ligation products bound by specific proteins. Immunoprecipitated ligation products were eluted, reverse crosslinked and ethanol precipitated. Purified DNA was further cleaned up by Dynabeads™ MyOne™ Streptavidin C1 beads (Invitrogen, #65001) to enrich for biotin-labeled ligation products. After end-repair, A-tailing and Truseq adapter ligation, PCR amplification was finally performed on beads by using Truseq barcoded primers to generate libraries for Illumina sequencing.
Truseq libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding adenosine to the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix. Nextera libraries were amplified with Nextera barcoded primers using the KAPA SYBR FAST qPCR Master Mix. Illumina libraries were sequenced paired-end at 50 bp length on Illumina Hiseq2500 v4 or NovaSeq 6000 instruments.

value: PGT stage

value: H9 hESCs

value: in vitro differentiated PGT cells

value: Pancreatic differentiation


title: PP_H3K4me1_DSG_MiCP_Rep1

description: Mi-ChIP

value: PP stage

value: in vitro differentiated PP cells

value: WT


title: PTRCF2_S14

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample207

value: saliva

value: Control-Unvax

value: White or Caucasian


title: PTRCC2_S11

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample201

value: Male

value: Not Hispanic


title: H9_H3K4me1_DSG_MiCP_Rep1

description: Mi-ChIP

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: DE_H3K4me1_DSG_MiCP_Rep1

description: Mi-ChIP

value: DE stage

value: in vitro differentiated DE cells


title: L36_sip63_Rep1

value: Pancreatic adenosquamous carcinoma cell line

value: P63 knockdown

value: P63 siRNA


title: BETA_H3K4me1_DSG_MiCP_Rep1

description: Mi-ChIP

value: SC-Beta stage

value: H9 hESCs

value: in vitro differentiated Beta cells

value: Pancreatic differentiation


title: PTRCC1_S3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample200

value: saliva

value: Control-Vax

value: Unknown/Other


title: PP_H3K27ac_DSG_MiCP_Rep1

description: Mi-ChIP

value: PP stage

value: in vitro differentiated PP cells

value: WT


title: L36_NT5_Rep3

value: non-targeting siRNA


title: PGT_H3K27ac_DSG_MiCP_Rep1

description: Mi-ChIP

value: PGT stage

value: in vitro differentiated PGT cells


title: L36_leChRO_NT5_Rep1

value: Pancreatic cancer cell line


title: PTRCB2_S10

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample199

value: Male

value: Black or African American

value: Hispanic


title: L36_NT5_Rep2

value: Pancreatic adenosquamous carcinoma cell line


title: PTRCB1_S2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample198

value: Control-Unvax

value: White or Caucasian

value: Not Hispanic


title: DE_H3K27ac_DSG_MiCP_Rep1

description: Mi-ChIP

value: DE stage

value: H9 hESCs

value: in vitro differentiated DE cells

value: Pancreatic differentiation


title: L36_NT5_Rep1


title: BETA_H3K27ac_DSG_MiCP_Rep1

description: Mi-ChIP

value: SC-Beta stage

value: in vitro differentiated Beta cells


title: L36_JQ1_500nm_Rep3

value: 500nM JQ1


title: PTRCA2_S9

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample197

value: saliva

value: Unknown/Other


title: PP_SA2_HiChIP_Rep1

description: Hi-ChIP

value: PP stage

value: in vitro differentiated PP cells

value: WT


title: PP_SA2_HiChIP_Rep2

description: Hi-ChIP


title: PH_SA2_HiChIP_Rep2

description: Hi-ChIP

value: PH stage

value: in vitro differentiated PH cells


title: L36_JQ1_500nm_Rep2

value: Pancreatic adenosquamous carcinoma cell line


title: PH_SA2_HiChIP_Rep1

description: Hi-ChIP


title: L36_JQ1_500nm_Rep1


title: PGT_SA2_HiChIP_Rep2

description: Hi-ChIP

value: PGT stage

value: in vitro differentiated PGT cells


title: L36_DMSO_Rep3

value: DMSO


title: H9_SA2_HiChIP_Rep2

description: Hi-ChIP

value: undifferentiated hESCs

value: H9 hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: PGT_SA2_HiChIP_Rep1

description: Hi-ChIP

value: Pancreatic differentiation


title: H9_SA2_HiChIP_Rep1

description: Hi-ChIP


title: PTRC9_S3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample195

value: Infected-Vax

value: Male

value: White or Caucasian

value: Not Hispanic


title: PTRC8_S11

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample194

value: saliva

value: Female


title: DE_SA2_HiChIP_Rep1

description: Hi-ChIP

value: DE stage

value: in vitro differentiated DE cells

value: WT


title: PTRC7_S3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample193


title: BETA_SA2_HiChIP_Rep2

description: Hi-ChIP

value: SC-Beta stage

value: in vitro differentiated Beta cells


title: H9_H3K27ac_DSG_MiCP_Rep1

description: Mi-ChIP


title: BETA_SA2_HiChIP_Rep1

description: Hi-ChIP


title: L36_DMSO_Rep1

value: Pancreatic adenosquamous carcinoma cell line

value: DMSO


title: PTRC6_S11

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample192

value: Infected-Unvax

value: Asian


title: PTRC5_S3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample191

value: Black or African American


title: PP_SA1_HiChIP_Rep2

description: Hi-ChIP

value: PP stage

value: H9 hESCs

value: in vitro differentiated PP cells

value: Pancreatic differentiation


title: PTRCA1_S1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample196

value: Control-Vax

value: Male

value: White or Caucasian

value: Not Hispanic


title: PP_SA1_HiChIP_Rep1

description: Hi-ChIP


title: PTRC4_S3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample190

value: saliva


title: PH_SA1_HiChIP_Rep1

description: Hi-ChIP

value: PH stage

value: in vitro differentiated PH cells

value: WT


title: PGT_SA1_HiChIP_Rep2

description: Hi-ChIP

value: PGT stage

value: in vitro differentiated PGT cells


title: PGT_SA1_HiChIP_Rep1

description: Hi-ChIP


title: PTRC3_S11

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample189

value: Infected-Unvax

value: Female


title: GöPDX21

value: PDX


title: H9_SA1_HiChIP_Rep2

description: Hi-ChIP

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: GöPDX19


title: PTRC2_S3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample188

value: Asian


title: DE_SA1_HiChIP_Rep1

description: Hi-ChIP

value: DE stage

value: H9 hESCs

value: in vitro differentiated DE cells

value: Pancreatic differentiation


title: GöPDX15


title: H9_SA1_HiChIP_Rep1

description: Hi-ChIP


title: L36_DMSO_Rep2

value: Pancreatic adenosquamous carcinoma cell line

value: DMSO


title: BETA_SA1_HiChIP_Rep2

description: Hi-ChIP

value: SC-Beta stage

value: in vitro differentiated Beta cells


title: PTRC1_S3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample187

value: saliva

value: White or Caucasian

value: Not Hispanic


title: PTRC12_S15

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample186

value: Control-Unvax

value: Female


title: BETA_SA1_HiChIP_Rep1

description: Hi-ChIP

value: WT


title: GöPDX13

value: PDX


title: PP_PolII_HiChIP_Rep2

description: Hi-ChIP

value: PP stage

value: in vitro differentiated PP cells


title: H9_S2P_HiChIP_Rep1

description: Hi-ChIP

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: GöPDX23


title: GöPDX14


title: PP_PolII_HiChIP_Rep1

description: Hi-ChIP

value: H9 hESCs

value: Pancreatic differentiation


title: PTRC11_S11

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample185

value: Control-Vax

value: Male


title: PH_PolII_HiChIP_Rep1

description: Hi-ChIP

value: PH stage

value: in vitro differentiated PH cells


title: GöPDX12


title: PH_SA1_HiChIP_Rep2

description: Hi-ChIP


title: PTRC10_S11

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample184

value: saliva

value: Infected-Vax

value: White or Caucasian


title: PTRB9_S2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample183

value: Not Hispanic


title: GöPDX11


title: GöPDX9


title: H9_PolII_HiChIP_Rep2

description: Hi-ChIP

value: WT


title: PGT_PolII_HiChIP_Rep2

description: Hi-ChIP

value: PGT stage

value: in vitro differentiated PGT cells


title: PGT_PolII_HiChIP_Rep1

description: Hi-ChIP


title: PTRB8_S10

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample182

value: Female


title: H9_PolII_HiChIP_Rep1

description: Hi-ChIP

value: undifferentiated hESCs


title: GöPDX8

value: PDX


title: DE_PolII_HiChIP_Rep1

description: Hi-ChIP

value: DE stage

value: in vitro differentiated DE cells


title: BETA_PolII_HiChIP_Rep1

description: Hi-ChIP

value: SC-Beta stage

value: H9 hESCs

value: in vitro differentiated Beta cells

value: Pancreatic differentiation


title: PTRB7_S2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample181


title: BETA_PolII_HiChIP_Rep2

description: Hi-ChIP


title: PTRB6_S10

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample180

value: Infected-Unvax

value: Male

value: Asian


title: GöPDX7


title: PH_PolII_HiChIP_Rep2

description: Hi-ChIP

value: PH stage

value: in vitro differentiated PH cells


title: GöPDX5


title: SPF, GL261, immune cells+tumor cells, high glucose diet

city: Duarte

first: Jaeho

last: Kim

address: 1500 E Duarte Rd

department: RadiationOncology

institute: City of Hope

description: 7-AAD- cells

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10X Genomics) was used for align reads, generate gene-cell matrices and perform clustering and gene expression analysis
Samples were aligned using the mouse genome 10-3.0.0 (Mm10, 10X genomics)
Assembly: Mm10
Supplementary files format and content: Feature, barcode, matrix

organism: Mus musculus

source_name: Brain

growth_protocol: Mice were housed in specific pathogen free (SPF) facility or KAIST, Korea. GL261 cells were cultured in DMEM supplied with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
To isolate single cells from the mouse GBM TME immediately after euthanasia via a CO2 gas chamber, we perfused 30 ml of cold DPBS solution through the heart to prevent blood contamination in the brain as much as possible. Then, only the right hemisphere, in which the cancer cells were inoculated, was extracted. The hemisphere was divided into small pieces using a blade and digested with 2 mg/ml collagenase IV (Worthington Biochemical Corporation, Columbus, OH, USA) and 30 μg/ml DNase I (Roche, Basel, Switzerland) at 37 °C for 30 minutes in a shaking incubator. Next, the tissues were filtered through a 70-µm strainer. To isolate immune cells, we resuspended the filtered cells in 5 ml of 30% Percoll solution (GE Healthcare, Chicago, IL) containing DMEM CM and then a 70% Percoll solution containing DPBS supplemented with 1% bovine serum (Thermo Fisher Scientific) was added slowly to the bottom, followed by centrifugation at room temperature for 20 minutes without applying a brake. After removing the immune cells at the interface of the two Percoll layers, the cells were incubated in ACK lysis buffer at room temperature for 5 minutes to remove the remaining red blood cells, and further analysis was performed. Suspensions were pooled into one sample from three mice in each group with a median of five mice. The single-cell suspensions were treated with an anti-CD16/32 antibody (2.4G2, Fc blocker) to block Fc receptors prior to staining with mouse-specific antibodies. The cells were then stained with CD45.2-PE. Live immune cells were isolated using a FACS Aria II (BD Biosciences) flow cytometer, and 7-AAD staining was performed before data acquisition to eliminate dead cells and 7-AAD-negative live cells were sorted with FACS Aria.
library were constructed with Single Cell 3' Reagent Kit v3 (10x genomics) following manufacturer's instruction.

treatment_protocol: For anti-PD-1 ICI administration, 200 µg of an InVivoMab anti-mouse PD-1 depletion antibody (BioXcell, BE0146) was diluted in 100 µl of DPBS and injected intraperitoneally into each mouse on days 9, 12, and 15 after GL261 tumor inoculation. For Desulfovibrio colonization, we supplied C57BL/6 wild type germ-free mice with Desulfovibrio vulgaris 1 × 10^8 cells/100 μl or DPBS for control through oral gavage, three times a week for 2 weeks before and after GL261 tumor inoculation.

value: Brain

tag: strain

value: immune cells + tumor cells

value: WT

value: high glucose diet


title: PTRB5_S14

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample179

value: saliva

value: Female

value: White or Caucasian

value: Not Hispanic


title: GöPDX4

value: PDX


title: PTRB4_S2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample178

value: Hispanic


title: SPF, GL261, immune cells+tumor cells, normal diet

description: 7-AAD- cells

value: normal water


title: PH_H3K9me3_HiChIP_Rep2

description: Hi-ChIP

value: H9 hESCs

value: Pancreatic differentiation


title: PTRB3_S10

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample177

value: Infected-Unvax


title: GöPDX1


title: SPF, GL261, immune cells, high glucose diet, anti PD-1

extract_protocol:
To isolate single cells from the mouse GBM TME immediately after euthanasia via a CO2 gas chamber, we perfused 30 ml of cold DPBS solution through the heart to prevent blood contamination in the brain as much as possible. Then, only the right hemisphere, in which the cancer cells were inoculated, was extracted. The hemisphere was divided into small pieces using a blade and digested with 2 mg/ml collagenase IV (Worthington Biochemical Corporation, Columbus, OH, USA) and 30 μg/ml DNase I (Roche, Basel, Switzerland) at 37 °C for 30 minutes in a shaking incubator. Next, the tissues were filtered through a 70-µm strainer. To isolate immune cells, we resuspended the filtered cells in 5 ml of 30% Percoll solution (GE Healthcare, Chicago, IL) containing DMEM CM and then a 70% Percoll solution containing DPBS supplemented with 1% bovine serum (Thermo Fisher Scientific) was added slowly to the bottom, followed by centrifugation at room temperature for 20 minutes without applying a brake. After removing the immune cells at the interface of the two Percoll layers, the cells were incubated in ACK lysis buffer at room temperature for 5 minutes to remove the remaining red blood cells, and further analysis was performed. Suspensions were pooled into one sample from three mice in each group with a median of five mice. The single-cell suspensions were treated with an anti-CD16/32 antibody (2.4G2, Fc blocker) to block Fc receptors prior to staining with mouse-specific antibodies. The cells were then stained with CD45.2-PE. Live immune cells were isolated using a FACS Aria II (BD Biosciences) flow cytometer, and 7-AAD staining was performed before data acquisition to eliminate dead cells and 7-AAD-negative and CD45.2-positive live immune cells were sorted with FACS Aria.
library were constructed with Single Cell 3' Reagent Kit v3 (10x genomics) following manufacturer's instruction.

treatment_protocol: For anti-PD-1 ICI administration, 200 µg of an InVivoMab anti-mouse PD-1 depletion antibody (BioXcell, BE0146) was diluted in 100 µl of DPBS and injected intraperitoneally into each mouse on days 9, 12, and 15 after GL261 tumor inoculation.  For Desulfovibrio colonization, we supplied C57BL/6 wild type germ-free mice with Desulfovibrio vulgaris 1 × 10^8 cells/100 μl or DPBS for control through oral gavage, three times a week for 2 weeks before and after GL261 tumor inoculation.

value: CD45.2+ immune cell

value: high glucose diet + anti PD-1


title: PP_H3K9me3_HiChIP_Rep1

description: Hi-ChIP

value: PP stage

value: in vitro differentiated PP cells


title: SPF, GL261, immune cells, normal diet, anti PD-1

value: Brain

value: normal water + anti PD-1


title: L36_HiCHIP_Rep2

data_processing:
HiChIP chromatin interaction data was analyzed using the HiC-Pro pipeline.
FitHiChIP was utilized to identify active p63-associated interactions using the “Peak-To-All” mode. Interactions not marked by H3K27ac on one of the ends were excluded.
The resulting bedpe files were subsequently used for downstream visualization and enhancer-gene association.
Assembly: hg19
Supplementary files format and content: bedpe file containing the active p63-interactions
Library strategy: HiChIP

extract_protocol:
After crosslinking the cells with 1% formaldehyde, cells were washed and lysed. The digestion was carried out with 200U of MboI, DpnII and HinfI (NEB) at 37°C for 2 hours. The overhangs were filled by adding dCTP, dGTP, dTTP and biotin labeled dATP (Jena biosciences) and DNA polymerase I Large (Klenow) Fragment (NEB). T4 DNA Ligase (NEB) mediated proximity ligation was carried out after the biotin incorporation. The samples were then resuspended in lysis buffer supplemented with protease inhibitors and sonicated. After verifying the size distribution of DNA fragments, the chromatin was precleared with 50% sepharose 4B (GE Healthcare) slurry and incubated with 6 μg of H3K27ac antibody (#196-050, Diagenode). Protein A-sepharose (GE Healthcare) beads were used to capture the immunocomplexes. After several rounds of washes, DNA was extracted with phenol/chloroform/isoamyl alcohol (25:24:1). Size selection using KAPApure beads (Roche) was performed according to manufacturer’s guidelines to exclude big DNA fragments prior to library preparation.
Libraries were prepared using KAPA HyperPrep (Roche) kit.  Before library amplification, biotin-labeled library DNA molecules were captured with Streptavidin T-1 beads (Invitrogen). The fragment distribution of HiChIP libraries was determined using Bioanalyzer (Agilent).

value: Pancreatic adenocarcinoma cell line

value: WT


title: PTRB2_S2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample176

value: saliva

value: Male

value: Black or African American


title: PH_H3K9me3_HiChIP_Rep1

description: Hi-ChIP

value: PH stage

value: in vitro differentiated PH cells


title: L36_HiCHIP_Rep1


title: GF, GL261, immune cells, DPBS

value: C57BL/6 (Germ-free)

value: DPBS oral gavage


title: GF, GL261, immune cells, D.vulgaris

value: D.vulgaris oral gavage


title: PTRB1_S2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample175

value: Infected-Unvax

value: Female

value: Hispanic


title: PGT_H3K9me3_HiChIP_Rep2

description: Hi-ChIP

value: PGT stage

value: H9 hESCs

value: in vitro differentiated PGT cells

value: Pancreatic differentiation


title: L36_sip63_H3K27ac_rep2

data_processing:
The fastq files were mapped to the human reference genome assembly hg19 using Bowtie2 with very-sensitive end-to-end mode.
The BAM files were filtered with MAPQ≥2 and PCR duplicates were removed using SAMTOOLS 1.9. The filtered BAM files from each replicate were merged within one condition using SAMTOOLS and the merged BAM files were normalized to 1x depth of coverage (reads per genomic content, RPGC) using Deeptools (3) 3.0.1 bamCoverage to generate bigwig files.
he filtered BAM files from each replicate were merged within one condition using SAMTOOLS and the merged BAM files were normalized to 1x depth of coverage (reads per genomic content, RPGC) using Deeptools (3) 3.0.1 bamCoverage to generate bigwig files.
Assembly: hg19
Supplementary files format and content: normalized bigwig files

extract_protocol:
PDX tissue samples were homogenized on dry-ice using the Sciences BioMascher® II Micro Tissue homogenizers. Powdered tissue and cell pellets from L3.6pl cells were fixed in 1% formaldehyde in PBS for 20 min and quenched with 125 mM glycine for 5 min at room temperature. Sonicated chromatin extract was immunoprecipitated overnight with corresponding antibodies. Protein A sepharose was used to capture immune complexes. Immune complexes were washed, de-crosslinked and DNA was extracted.
ChIP-seq libraries except the H3K4me1 and H3K4me3 were prepared using the KAPA HyperPrep (Roche) kit. H3K4me1 and H3K4me3 libraries were prepared using the MicroPlex Library Preparation Kit (Diagenode) according to the manufacturer's instructions. The library size was estimated using a Bioanalyzer 2100.

value: Pancreatic adenocarcinoma cell line

tag: antibody

value: H3K27ac (Diagenode #C15410196)

value: P63 knockdown

value: P63 siRNA


title: PGT_H3K9me3_HiChIP_Rep1

description: Hi-ChIP

value: WT


title: SPF, GL261, immune cells, high glucose diet

description: HGD

value: Brain

value: CD45.2+ immune cell

value: high glucose diet


title: PP_H3K9me3_HiChIP_Rep2

description: Hi-ChIP

value: PP stage

value: in vitro differentiated PP cells


title: PTRB12_S14

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample174

value: saliva

value: Control-Unvax

value: Black or African American

value: Unknown/Other


title: H9_H3K9me3_HiChIP_Rep2

description: Hi-ChIP

value: undifferentiated hESCs

value: H9 hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: L36_sip63_H3K27ac_rep1

value: Pancreatic adenocarcinoma cell line

value: H3K27ac (Diagenode #C15410196)


title: SPF, GL261, immune cells, normal diet

description: CD

value: normal water


title: PTRB11_S10

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample173

value: Male

value: Asian

value: Not Hispanic


title: L36_NT5_H3K27ac_rep2

value: WT

value: non-targeting siRNA


title: H9_H3K9me3_HiChIP_Rep1

description: Hi-ChIP


title: L36_NT5_H3K27ac_rep1


title: Pool4-RNA-multiome

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Multiome fastq files were processed using CellRanger-ARC pipeline v2
After read alignment with bwa for ATAC, fragment files were generated by offsetting Tn5 inserts and deduplicating
After read alignment with STAR for RNA, a cell x genes count matrix was generated using the featureCounts options
Assembly: mm10
Supplementary files format and content: fragments file containing trimmed, deduplicated, high quality atac-seq fragments and cell barcodes; h5 files containing the cell x feature matrices

source_name: tissue resident memory T cells

extract_protocol:
Nuclei were isolated from frozen, flow cytometry sorted CD8+ T cell subsets
scATAC-seq libraries were constructed using 10X genomics reagents and protocols

value: Liver + Spleen

tag: days p.i.

tag: replicate


title: DE_H3K9me3_HiChIP_Rep2

description: Hi-ChIP

value: DE stage

value: in vitro differentiated DE cells

value: Pancreatic differentiation


title: PTRA8_S9

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample170

tag: tissue

value: saliva

tag: group

value: Infected-Vax

value: Female

value: White or Caucasian


title: Pool3-RNA-multiome


title: Pool2-RNA-multiome


title: DE_H3K9me3_HiChIP_Rep1

description: Hi-ChIP

value: H9 hESCs


title: GöPDX4_Input

value: PDX


title: GöPDX4_P63

value: P63 (Santa Cruz, sc-8431)


title: PTRA9_S1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample171

tag: Sex

tag: race

value: Unknown/Other


title: BETA_H3K9me3_HiChIP_Rep2

description: Hi-ChIP

value: SC-Beta stage

value: in vitro differentiated Beta cells


title: Pool4-ATAC-multiome


title: BETA_H3K9me3_HiChIP_Rep1

description: Hi-ChIP


title: GöPDX4_H3K27ac

value: H3K27ac (Diagenode #C15410196)


title: Pool1-RNA-multiome


title: PTRA7_S1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample169

tag: ethnicity

value: Not Hispanic

tag: age


title: PP_H3K4me1_HiChIP_Rep2

description: Hi-ChIP

tag: developmental stage

value: PP stage

tag: cell line

value: in vitro differentiated PP cells

value: WT


title: Pool3-ATAC-multiome

value: Liver + Spleen


title: PTRA5_S1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample167

value: Infected-Unvax

value: Black or African American

value: Hispanic


title: PP_H3K4me1_HiChIP_Rep1

description: Hi-ChIP

tag: cell type

tag: genotype

value: Pancreatic differentiation


title: PTRB10_S10

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample172

value: saliva

value: Infected-Vax

value: Female

value: White or Caucasian


title: PTRA4_S1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample166


title: Pool2-ATAC-multiome


title: Pool1-ATAC-multiome


title: PTRA3_S9

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample165


title: rtfl9.2

city: Valencia

first: Ana

last: Alarcia

address: Campus de la Univ. Politécnica de Valencia. CPI Edif. 8E. Av de los Naranjos s/

country: Spain

institute: Instututo de Biologia Molecular y Celular de Plantas (CSIC-UPV)

description:
R18
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv

data_processing:
For the bioinformatic and statistical analysis, the input files were processed using the cutadapt software (http://cutadapt.readthedocs.io/en/stable/guide.html)
RNA-seq reads were aligned to the reference genome of Arabidopsis available at the TAIR database (http://arabidopsis.org; Lamesch et al., 2012) using hisat2  software (https://ccb.jhu.edu/software/hisat2/index.shtml).
The abundance estimation of the transcripts was performed using the htseq-count software (https://htseq.readthedocs.io/en/release_0.11.1/count.html),
Supplementary files format and content: .tvs format file including raw counts for ecah sample

organism: Arabidopsis thaliana

source_name: inflorescence apices

extract_protocol:
RNA for RNA-seq was extracted with the RNeasy Plant Mini Kit (Qiagen) from inflorescences and flowers in post-anthesis, adding the DNase to the column with the RNase-Free DNase Set (Qiagen) according to manufacturer’s instructions. RNA concentration and purity were verified using a NanoDrop Spectrophotometer ND1000 and a Bioanalyzer 2100 (Agilent Technologies).
The cDNA libraries preparation, sequencing and analysis were made by Novogene (UK) Company Ltd. using Illumina Novaseq6000 system with a PE150 strategy (pair end – 150 pb simple ends).

value: inflorescence apices

value: dvl8 dvl11 rtfl9 rtfl11 dvl19


title: rtfl9.3

description:
R19
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv


title: in situ Hi-C on olfactory receptor cell with DpnII - 4DNEXH1YN2XB

city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEXH1YN2XB
description: HiC from mature olfactory sensory neurons expressing Olfr17 - bioreplicate 2
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 20000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXH1YN2XB/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/e96c05f9-a27b-46f3-b436-5eddb4dec619/
genome_assembly: GRCm38
derived_from: 4DNFII9EDMZJ.bam, 4DNFIBGPDQ5D.bam, 4DNFICYMMOQF.bam, 4DNFIPG4G75Z.bam, 4DNFICHERKF6.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIEIEFZMD.pairs.gz

source_name: biosource_summary: olfactory receptor cell

extract_protocol:
description: The Official 4DN Standard in situ Hi-C protocol adapted from Rao et al. 2014 PMID: 25497547 - with accepted deviations approved by SC 02/21/2017
download: https://data.4dnucleome.org/protocols/fdc20e37-f22e-42dc-8026-0a132739bad1/@@download/attachment/4DN_in_situ_Hi-C_protocol_20170729.pdf

treatment_protocol:
description: FACS plots for mature olfactory sensory neurons expressing Olfr17 (P2) from P2-GFP mice. HiC from P3 in FACS plot
download: https://data.4dnucleome.org/protocols/bee5ee6c-4134-47fc-bfd6-983225355ade/@@download/attachment/FACS.P2.171101.pdf

value: olfactory receptor cell

value: olfactory epithelium

tag: description

value: FACs-sorted Olfr17+ cells - biological replicate 2

value: mixed

value: adult

value: primary cells

tag: url


title: rtfl9.1

description:
R17
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv


title: rtfl9.4

description:
R20
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv


title: PH_H3K4me1_HiChIP_Rep2

description: Hi-ChIP

value: PH stage

value: H9 hESCs

value: in vitro differentiated PH cells

value: WT

tag: treatment


title: PTRA2_S1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample164

value: Infected-Unvax

value: Male

value: Black or African American

value: Not Hispanic


title: PGT_H3K4me1_HiChIP_Rep2

description: Hi-ChIP

value: PGT stage

value: in vitro differentiated PGT cells

value: Pancreatic differentiation


title: dvl1.4

description:
R16
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv

value: inflorescence apices

value: dvl1 dvl8 dvl11 rtfl11 dvl19


title: in situ Hi-C on olfactory receptor cell with DpnII - 4DNEXDSNPZOU

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEXDSNPZOU
description: HiC from mature olfactory sensory neurons expressing Olfr17 - bioreplicate 1
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 23000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXDSNPZOU/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/ff4d70b3-b589-412a-a35b-004e45100e97/
genome_assembly: GRCm38
derived_from: 4DNFIIIGLA5K.bam, 4DNFI2P1LBCI.bam, 4DNFI318P6AP.bam, 4DNFI7Z5OJAU.bam, 4DNFI5K4EJ2A.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFICY5CI8Q.pairs.gz

value: olfactory receptor cell

value: olfactory epithelium

value: FACs-sorted Olfr17+ cells - biological replicate 1


title: PTRA1_S1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample163

value: saliva

value: Infected-Vax

value: Female

value: White or Caucasian


title: in situ Hi-C on olfactory receptor cell with DpnII - 4DNEX4KRGMAQ

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEX4KRGMAQ
description: HiC from mature olfactory sensory neurons expressing Olfr1507 - bioreplicate 2
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 220000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEX4KRGMAQ/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/b858626b-c1b7-4ab0-ac15-61d8b3a9d461/
genome_assembly: GRCm38
derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIZ32E4IH.bam, 4DNFIC2GWTU7.bam, 4DNFIV1M1SN8.bam, 4DNFIEMLVQQK.bam, 4DNFI537T8V6.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFI72AHX9H.pairs.gz

treatment_protocol:
description: FACS plots for mature olfactory sensory neurons expressing Olfr1507 (MOR28) from MOR28-GFP mice
download: https://data.4dnucleome.org/protocols/0ef5a90b-43dc-4db0-abde-df398b44f343/@@download/attachment/FACS.MOR28.171002.pdf

value: FACs-sorted Olfr1507+ cells - biological replicate 2

value: mixed

value: adult

value: primary cells


title: PGT_H3K4me1_HiChIP_Rep1

description: Hi-ChIP

value: H9 hESCs

value: WT


title: dvl1.2

description:
R14
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv


title: in situ Hi-C on olfactory receptor cell with DpnII - 4DNEXOHPSJTN

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEXOHPSJTN
description: HiC from mature olfactory sensory neurons expressing Olfr1507 - bioreplicate 1
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 170000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXOHPSJTN/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/ca761468-f995-466c-810a-914c9d307b62/
genome_assembly: GRCm38
derived_from: 4DNFIE6IPZ1V.bam, 4DNFINPBVMOY.bam, 4DNFI92NBOUB.bam, 4DNFIO6UFAGH.bam, 4DNFIXN33T8L.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFI3CBEV3I.pairs.gz

value: FACs-sorted Olfr1507+ cells - biological replicate 1


title: PTRA6_S9

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample168

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt 1.2.1
Trimmed sequence reads were quantified to hg38 Ensembl transcripts release 105 using Salmon, using minimum assigned fragments of 10, minimum score fraction of 0.65, match value 2, mismatch value -4, gap opening value 6 and gap extension value of 2
Quantified features were filtered to eliminate those with less than 1 count in 80% or more of the samples
Normalization performed on filtered features using TPM followed by quantile and log2 transformation
Assembly: Homo sapiens hg38
Supplementary files format and content: Tab-separated values matrix file containing raw Salmon feature counts
Supplementary files format and content: Tab-separated matrix file containing filtered and normalized feature abundances

value: Infected-Unvax

value: Male

value: Hispanic


title: PTRA12_S13

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample162

value: Control-Vax

value: Not Hispanic


title: PTRA11_S9

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample161


title: PTRA10_S9

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample160

value: Unknown/Other


title: dvl1.1

description:
R13
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv

value: inflorescence apices

value: dvl1 dvl8 dvl11 rtfl11 dvl19


title: in situ Hi-C on olfactory receptor cell with DpnII - 4DNEXBSGTVWJ

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEXBSGTVWJ
description: HiC from mature olfactory sensory neurons expressing Olfr16 - bioreplicate 2
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 24400 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXBSGTVWJ/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/9601c8a9-b15e-4067-87fb-177c9ca5d288/
genome_assembly: GRCm38
derived_from: 4DNFIJNBGRZW.bam, 4DNFIAPOCTLV.bam, 4DNFISOLX3OU.bam, 4DNFIASZ3TVB.bam, 4DNFIWC9MHY4.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFI3O8M6SZ.pairs.gz

treatment_protocol:
description: FACS plots for mature olfactory sensory neurons expressing Olfr16 (MOR23) from MOR23-GFP mice. HiC from P3 in FACS plot
download: https://data.4dnucleome.org/protocols/a1b28594-703f-4109-8fcd-7222c83cb7bb/@@download/attachment/FACS.MOR23.171101.pdf

value: olfactory receptor cell

value: Not Specified

value: olfactory epithelium

value: FACs-sorted Olfr16+ cells - biological replicate 2


title: 35S.DVL8.2.4

description:
R12
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv


title: DE_H3K4me1_HiChIP_Rep1

description: Hi-ChIP

value: DE stage

value: in vitro differentiated DE cells

value: Pancreatic differentiation


title: PH_H3K4me1_HiChIP_Rep1

description: Hi-ChIP

value: PH stage

value: H9 hESCs

value: in vitro differentiated PH cells

value: WT


title: DeltaH4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample111

value: saliva

value: Infected-Unvax

value: Female

value: Black or African American

value: Hispanic


title: in situ Hi-C on olfactory receptor cell with DpnII - 4DNEXMM7MN7V

description:
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEXMM7MN7V
description: HiC from mature olfactory sensory neurons expressing Olfr16 - bioreplicate 1
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 28000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXMM7MN7V/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/eb4c644b-5fdc-4194-b6c0-571e04332461/
genome_assembly: GRCm38
derived_from: 4DNFIBYQIHSL.bam, 4DNFIY7AVX6K.bam, 4DNFI8O2NBME.bam, 4DNFIIG5TPYG.bam, 4DNFI9UTY34B.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIBEV8M9E.pairs.gz

value: FACs-sorted Olfr16+ cells - biological replicate 1

value: mixed

value: adult

value: primary cells


title: BETA_H3K4me1_HiChIP_Rep2

description: Hi-ChIP

value: SC-Beta stage

value: in vitro differentiated Beta cells


title: 35S.DVL8.2.3

description:
R11
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv

value: inflorescence apices


title: DeltaH3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample110

value: Male

value: White or Caucasian

value: Not Hispanic


title: dvl1.3

description:
R15
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv

value: dvl1 dvl8 dvl11 rtfl11 dvl19


title: Adipose, HF/HS, EndoMT, rep2

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

description:
EndoMT_2
Adipose_EndoMT_RNAseq.csv

data_processing:
Raw sequencing reads were demultiplexed into sample specific Fastq files, which were analyzed by aligning to reference genomes (mouse mm10 or human hg38) by Kallisto v0.46.2
Differential gene expression analysis was performed with Sleuth v0.30.0
Assembly: mm10 or hg38
Supplementary files format and content: Normalized read output per aligned gene as analyzed by Kallisto, statistical outputs of differential gene expression between groups as analyzed by Sleuth

source_name: Visceral Adipose Tissue

extract_protocol:
RNA was purified using the RNeasy MinElute kit (Qiagen, Cat # 74204)
Purified RNA was submitted to the Yale Center for genome analysis for quality control analysis, low-input RNA sequencing amplification, PolyA RNA library preparation, and paired-end 100bp sequencing (NovaSeq v2, Illumina)

value: Visceral Adipose Tissue

value: Cdh5CreERT2; Rosa26eYFP

value: HF/HS

tag: time point

value: 12 months


title: 35S.DVL8.2.2

description:
R10
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv


title: BETA_H3K4me1_HiChIP_Rep1

description: Hi-ChIP

value: H9 hESCs

value: WT

value: Pancreatic differentiation


title: DeltaH2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample109

value: saliva

value: Infected-Vax

value: Female

value: Unknown/Other


title: 35S.DVL8.2.1

description:
R9
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv


title: DeltaH1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample108


title: H9_H3K4me1_HiChIP_Rep2

description: Hi-ChIP

value: undifferentiated hESCs

value: H9 human embryonic stem cells

value: undifferentiated state


title: Adipose, HF/HS, EndoMT, rep1

description:
EndoMT_1
Adipose_EndoMT_RNAseq.csv


title: H9_H3K4me1_HiChIP_Rep1

description: Hi-ChIP


title: PP_H3K27ac_HiChIP_Rep2

description: Hi-ChIP

value: PP stage

value: in vitro differentiated PP cells


title: PP_H3K27ac_HiChIP_Rep1

description: Hi-ChIP


title: DVL1.1D.4

description:
R8
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv

value: inflorescence apices


title: Adipose, HF/HS, Endothelial, rep3

description:
EC_3
Adipose_EndoMT_RNAseq.csv

value: Visceral Adipose Tissue


title: Adipose, HF/HS, Endothelial, rep2

description:
EC_2
Adipose_EndoMT_RNAseq.csv

value: Cdh5CreERT2; Rosa26eYFP


title: DeltaG4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample107

value: Infected-Unvax

value: Black or African American

value: Not Hispanic


title: DeltaG3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample106

value: Male

value: White or Caucasian


title: PH_H3K27ac_HiChIP_Rep2

description: Hi-ChIP

value: PH stage

value: H9 hESCs

value: in vitro differentiated PH cells

value: WT

value: Pancreatic differentiation


title: PH_H3K27ac_HiChIP_Rep1

description: Hi-ChIP


title: Adipose, HF/HS, EndoMT, rep3

description:
EndoMT_3
Adipose_EndoMT_RNAseq.csv

value: HF/HS

value: 12 months


title: DeltaG2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample105

value: saliva

value: Infected-Vax

value: Female


title: DVL1.1D.3

description:
R7
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv

value: inflorescence apices


title: Adipose, HF/HS, Endothelial, rep1

description:
EC_1
Adipose_EndoMT_RNAseq.csv

value: Visceral Adipose Tissue

value: Cdh5CreERT2; Rosa26eYFP


title: DVL1.1D.2

description:
R6
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv


title: PGT_H3K27ac_HiChIP_Rep2

description: Hi-ChIP

value: PGT stage

value: in vitro differentiated PGT cells


title: MEF-IGF2BP1-KO-Wnt3a, Biol rep 3

city: Hershey

first: Vonn

last: Walter

state: PA

address: 500 University Drive

department: Public Health Sciences

institute: Penn State College of Medicine

data_processing:
De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12, Illumina), allowing no mismatches in the index read. After the quality and polyA trimming by BBDuk and alignment by HISAT2 (version 2.1.0), read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCm38.78).
Assembly: GRCm38
Supplementary files format and content: raw read counts are provided in txt file

source_name: Embryonic

growth_protocol: Cells were cultured in DMEM Medium supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit from Qiagen (74104)
The cDNA libraries were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) as per the manufacturer’s instructions. Briefly, total RNA was reverse transcribed using oligo (dT) primers. The second cDNA strand was synthesized by random priming, in a manner that DNA polymerase is efficiently stopped when reaching the next hybridized random primer, so only the fragment close to the 3’ end gets captured for later indexed adapter ligation and PCR amplification. The processed libraries were assessed for their size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).

treatment_protocol: 90% confluent cells were treated/untreated with Wnt3a(100ng/ml) for 24hrs to induce the Wnt signaling

value: Embryonic

value: Mouse Embryonic Fibroblast Cells-IGF2BP1 knockout

tag: biological repeats

value: Biol rep 3

value: Fibroblast


title: WT Col.0.4

description:
R4
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv

value: Col. O


title: DeltaG1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample104

value: Male

value: White or Caucasian

value: Not Hispanic


title: DVL1.1D.1

description:
R5
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv


title: PGT_H3K27ac_HiChIP_Rep1

description: Hi-ChIP

value: H9 hESCs

value: WT

value: undifferentiated state


title: MEF-IGF2BP1-KO-UT, Biol rep 3

value: Untreated


title: H9_H3K27ac_HiChIP_Rep2

description: Hi-ChIP

value: undifferentiated hESCs

value: H9 human embryonic stem cells


title: DeltaF3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample102

value: saliva

value: Infected-Unvax


title: WT Col.0.3

description:
R3
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv

value: inflorescence apices


title: WT Col.0.2

description:
R2
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv


title: H9_H3K27ac_HiChIP_Rep1

description: Hi-ChIP

value: Pancreatic differentiation


title: MEF-WT-Wnt3a, Biol rep 3

value: Embryonic

value: Mouse Embryonic Fibroblast Cells


title: WT Col.0.1

description:
R1
DVL_selected.htseq-count.unstranded.tsv.rpkms.tsv


title: DE_H3K27ac_HiChIP_Rep1

description: Hi-ChIP

value: DE stage

value: in vitro differentiated DE cells


title: MEF-WT-UT, Biol rep 3

value: Biol rep 3

value: Fibroblast


title: DeltaF2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample101

value: Infected-Vax

value: Female

value: White or Caucasian

value: Not Hispanic


title: MEF-IGF2BP1-KO-UT, Biol rep 2

value: Mouse Embryonic Fibroblast Cells-IGF2BP1 knockout

value: Biol rep 2

value: Untreated


title: DeltaE3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample98

value: saliva


title: DeltaE4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample99

value: Infected-Unvax

value: Black or African American


title: MEF-WT-Wnt3a, Biol rep 2


title: MEF-IGF2BP1-KO-Wnt3a, Biol rep 1

value: Biol rep 1


title: SC-β_HiC_Rep2

description: Hi-C

data_processing:
Hi-C data processing.   Paired-end reads from Hi-C experiments were aligned to the human hg38 reference genome using HiC-Pro v2.10.0. After PCR duplicates and low-quality reads were removed, high-quality reads were assigned to DpnII restriction fragments, filtered for valid interaction PETs, and used to generate binned contact matrix hic files. For visualization and further analysis of Hi-C contact maps, Knight-Ruiz (KR) normalized signal for the interaction matrices were derived using the Juicebox tools dump command. HiCCUPS (https://github.com/aidenlab/juicer/wiki/CPU-HiCCUPS) and SIP v1.3.3 (https://github.com/PouletAxel/SIP/releases) were used to call CTCF loops in the Hi-C interaction matrix. Fit-Hi-C (https://github.com/ay-lab/fithic) was used to call significant interaction at 5,10 and 25kb resolution with a q value cutoff of > 0.001 and merged together for all the rest analysis.
Assembly: hg38
Supplementary files format and content: .hic; matrix showing long-range contacts in Hi-C data, visible in Juicebox browser

extract_protocol:
For in-situ Hi-C, H9 cells and their in vitro differentiated organoids were collected, fixed with 1% formaldehyde for 10 min at room temperature and quenched with glycine, washed with PBS and stored frozen at -80°C. For library preparation, fixed organoids were gently homogenized in Hi-C lysis buffer with pestle A to release nuclei. To derive the proximity ligation products of chromatin, DpnII digestion, biotin-dCTP fill in and re-ligation were applied to released nuclei sequentially. To extract and purify re-ligated DNA, samples were digested by Proteinase K, reverse-crosslinked at 65°C overnight, and then precipitated by ethanol to get pure DNA. Purified DNA were further sheared by sonication to 200-500 bp in length. After that, streptavidin dynal beads were incubated with sheared DNA to pull down biotin-labeled proximity ligation products for library preparation on beads. After end-repair, A-tailing and Truseq adapter ligation, PCR amplification was finally performed by using Truseq barcoded primers to generate libraries for Illumina sequencing.
Truseq libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding adenosine to the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligated at room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.

value: SC-Beta stage

value: H9 hESCs

value: in vitro differentiated Beta cells

value: WT

value: Pancreatic differentiation


title: DeltaF1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample100

extract_protocol:
RNA was purified from saliva swabs used for clinical PCR COVID-19 testing, using Zymo Quick-RNA Viral 96 Kit or the KingFisher MagMAX Viral/Pathogen Nucleic Acid Isolation Kit
RNA-seq libraries were synthesized using TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina) according to manufacturer protocol

value: Male


title: MEF-WT-UT, Biol rep 2

value: Embryonic

value: Mouse Embryonic Fibroblast Cells

value: Fibroblast


title: BETA_H3K27ac_HiChIP_Rep2

description: Hi-ChIP


title: BETA_H3K27ac_HiChIP_Rep1

description: Hi-ChIP


title: PH_HiC_Rep1

description: Hi-C

value: PH stage

value: in vitro differentiated PH cells


title: PH_HiC_Rep2

description: Hi-C


title: MEF-IGF2BP1-KO-UT, Biol rep 1

value: Mouse Embryonic Fibroblast Cells-IGF2BP1 knockout


title: SC-β_HiC_Rep1

description: Hi-C


title: DeltaD3

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample95

value: White or Caucasian

value: Not Hispanic


title: DeltaD2

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample94

value: saliva

value: Infected-Vax

value: Female


title: DeltaF4

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample103

value: Infected-Unvax


title: C5aR KO-TAM2

city: Chongqing

first: Xiaojin

last: Luan

address: yuzhong road

institute: Chongqing medical university

data_processing:
Illumia Casva 1.7 software used for base-calling.
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2  software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
To identify DEGs between two different samples, the expression level of each transcript was  calculated  according  to  the  transcripts per million  reads method.  RSEM was used to quantify  gene  abundances.  Essentially,  differential  expression  analysis  was  performed  using  the  DESeq2 or DEGseq .
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM and count values for each sample

source_name: tumor

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000.
RNA purification,  reverse  transcription,  library  construction  and  sequencing  were performed  at  Shanghai Majorbio  Bio-pharm  Biotechnology  Co.,  Ltd.  (Shanghai,  China)  according  to  the  manufacturer’s  instructions (Illumina, San Diego, CA).

value: tumor

value: ID8 cells injected into C5aR knockout mice

value: tumor associated macrophages


title: MEF-WT-Wnt3a, Biol rep 1

value: Biol rep 1


title: DeltaD1

description:
matrix includes transcript ID, gene ID, and values for each sample ID
sample93

value: Male


title: C5aR KO-TAM3


title: WT-TAM3

value: ID8 cells injected into WT mice