title: 4w, Middle, M, M3, Rep2

description: Library name: L9CN83_D2

data_processing:
ST cDNA libraries were diluted to 4nM and 1.08pm libraries loaded for sequencing on an Illumina NextSeq 550 (Illumina, USA) using paired-end sequencing (R1 30bp, R2 55bp). Samples were sequenced at a mean depth of 65.6 million paired-end reads depth. fastq reads were generated with bcl2fastq2. ST Pipeline155 was used to process the resulting fastq files. Briefly, 5nt trimmed R2 was used for mapping to the mouse genome using STAR156. After that, mapped reads were annotated using HTseq-count157. Spatial barcodes were collapsed using TagGD155,158 modified demultiplexer (k-mer 6, mismatches 2). Then, unique molecular identifiers (UMIs) mapped to the same transcript and spatial barcode were collapsed using naive clustering with one mismatch allowed in the mapping process as described in umi-tools159. The output genes-by-barcode matrix was used in all further processing steps. Average library saturation was 78.3%. To focus on reliably detected genes across spots, genes detected in fewer than 2% of spots were removed, as were spots with fewer than 100 UMIs across all genes. The resulting median number of genes and UMI transcripts per spatial spot was 2,164 (10th percentile was 829 and 90th percentile was 4,370) and 4,343 (10th percentile was 1,246 and 90th percentile was 13,055).
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: JPEG-formatted image files containing H&E staining of each Sample

extract_protocol:
After imaging, coverslips were removed in deionized water and permeabilization reactions immediately started. First, tissue samples were permeabilized with 120µl reagent per reaction of collagenase I (200U) in 1x HBSS (both from ThermoFisher Scientific, USA). Pre-permeabilization reagent removal was followed by a 180µl wash in 0.1X Saline Sodium Citrate (SSC, Sigma-Aldrich, USA) at 37°C. Next, tissue was permeabilized with 75µl 0.1% pepsin (pH 1, Sigma-Aldrich, USA) at 37°C for 10min, followed by another wash with 0.1x SCC. Reverse transcription (RT) was performed by the addition of 75µl RT reagents: 50ng/µl actinomycin D (Sigma-Aldrich, USA), 0.5mM dNTPs (ThermoFisher Scientific, USA), 0.20µg/µl BSA, 1X First strand buffer, 5mM DTT, 2U/µl RNaseOUT, 20U/µl Superscript III (all from ThermoFisher Scientific, USA). Tissues were digested from the slide surface by 1h incubation in proteinase K (Qiagen, Germany) at 56°C. Slides were washed as suggested by the slide manufactures (Codelink, Surmodics): 10min 2x SCC with 0.1% SDS (Sigma Aldrich), 1min 0.2x SCC and 1min 0.1X SSC. To remove spatial cDNA:mRNA hybrids from the array surface, Uracil-Specific Excision Reagent (NEB, USA) was used as previously described153.The reaction was run for 2h at 37°C and the resulting spatially barcoded cDNA libraries were collected and libraries prepared
cDNA:RNA hybrids collected from the array surface were used as input in the first part of library preparation reactions. RNA strands were digested and used as primer to make dsDNA using DNA Polymerase I and RNaseH (2.7X First strand buffer, 3.7 U/µl DNA polymerase I and 0.2 U/µl Ribonuclease H (all from ThermoFisher Scientific, USA)) for 2h at 16°C. The material was made into blunt-end dsRNA products with 15U T4 DNA polymerase (NEB, USA) for 20 minutes at 16°C and reactions stopped by addition of 20mM EDTA (pH 8.0, ThermoFisher Scientific, USA). dsDNA was purified using Ampure XP (Beckman Coulter, USA) at a bead to cDNA ratio of 1:1. Next, the material was linearly amplified using a T7 promoter sequencing initially embedding in the oligonucleotides on the array surface by adding 27.8µl of the T7 reaction mix (46.2mM rNTPs, 1.5X T7 reaction buffer, 1.54 U/µl SUPERaseIN inhibitor and 2.3U/µl T7 enzyme; all from ThermoFisher Scientific, USA) for 14h at 37°C. This was followed by a bead cleanup with RNAclean Ampure XP beads (Beckman Coulter, USA) at a beads:aRNA ratio of 1.8:1. 8µl of the eluted aRNA was used as input to the following reactions. 2.5µl of 3µM aRNA adapters [rApp]AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC[ddC] were added to 8µl of aRNA. The reaction was then incubated at 70°C in a PCR machine for 2min and immediately chilled on wet ice. To ligate the adaptors, 4.5µl T4 RNA ligation mix (3.3X T4 RNA ligase buffer, 66U/µl truncated T4 ligase 2 and 13U/µl murine RNAse inhibitor (all from NEB, USA)) were added at 25°C for 1h, followed by an Ampure XP (Beckam Coulter, USA) bead purification at a bead:cDNA ratio of 1.8:1. 1:1 v/v of 20µM GTGACTGGAGTTCAGACGTGTGCTCTTCCGA and 10mM dNTPs were added to the ligated samples and heated to 65°C for 5min. Reverse transcription took place by adding 2.5X First strand buffer, 13mM DTT, 5 U/µl RNaseOUT and 25 U/µl Superscript III (all from Thermo Fisher Scientific, USA). Samples were incubated at 50°C for 1h. 10µl of nuclease-free water were added followed by a final Ampure XP bead purification at bead:cDNA ratio of 1.7:1 with a final elution of 10µl nuclease-free water. qPCR library quantification and indexing were performed as previously described153.

treatment_protocol: Colons were collected within 5 min of death and flushed using ice-cold 1x PBS (Gibco) using a straight gauge needle with a 2.4mm tip (Kent Scientific Corporation, USA) for mice >3 weeks of age or a newborn feeding needle (Cadence Science, USA) for mice ages 3 weeks. The rest of the mice were processed without colon flushing prior to freezing. Tissues were then dried and embedded in Optimal Cutting Temperature (OCT, Fisher Healthcare, USA) in large molds (VWR, USA). Samples were then plunged onto a metal plate pre-chilled and sitting on top of dry ice for 2min or until complete freezing. Samples were transferred and stored at -80°C until use. Cryosections were cut at 10μm thickness onto ST slides, and stored at -80°C for at most 2 days. Approximately 0.5cm of tissue from three different colon regions was placed on a tissue and dried before transfer to a sterile dish to ensure all excess water was gently removed from the sample. Tissues were then placed in a 1.5 mL tube on dry ice and, upon freezing, transferred to −80°C until subsequent tissue processing.

value: M


title: 1yr_All_M_M1

status: Public on Aug 14 2025

type: SRA

city: Columbia

first: Aidan

last: Daly

state: SC

address: 2230 Rembert Street

country: USA

institute: New York Genome Center

description: Library name: 1yr

library_source: transcriptomic single cell

data_processing:
CellRanger v3.0 was used for all initial data pre-processing. Fastq reads were first demultiplexed and then mapped to the reference mm10 transcriptome, augmented to allow for counting of all transcript tags in addition to counting exons as suggested by 10X Genomics. Each barcode was connected to a particular cell and UMIs were collapsed to account for duplicated transcripts. Filtered matrices reflecting digital gene expression (DGE) for each sample and cell were extracted from the pipeline.
Assembly: mm9
Supplementary files format and content: MTX-formatted file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file including annotation metadata for each cell (rows)
Supplementary files format and content: tab-delimited text file containing gene names and expression metadata (columns)
Supplementary files format and content: tab-delimited text file containing barcode names for each cell (rows)

molecule: polyA RNA

organism: Mus musculus

source_name: All colon

growth_protocol: C57BL/6J mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and maintained in accordance with ethical guidelines monitored by the Institutional Animal Care and Use Committees (IACUC) established by the Division of Comparative Medicine at the Broad Institute of MIT and Harvard and Columbia University, and consistent with the Guide for Care and Use of Laboratory Animals, National Research Council, 1996 (institutional animal welfare assurance no. A4711-01), with protocols 0122-10-16 and AABI3617, respectively.

extract_protocol:
Frozen tissues were taken from 1.5ml tubes used for storage at −80°C and placed in pre-chilled 1 mL extraction buffer (0.03% Tween-20, 146mM NaCl, 10mM Tris pH 8.0, 1mMM CaCl2 and 21mM MgCl2; all from Sigma Aldrich, USA), supplemented with 400U RNasin Plus inhibitor (Promega Corporation, USA) and 200U SUPERaseIn RNase Inhibitor (ThermoFisher Scientific, USA). Tissues were disintegrated by chopping with tungsten Carbide Straight 11.5 cm Fine Scissors (14558-11, Fine Science Tools, Foster City, CA) for 10 minutes on ice. To avoid clogging, samples were filled through a 40 μm strainer (Falcon). To release any leftover material from the strainer, it was cleaned with the extraction buffer without the addition of Tween-20, followed by centrifugation to pellet the nuclei at 500g for 5 mins at 4°C. Supernatants were removed and nuclei were resuspended in a 100μL extraction buffer without the addition of Tween-20 before filtering through a 40 μm strainer-capped into a round bottom tube (Falcon). Nuclei were counted and ~8,000 nuclei were loaded per channel on the GemCode Single Cell Platform using the GemCode Gel Bead kit, Chip and Library Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol.
Nuclei were partitioned into Gel Beads in Emulsion (GEMs), lysed and barcoded using reverse transcription reactions, followed by amplification, shearing and 5′ adapter and library indexing. Libraries were sequenced on an Illumina NextSeq 550 (R1: 26 bases; R2: 55 bases) or a NovaSeq 6000 (R1: 28 bases; R2: 94 bases).

treatment_protocol: Colons were collected within 5 min of death and flushed using ice-cold 1x PBS (Gibco) using a straight gauge needle with a 2.4mm tip (Kent Scientific Corporation, USA) for mice >3 weeks of age or a newborn feeding needle (Cadence Science, USA) for mice ages 3 weeks. The rest of the mice were processed without colon flushing prior to freezing. Tissues were then dried and embedded in Optimal Cutting Temperature (OCT, Fisher Healthcare, USA) in large molds (VWR, USA). Samples were then plunged onto a metal plate pre-chilled and sitting on top of dry ice for 2min or until complete freezing. Samples were transferred and stored at -80°C until use. For nucleus extractions, colons were separated from the animals within 5 minutes of death and each colon was separately flushed similar to collecting tissue for ST. Approximately 0.5cm of tissue from three different colon regions was placed on a tissue and dried before transfer to a sterile dish to ensure all excess water was gently removed from the sample. Tissues were then placed in a 1.5 mL tube on dry ice and, upon freezing, transferred to −80°C until subsequent tissue processing.

tag: tissue

value: All colon

tag: strain

tag: Sex

value: male

tag: age


title: 4w, Distal, M, M3, Rep1

description: Library name: L9CN83_E1

library_source: transcriptomic

source_name: Distal colon

value: Distal colon

tag: genotype

tag: treatment

tag: batch


title: 4w, Proximal, M, M3, Rep2

description: Library name: L9CN83_C2

source_name: Proximal colon

value: Proximal colon


title: 4w, Distal, M, M3, Rep2

description: Library name: L9CN83_E2


title: 4w, Middle, M, M3, Rep1

description: Library name: L9CN83_D1

source_name: Middle colon

value: Middle colon


title: 4w, Proximal, M, M3, Rep1

description: Library name: L9CN83_C1


title: 12w, Distal, M, M2, Rep2

description: Library name: L9CN82_E2


title: 8w_Distal_M_M4

description: Library name: 8w_v2_rep2


title: 4w_Middle_M_M4

description: Library name: 4w_v2_rep5


title: 12w, Middle, M, M2, Rep1

description: Library name: L9CN82_D1


title: 12w, Middle, M, M2, Rep2

description: Library name: L9CN82_D2


title: 8w_Distal_M_M3

description: Library name: 8w_v2_rep1


title: 12w, Proximal, M, M2, Rep2

description: Library name: L9CN82_C2


title: 12w, Proximal, M, M2, Rep1

description: Library name: L9CN82_C1


title: 4w_Proximal_M_M4

description: Library name: 4w_v2_rep6


title: 4w_Distal_F_M2

description: Library name: 4w_v2_rep1

value: female


title: 4w, Middle, M, M4, Rep2

description: Library name: L9CN81_D2


title: 4w, Middle, M, M4, Rep1

description: Library name: L9CN81_D1


title: 8w, Middle, F, M3, Rep1

description: Library name: L9CN49_E1

value: F


title: 4w, Proximal, M, M4, Rep1

description: Library name: L9CN81_C1


title: 8w, Distal, F, M3, Rep1

description: Library name: L9CN49_C1


title: 4w, Middle, M, M5, Rep1

description: Library name: L9CN44_E1


title: 8w, Proximal, F, M3, Rep1

description: Library name: L9CN49_D1


title: 12w, Distal, M, M2, Rep1

description: Library name: L9CN82_E1


title: 4w, Proximal, M, M5, Rep2

description: Library name: L9CN44_D2


title: 12w, Middle, M, M3, Rep1

description: Library name: L9CN43_E1


title: 12w, Proximal, M, M3, Rep2

description: Library name: L9CN43_D2


title: 12w, Middle, M, M3, Rep2

description: Library name: L9CN43_E2


title: 4w, Distal, M, M5, Rep1

description: Library name: L9CN44_C1


title: 4w, Proximal, M, M5, Rep1

description: Library name: L9CN44_D1


title: 4w, Distal, M, M5, Rep2

description: Library name: L9CN44_C2


title: 12w, Proximal, M, M3, Rep1

description: Library name: L9CN43_D1


title: 4w, Distal, M, M4, Rep1

description: Library name: L9CN81_E2


title: 12w, Distal, M, M3, Rep1

description: Library name: L9CN43_C1


title: 12w, Distal, M, M3, Rep2

description: Library name: L9CN43_C2


title: 8w, Distal, F, M1, Rep3

description: Library name: L9CN40_C1


title: 8w, Middle, F, M1, Rep3

description: Library name: L9CN40_E1


title: 8w, Middle, F, M1, Rep4

description: Library name: L9CN40_E2


title: 8w, Proximal, F, M1, Rep4

description: Library name: L9CN40_D2


title: 8w, Proximal, F, M1, Rep3

description: Library name: L9CN40_D1


title: 8w, Distal, M, M3, Rep2

description: Library name: L9CN39_E2


title: 8w, Distal, M, M3, Rep1

description: Library name: L9CN39_E1


title: 4w, Proximal, M, M4, Rep2

description: Library name: L9CN81_C2


title: WT - AB

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description:
Library name: SHE6920A9
single cell RNA sequencing, 10X genomics

library_source: other

data_processing:
CellRanger multi run with chemistry = SC5P-R2
Single cell BCR sequencing analysis. B-cell receptor (BCR) repertoire analysis was conducted with the Immcantation framework, implemented in a Python environment (v.3.11.10)
Assembly: mm10-2020
Supplementary files format and content: CellRanger verison 7.0.1 outputs file for expression, HTO and BCR .
Supplementary files format and content: Only B-1 cells from peritoneal cavity labelled with hashtag antibodies (C0303, C0304, C0306, Biolegend) are used for the further VDJ and diversity analysis
Library strategy: CITE-seq

molecule: protein

source_name: foetal liver, bone marrow, spleen and peritoneal cavity

extract_protocol: B-1 progenitor cells (Lin-CD93+IgM-CD19+B220neg-lo) from E18.5 foetal livers (three foetal livers were pooled together as one replicate) or bone marrow from three 8 weeks mice, B-1 cells (CD19+B220neg-lo ) from peritoneal cavity and spleen from three 8 weeks old mice were sorted by the FACS Aria II cell sorting system (BD Immunocytometry Systems, San Jose, CA, USA)

tag: cell type

value: B-1 progenitor cells and B-1 cells

value: WT

value: E18.5 and 8 weeks old


title: 8w, Distal, F, M1, Rep4

description: Library name: L9CN40_C2


title: 8w, Middle, M, M3, Rep1

description: Library name: L9CN39_D1


title: 8w, Proximal, F, M3, Rep2

description: Library name: L9CN49_D2


title: 8w, Proximal, M, M3, Rep2

description: Library name: L9CN39_C2


title: 4w, Middle, M, M5, Rep2

description: Library name: L9CN44_E2


title: 4w, Distal, F, M4, Rep2

description: Library name: L9CN37_E2


title: 4w, Distal, F, M4, Rep1

description: Library name: L9CN37_E1


title: 8w, Proximal, M, M3, Rep1

description: Library name: L9CN39_C1


title: 4w, Middle, F, M4, Rep1

description: Library name: L9CN37_D2


title: 4w, Proximal, F, M4, Rep1

description: Library name: L9CN37_C1


title: 4w, Proximal, F, M4, Rep2

description: Library name: L9CN37_C2


title: 4w, Proximal, F, M3, Rep2

description: Library name: L9CN36_C2


title: 4w, Distal, F, M3, Rep2

description: Library name: L9CN36_E2


title: 4w, Middle, F, M3, Rep2

description: Library name: L9CN36_D2


title: 4w, Middle, F, M3, Rep1

description: Library name: L9CN36_D1


title: 4w, Distal, F, M3, Rep1

description: Library name: L9CN36_E1


title: 4w, Proximal, F, M3, Rep1

description: Library name: L9CN36_C1


title: 4w, Distal, F, M2, Rep2

description: Library name: L9CN35_E2


title: 4w, Middle, F, M2, Rep2

description: Library name: L9CN35_D2


title: 4w, Middle, F, M2, Rep1

description: Library name: L9CN35_D1


title: 4w, Proximal, F, M2, Rep2

description: Library name: L9CN35_C2


title: 6w, Middle, F, M3, Rep2

description: Library name: L9CN33_D2


title: 6w, Proximal, F, M3, Rep2

description: Library name: L9CN33_C2


title: 4w, Distal, F, M2, Rep1

description: Library name: L9CN35_E1


title: 8w, Middle, M, M3, Rep2

description: Library name: L9CN39_D2


title: 6w, Distal, F, M2, Rep2

description: Library name: L9CN32_E2


title: 6w, Distal, F, M3, Rep2

description: Library name: L9CN33_E2


title: 6w, Middle, F, M3, Rep1

description: Library name: L9CN33_D1


title: 6w, Distal, F, M3, Rep1

description: Library name: L9CN33_E1


title: 6w, Middle, F, M2, Rep2

description: Library name: L9CN32_D2


title: 6w, Middle, F, M2, Rep1

description: Library name: L9CN32_D1


title: 6w, Proximal, F, M2, Rep2

description: Library name: L9CN32_C2


title: 6w, Middle, F, M4, Rep2

description: Library name: L9CN31_D2


title: 6w, Proximal, F, M4, Rep2

description: Library name: L9CN31_C2


title: 6w, Distal, F, M4, Rep1

description: Library name: L9CN31_E1


title: 6w, Middle, F, M4, Rep1

description: Library name: L9CN31_D1


title: 6w, Proximal, F, M4, Rep1

description: Library name: L9CN31_C1


title: 8w, Proximal, F, M2, Rep2

description: Library name: L9CN16_D2


title: 8w, Proximal, F, M2, Rep1

description: Library name: L9CN16_D1


title: 6w, Proximal, F, M2, Rep1

description: Library name: L9CN32_C1


title: 4w, Proximal, F, M2, Rep1

description: Library name: L9CN35_C1


title: 6w, Proximal, F, M3, Rep1

description: Library name: L9CN33_C1


title: 8w, Middle, F, M2, Rep2

description: Library name: L9CN16_E2


title: 8w, Distal, F, M2, Rep1

description: Library name: L9CN16_C1


title: 8w, Distal, F, M2, Rep2

description: Library name: L9CN16_C2


title: 12w, Distal, M, M1, Rep1

description: Library name: L9CN150_E1


title: 8w, Middle, F, M2, Rep1

description: Library name: L9CN16_E1


title: 12w, Distal, M, M1, Rep2

description: Library name: L9CN150_E2


title: 12w, Proximal, M, M1, Rep1

description: Library name: L9CN150_C1


title: 12w, Middle, M, M1, Rep1

description: Library name: L9CN150_D1


title: 4w, Distal, M, M2, Rep2

description: Library name: L9CN14_E2


title: 4w, Middle, M, M2, Rep1

description: Library name: L9CN14_D1


title: 4w, Distal, M, M2, Rep1

description: Library name: L9CN14_E1


title: 4w, Proximal, M, M2, Rep1

description: Library name: L9CN14_C1


title: 6w, Distal, F, M2, Rep1

description: Library name: L9CN32_E1


title: 4w, Proximal, M, M2, Rep2

description: Library name: L9CN14_C2


title: 12w, Proximal, M, M1, Rep2

description: Library name: L9CN150_C2


title: 6w, Distal, F, M4, Rep2

description: Library name: L9CN31_E2


title: 8w, Distal, M, M2, Rep2

description: Library name: L9CN148_E2


title: 8w, Middle, M, M2, Rep2

description: Library name: L9CN148_D2


title: 8w, Distal, M, M2, Rep1

description: Library name: L9CN148_E1


title: 8w, Middle, M, M2, Rep1

description: Library name: L9CN148_D1


title: 8w, Proximal, M, M2, Rep2

description: Library name: L9CN148_C2


title: 8w, Proximal, M, M2, Rep1

description: Library name: L9CN148_C1


title: 8w, Distal, M, M1, Rep2

description: Library name: L9CN141_E2


title: 8w, Middle, M, M1, Rep2

description: Library name: L9CN141_D2


title: 8w, Middle, M, M1, Rep1

description: Library name: L9CN141_D1


title: 8w, Distal, M, M1, Rep1

description: Library name: L9CN141_E1


title: 8w, Proximal, M, M1, Rep2

description: Library name: L9CN141_C2


title: 4w, Middle, M, M2, Rep2

description: Library name: L9CN14_D2


title: 8w, Proximal, M, M1, Rep1

description: Library name: L9CN141_C1


title: BHLHE40-overexpressing CD4 T cells, input1, CUT&RUN

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA85591

library_source: genomic

data_processing:
Sequencing was performed on NovaSeq X Plus platform in a 101+101-base paired-end mode.
Illumina RTA4 software was used for base calling.
Trimmomatic software was used for adapter trimming.
Bowtie 2 software was used for alignment.
Picard MarkDuplicates software was used for deduplication.
MACS2 software was used for pileup and peak calling.
deepTools bamCoverage software was used for convert bam file into bigwig file.
Assembly: hg19
Supplementary files format and content: Bigwig format files including genome coverage tracks
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Chromatin fragments bound by specific antibodies were isolated from human PBMC-derived CD4 T cells infected with lentivirus using the ChIC/CUT&RUN Assay Kit (Active Motif, Carlsbad, CA, USA).
According to the manufacturer's instructions, library preparation was performed using a NEBNext Ultra II DNA Library Prep Kit for Ilumina (New England Biolabs, Ipswitch, MA, USA).

value: Blood

value: CD4 positive T cells overexpressing BHLHE40

tag: group

value: IgG

value: BHLHE40 overexpression


title: BHLHE40-overexpressing CD4 T cells, input2, CUT&RUN

description: Library name: GA85592


title: BHLHE40-overexpressing CD4 T cells, H3K27ac, CUT&RUN

description: Library name: GA85589


title: 6w, Distal, F, M1, Rep1

description: Library name: L9CN12_E1


title: 6w, Distal, F, M1, Rep2

description: Library name: L9CN12_E2


title: BHLHE40-overexpressing CD4 T cells, H3K27me3, CUT&RUN

description: Library name: GA85590


title: 6w, Middle, F, M1, Rep2

description: Library name: L9CN12_D2


title: BHLHE40-overexpressing CD4 T cells, BHLHE40, CUT&RUN

description: Library name: GA85587


title: RUNX2-overexpressing CD4 T cells, input2, CUT&RUN

description: Library name: GA85586

value: CD4 positive T cells overexpressing RUNX2

value: RUNX2 overexpression


title: BHLHE40-overexpressing CD4 T cells, RUNX2, CUT&RUN

description: Library name: GA85588


title: RUNX2-overexpressing CD4 T cells, input1, CUT&RUN

description: Library name: GA85585


title: RUNX2-overexpressing CD4 T cells, H3K27me3, CUT&RUN

description: Library name: GA85584


title: 6w, Proximal, F, M1, Rep2

description: Library name: L9CN12_C2


title: 6w, Proximal, F, M1, Rep1

description: Library name: L9CN12_C1


title: 6w, Distal, M, M4, Rep2

description: Library name: L8CN183_E2

value: M


title: RUNX2-overexpressing CD4 T cells, H3K27ac, CUT&RUN

description: Library name: GA85583


title: 6w, Distal, M, M4, Rep1

description: Library name: L8CN183_E1


title: RUNX2-overexpressing CD4 T cells, RUNX2, CUT&RUN

description: Library name: GA85582


title: 6w, Middle, M, M4, Rep2

description: Library name: L8CN183_D2


title: 6w, Proximal, M, M4, Rep2

description: Library name: L8CN183_C2


title: 6w, Middle, M, M4, Rep1

description: Library name: L8CN183_D1


title: CD12_CITE, ADT,HTO-derived cDNA

description: Library name: GA89195

data_processing:
Sequencing was performed on NovaSeq X Plus platform in 51+90, 51+91 or 151+151 base paired-end mode.
Illumina Real Time Analysis v4 (RTA4) software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-8.0.1 or 9.0.1, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: refdata-gex-GRCh38-2024-A
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format files including filtered counts data for each gene (or tag sequence) and cell (barcode) combination
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 format files including raw counts data for each gene (or tag sequence) and cell (barcode) combination
Supplementary files format and content: airr_rearrangement.tsv : tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv : comma-delimited text file including the TCR clonotype information
Library strategy: CITE-seq

source_name: inflamed colon, mildly inflamed colon, mesenteric lymph nodes, blood

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. Antibody-derived tag (ADT), hashtag oligonucleotides (HTO) or cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Next GEM Single Cell 5' Reagent Kits v3 with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping User Guide.

value: CD4+ T cells

tag: disease

value: Crohn's disease

tag: library type

value: ADT,HTO


title: CD12_CITE, TCR-derived cDNA

description: Library name: GA89194

molecule: total RNA

value: inflamed colon, mildly inflamed colon, mesenteric lymph nodes, blood

value: TCR V(D)J


title: 6w, Proximal, M, M4, Rep1

description: Library name: L8CN183_C1

value: Proximal colon


title: CD12_CITE, mRNA-derived cDNA

description: Library name: GA89193

value: mRNA


title: 6w, Distal, M, M2, Rep2

description: Library name: L8CN182_E2

value: Distal colon


title: CD11_CITE, ADT,HTO-derived cDNA

description: Library name: GA94532


title: 6w, Distal, M, M2, Rep1

description: Library name: L8CN182_E1


title: 6w, Middle, M, M2, Rep2

description: Library name: L8CN182_D2

value: Middle colon


title: CD11_CITE, TCR-derived cDNA

description: Library name: GA94531


title: 6w, Proximal, M, M2, Rep1

description: Library name: L8CN182_C1


title: 6w, Proximal, M, M2, Rep2

description: Library name: L8CN182_C2


title: CD10_CITE, ADT,HTO-derived cDNA

description: Library name: GA96536


title: 6w, Middle, F, M1, Rep1

description: Library name: L9CN12_D1

value: F


title: CD11_CITE, mRNA-derived cDNA

description: Library name: GA94530


title: 6w, Middle, M, M2, Rep1

description: Library name: L8CN182_D1


title: 6w, Middle, M, M1, Rep1

description: Library name: L8CN181_D1


title: CD10_CITE, TCR-derived cDNA

description: Library name: GA96535


title: 6w, Middle, M, M1, Rep2

description: Library name: L8CN181_D2


title: CD10_CITE, mRNA-derived cDNA

description: Library name: GA96534


title: HLA-DR_positive3, mRNA-derived cDNA

description: Library name: GA97031

data_processing:
Sequencing was performed on NovaSeq X Plus platform in a 101-base single-end mode.
Illumina RTA4 software was used for base calling.
Generated reads were mapped to the human (GRCh38) reference genome using HISAT2 ver.2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: inflamed colon

extract_protocol:
Total RNA was extracted from cells using the RNeasy Micro kit (QIAGEN N.V.) according to the enclosed instructions.
A full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio), following the instructions provided with the kit. Then, a NexteraXT DNA Library Preparation Kit (Illumina) was used to prepare the cDNA library.

value: inflamed colon

value: CD4+ CD103+ HLA-DR+ T cells


title: HLA-DR_positive2, mRNA-derived cDNA

description: Library name: GA97029


title: HLA-DR_positive1, mRNA-derived cDNA

description: Library name: GA97027


title: 6w, Proximal, M, M1, Rep1

description: Library name: L8CN181_C1


title: 12w, Distal, F, M3, Rep1

description: Library name: L8CN180_E2


title: HLA-DR_negative3, mRNA-derived cDNA

description: Library name: GA97032

value: CD4+ CD103+ HLA-DR- T cells


title: 6w, Proximal, M, M1, Rep2

description: Library name: L8CN181_C2


title: 12w, Middle, F, M3, Rep2

description: Library name: L8CN180_D2


title: RUNX2-overexpressing CD4 T cells, BHLHE40, CUT&RUN

description: Library name: GA85581

value: Blood


title: 12w, Middle, F, M3, Rep1

description: Library name: L8CN180_D1


title: 12w, Proximal, F, M3, Rep2

description: Library name: L8CN180_C2


title: HCT116 Xenograft Tumor, 3-oxo-LCA_3

city: Madison

first: TING

last: FU

state: Wisconsin

address: Attn: TING FU LAB, Suite/Rm:, 777 HIGHLAND AVE, RENNEBOHM HALL, ZN 3, MADISON, WI 53705-2222, United States

institute: University of Wisconsin-Madison

description:
Library name: Sample 6
Column name in raw _counts_All_Samples.txt: 3-oxo-LCA_3

data_processing:
Reads were mapped against the reference genome and transcript annotation (hg38) using STAR
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: HCT116 Xenograft tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen), 1.0μg of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared from three biological replicates for each experimental condition and sequenced on the Illumina NovaSeq X Plus Series using barcoded multiplexing and paired-end sequencing with a 150-bp read length.

value: HCT116 Xenograft tumor

value: WT


title: HLA-DR_negative2, mRNA-derived cDNA

description: Library name: GA97030


title: 12w, Proximal, F, M3, Rep1

description: Library name: L8CN180_C1


title: 12w, Distal, F, M1, Rep2

description: Library name: L8CN174_E2


title: HCT116 Xenograft Tumor, Vehicle_3

description:
Library name: Sample 3
Column name in raw _counts_All_Samples.txt: Ctl_3

value: Vehicle


title: 12w, Distal, F, M1, Rep1

description: Library name: L8CN174_E1


title: HCT116 Xenograft Tumor, 3-oxo-LCA_2

description:
Library name: Sample 5
Column name in raw _counts_All_Samples.txt: 3-oxo-LCA_2


title: HCT116 Xenograft Tumor, Vehicle_2

description:
Library name: Sample 2
Column name in raw _counts_All_Samples.txt: Ctl_2


title: HCT116 Xenograft Tumor, 3-oxo-LCA_1

description:
Library name: Sample 4
Column name in raw _counts_All_Samples.txt: 3-oxo-LCA_1


title: 12w, Middle, F, M1, Rep1

description: Library name: L8CN174_D1


title: 12w, Middle, F, M1, Rep2

description: Library name: L8CN174_D2


title: HCT116 Xenograft Tumor, Vehicle_1

description:
Library name: Sample 1
Column name in raw _counts_All_Samples.txt: Ctl_1


title: 12w, Proximal, F, M1, Rep2

description: Library name: L8CN174_C2


title: 12w, Proximal, F, M1, Rep1

description: Library name: L8CN174_C1


title: ICL - NE-3

city: Palo Alto

first: Michael

middle: Seth

last: Kapiloff

state: California

address: 1651 Page Mill Road, Room 2112

institute: Stanford University

description: Library name: ICL_NE_s38

data_processing:
The nf-core/rnaseq v3.18.0 (https://nf-co.re/rnaseq) pipeline was used to process the data.
The pipeline was executed with Nextflow v24.10.4 (https://www.nextflow.io/).
STAR v2.7.10a alignment and RSEM v1.3.1 transcript quantification were performed.
Assembly: mRatBN7.2 (Ensembl release-112)
Supplementary files format and content: tab-delimited text file includes expected raw counts for each sample

organism: Rattus norvegicus

source_name: Heart

growth_protocol: primary cultured rat adult cardiomoctes

extract_protocol:
Total RNA extracted  via RNeasy micro kit (Qiagen #74004)
The NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) was utilized according to the manufacturer's recommendations. ERCC RNA Spike-In Mix (ThermoFisher, #4456740) was added to normalized total RNA prior to library preparation following manufacturer’s protocol.

treatment_protocol: 2 days after adenoviral infection, cells were treated with 10nmol/L norepinephrine or vehicle control for 1 hour

value: Heart

tag: cell line

value: primary cultured adult cardiomyocytes

value: cardiomyocytes

value: Sprague-Dawley Rat

value: Adeno-ICL3-9-mCherry-Nesprin + treatment with 10nmol/L norepinephrine for 1 hour


title: Nb80- NE-3

description: Library name: Nb80_NE_s36

value: Adeno-Nb80-mCherry-Nesprin + treatment with 10nmol/L norepinephrine for 1 hour


title: 12w, Distal, F, M2, Rep2

description: Library name: L8CN173_E2


title: 12w, Distal, F, M2, Rep1

description: Library name: L8CN173_E1


title: ICL - BL-3

description: Library name: ICL_BL_s37

value: Adeno-ICL3-9-mCherry-Nesprin + treatment with water for 1 hour


title: 12w, Middle, F, M2, Rep2

description: Library name: L8CN173_D2


title: Control - NE-3

description: Library name: Control_NE_s34

value: Adeno-myc-mCherry-Nesprin + treatment with 10nmol/L norepinephrine for 1 hour


title: 12w, Proximal, F, M2, Rep1

description: Library name: L8CN173_C2

value: Proximal colon


title: 2yr, Proximal, F, M3, Rep6

description: Library name: 10015CN99_E2

value: F


title: Control - BL-3

description: Library name: Control_BL_s33

value: Adeno-myc-mCherry-Nesprin + treatment with water for 1 hour


title: NI - NE-3

description: Library name: NI_NE_s32

value: no Adenovirus transduction + treatment with 10nmol/L norepinephrine for 1 hour


title: 12w, Middle, F, M2, Rep1

description: Library name: L8CN173_D1

value: Middle colon


title: NI - BL-3

description: Library name: NI_BL_s31

value: no Adenovirus transduction + treatment with water for 1 hour


title: HLA-DR_negative1, mRNA-derived cDNA

description: Library name: GA97028

value: inflamed colon

value: CD4+ CD103+ HLA-DR- T cells


title: ICL - NE-2

description: Library name: ICL_NE_s28


title: 2yr, Proximal, F, M3, Rep4

description: Library name: 10015CN99_D2


title: ICL - BL-2

description: Library name: ICL_BL_s27


title: 2yr, Proximal, F, M3, Rep3

description: Library name: 10015CN99_D1


title: Nb80- NE-2

description: Library name: Nb80_NE_s26


title: Control - NE-2

description: Library name: Control_NE_s24


title: Control - BL-2

description: Library name: Control_BL_s23


title: 2yr, Proximal, F, M3, Rep2

description: Library name: 10015CN99_C2


title: 2yr, Distal, F, M3, Rep6

description: Library name: 10015CN98_E2

value: Distal colon


title: 2yr, Proximal, F, M3, Rep1

description: Library name: 10015CN99_C1


title: 2yr, Distal, F, M3, Rep5

description: Library name: 10015CN98_E1


title: NI - NE-2

description: Library name: NI_NE_s22

value: Heart


title: Nb80 - BL-3

description: Library name: Nb80_BL_s35

value: primary cultured adult cardiomyocytes

value: Adeno-Nb80-mCherry-Nesprin + treatment with water for 1 hour


title: 2yr, Distal, F, M3, Rep3

description: Library name: 10015CN98_D1


title: NI - BL-2

description: Library name: NI_BL_s21

value: cardiomyocytes

value: Sprague-Dawley Rat


title: ICL - NE-1

description: Library name: ICL_NE_s8

value: Adeno-ICL3-9-mCherry-Nesprin + treatment with 10nmol/L norepinephrine for 1 hour


title: 2yr, Distal, F, M3, Rep4

description: Library name: 10015CN98_D2


title: 2yr, Distal, F, M3, Rep2

description: Library name: 10015CN98_C2


title: ICL - BL-1

description: Library name: ICL_BL_s7

value: Adeno-ICL3-9-mCherry-Nesprin + treatment with water for 1 hour


title: 2yr, Distal, F, M3, Rep1

description: Library name: 10015CN98_C1


title: Nb80- NE-1

description: Library name: Nb80_NE_s6

value: Adeno-Nb80-mCherry-Nesprin + treatment with 10nmol/L norepinephrine for 1 hour


title: 6m, Distal, M, M3, Rep2

description: Library name: 10015CN94_E2

value: M


title: Nb80 - BL-1

description: Library name: Nb80_BL_s5


title: 2yr, Proximal, F, M3, Rep5

description: Library name: 10015CN99_E1

value: Proximal colon

value: F


title: Control - BL-1

description: Library name: Control_BL_s3

value: Adeno-myc-mCherry-Nesprin + treatment with water for 1 hour


title: Control - NE-1

description: Library name: Control_NE_s4

value: Adeno-myc-mCherry-Nesprin + treatment with 10nmol/L norepinephrine for 1 hour


title: 6m, Proximal, M, M3, Rep1

description: Library name: 10015CN94_D1


title: 6m, Distal, M, M3, Rep1

description: Library name: 10015CN94_D2


title: Nb80 - BL-2

description: Library name: Nb80_BL_s25


title: NI - NE-1

description: Library name: NI_NE_s2

value: no Adenovirus transduction + treatment with 10nmol/L norepinephrine for 1 hour


title: NI - BL-1

description: Library name: NI_BL_s1

value: no Adenovirus transduction + treatment with water for 1 hour


title: 6m, Middle, F, M7, Rep2

description: Library name: 10015CN93_E1

value: Middle colon


title: K562-IgG_ChIP-exo_5.0_control_(SPRI+TP)_rep2_236-211

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description: Library name: K562-IgG ChIP-exo 5.0 control (SPRI+TP) - Rep 2

data_processing:
Read alignment: Adapter sequences were first trimmed from the paired-end fastq files using fastp (v.0.23.2) (S. Chen et al. 2018). Paired-end reads were aligned using BWA-MEM (v.0.7.17) (Li and Durbin 2010) with parameter -M against the human (hg38) or mouse (mm10) genomes. BAM files were sorted using samtools sort (v.1.16.1) (Li et al. 2009) and duplicate read pairs were marked using Picard MarkDuplicates (v.2.24.1) with arguments REMOVE_DUPLICATES='false' ASSUME_SORTED='true' DUPLICATE_SCORING_STRATEGY='SUM_OF_BASE_QUALITIES' READ_NAME_REGEX='[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.'. BAM files were then filtered to remove reads that are duplicated, unmapped, or not in proper pairs using samtools view (v.1.16.1) with arguments -h -b -f 0x3 -F 0x404.
Peak-finding: Peaks for each individual ChIP-exo sample were determined using ChExMix (v0.52) (Yamada et al. 2018) using the following parameters: --threads 4 --expt ${expt} --ctrl ${ctrl} --format BAM --scalewin 1000 --noread2 --round 3 --minmodelupdateevents 50 --prlogconf -4 --alphascale 1.0 --betascale 0.05 --epsilonscale 0.2 --minroc 0.7 --minmodelupdaterefs 25 --pref -0.1 --numcomps 500 --win 250 --back ${back} --memepath ${memePath} --mememinw 6 --mememaxw 18 --seq ${genome} --exclude ${exclude} --q 0.01 --minfold 1.5. Blacklist files (the ${exclude} argument) were sourced from ENCODE. Background files (the ${back} argument) are 2nd-order Markov models created from the human or mouse genomes. Control samples (the ${ctrl} argument) represent pooled BAM files of all relevant control samples in each cell type, merged using samtools merge (v.1.16.1) (Li et al. 2009). This merger was performed across 13 K562 control samples (totaling 40,362,133 read pairs), 5 HepG2 control samples (13,990,398 read pairs), and 14 mES control samples (93,023,738 read pairs).
Assembly: hg38 and mm10
Supplementary files format and content: BED: ChExMix peak locations in BED format. If a BED file is not provided for a sample, either no peaks were found or peak-finding was not provided on the sample (e.g., for control files)
Supplementary files format and content: BW: bigwig files showing only the read1 5' positions after de-duplication. Only the 5' positions are shown because this reflects the exonuclease digestion stop point and is the most relevant position for ChIP-exo analysis. Positive strand and negative strand reads are separated into different bigwig files.

growth_protocol: K562 (CCL-243) and HepG2 (HB-8065) cells were obtained from the American Type Culture Collection (ATCC) handled and sub-cultured following the manufacturers recommendations. A17 A2Lox.cre mES cells (H2B-GFP_iGFP; iFoxA1.Flag) were cultured as previously described (Bulajić et al. 2020).

extract_protocol:
K562 suspension cells were counted and directly crosslinked in media or pelleted and resuspended for crosslinking in PBS. Adherent cells were washed with PBS, trypsinized, quenched and resuspended in media or PBS for counting and crosslinking. All cell counts were performed with a trypan blue dye exclusion test using a hemocytometer. For MO-ChIP-exo, 10 min of crosslinking with 1% formaldehyde was quenched with a 3M Tris pH 7.8. Variations of the crosslinking time, formaldehyde concentration and quencher were used as reported. Crosslinked cells were washed with PBS + 1X CPI and flash frozen in liquid nitrogen.
Crosslinked cell pellets (10 M cells per reaction) were subjected to cell and nuclear lysis. Lysates were resuspended in PBS + 1X CPI for sonication in a Diagenode Bioruptor Pico. The ‘Go & Shear’ setting was used with the validated parameters on the ‘Easy Mode’ for 30’’ON/OF with increasing cycles (1-11 as described). An aliquot of 15 μL (~0.5 M cells) was used to reverse crosslink and purify the DNA for a sonication assessment using the Agilent Tape Station D5000 kit. The sonicated crosslinked chromatin was pre-cleared before ChIP using high speed centrifugation (14k rpm at 4C for 15 min). ChIP antibodies [Anti-CTCF (Sigma 07-729), Anti-USF1-1B8 (DSHB USF1-1B8-6/13/19), IgG (Sigma i5006), Anti-GATA1 (Santa Cruz Biotechnology  SC-266), Anti-FoxA1 (Santa Cruz Biotechnology SC-101058), Anti-SOX2 (R&D AF2018)] were pre-conjugated to 50 μL Protein A or G Dynabeads (Invitrogen) before an overnight incubation with the antibody of interest at 4C. Bead-bound chromatin was washed and subjected to simultaneous End-repair and A-tailing with a subsequent TA ligation of the first HPLC-purified adapter using the NEBNext® Ultra™ II DNA Library Prep Kit. After washes, a fill-in reaction was performed using Phi29 DNA Polymerase (NEB). This reaction was followed by another wash and Lambda Exonuclease (NEB) digestion. Reverse crosslinking was performed overnight to release the DNA. Released DNA was purified using Mag-Bind® TotalPure NGS beads (Omega Bio-Tek) before ligating the 2nd HPLC-purified adapter using T4 DNA ligase (Qiagen). A DNA cleanup was performed using Mag-Bind® TotalPure NGS beads before PCR enrichment for 12 cycles. This was followed by size selection using SPRI select beads (Beckman Coulter) and an additional DNA cleanup to remove excess adapters. Completed libraries were analyzed in the Tape Station using High Sensitivity D5000 ScreenTape and Reagents. Finally, libraries were individually quantified through qPCR using NEBNext® Library Quantification Kit, For Illumina® (NEB) in an ABI StepOne Plus Real Time PCR System. Completed libraries were pooled for each sequencing run based on their concentration and read allocation with a 1% PhiX spike-in, treated with Illumina’s Free Adapter Blocking Reagent and cleaned up using Mag-Bind® TotalPure NGS beads. Final pool concentration was determined through qPCR using NEB Next® Library Quantification Kit, For Illumina® in an ABI StepOne Plus Real Time PCR System before diluting to 0.65 nM for loading. An Illumina NextSeq 2000 Sequencing System was used with a NextSeq™ 1000/2000 P2 XLEAP-SBS™ Reagent Kit (100 Cycle) for paired-end sequencing with 50 bp each for read1 and read2.

value: Leukemia

value: IgG Sigma i5006 Lot SLCB7084


title: 6m, Proximal, F, M7, Rep1

description: Library name: 10015CN93_D1


title: 6m, Middle, F, M7, Rep1

description: Library name: 10015CN93_C2


title: K562-IgG_ChIP-exo_5.0_control_(0.2X_Ab_SPRI+TP)_rep1_236-111

description: Library name: K562-IgG ChIP-exo 5.0 control (0.2X Ab, SPRI+TP) - Rep 1


title: 6m, Distal, F, M7, Rep1

description: Library name: 10015CN93_D2

value: Distal colon


title: K562-IgG_MO-ChIP-exo_control_rep1_099-111

description: Library name: K562-IgG MO-ChIP-exo control - Rep 1


title: 1yr, Distal, F, M2, Rep2

description: Library name: 10015CN92_E2


title: 1yr, Middle, F, M2, Rep2

description: Library name: 10015CN92_E1


title: 1yr, Distal, F, M2, Rep1

description: Library name: 10015CN92_D2


title: K562-IgG_ChIP-exo_5.0_control_(Alt_Lysis;_HPLC;_SPRI)_rep1_089-111

description: Library name: K562-IgG ChIP-exo 5.0 control (Alt Lysis; HPLC; SPRI) - Rep 1


title: K562-IgG_MO-ChIP-exo_control_(0.2%SDS)_rep1_091-111

description: Library name: K562-IgG MO-ChIP-exo control (0.2pSDS) - Rep 1


title: K562-IgG_MO-ChIP-exo_control_(SPRI_only)_rep1_090-111

description: Library name: K562-IgG MO-ChIP-exo control (SPRI only) - Rep 1


title: 1yr, Proximal, F, M2, Rep2

description: Library name: 10015CN92_D1


title: 1yr, Middle, F, M2, Rep1

description: Library name: 10015CN92_C2


title: K562-IgG_ChIP-exo_5.0_control_(SPRI)_rep2_076-111

description: Library name: K562-IgG ChIP-exo 5.0 control (SPRI) - Rep 2


title: K562-IgG_ChIP-exo_5.0_control_(SPRI)_rep1_075-111

description: Library name: K562-IgG ChIP-exo 5.0 control (SPRI) - Rep 1


title: 1yr, Proximal, F, M2, Rep1

description: Library name: 10015CN92_C1


title: 6m, Middle, M, M3, Rep2

description: Library name: 10015CN94_E1


title: K562-IgG_ChIP-exo_5.0_control_rep2_047-111

description: Library name: K562-IgG ChIP-exo 5.0 control - Rep 2


title: 1yr, Distal, M, M7, Rep2

description: Library name: 10015CN91_E2


title: 1yr, Middle, M, M7, Rep2

description: Library name: 10015CN91_E1


title: K562_(Frozen_Chromatin)-IgG_ChIP-exo_5.0_control_rep2_012-112

description: Library name: K562 (Frozen Chromatin)-IgG ChIP-exo 5.0 control - Rep 2


title: HepG2-IgG_MO-ChIP-exo_5.0_control_rep2_240-211

description: Library name: HepG2-IgG MO-ChIP-exo 5.0 control - Rep 2

value: Hepatocellular carcinoma


title: 6m, Middle, M, M3, Rep1

description: Library name: 10015CN94_C2


title: HepG2-IgG_MO-ChIP-exo_5.0_control_rep1_240-111

description: Library name: HepG2-IgG MO-ChIP-exo 5.0 control - Rep 1


title: 1yr, Proximal, M, M7, Rep2

description: Library name: 10015CN91_D1


title: 1yr, Distal, M, M7, Rep1

description: Library name: 10015CN91_D2


title: HepG2_(Frozen_Chromatin)-IgG_ChIP-exo_5.0_control_rep2_026-112

description: Library name: HepG2 (Frozen Chromatin)-IgG ChIP-exo 5.0 control - Rep 2


title: 0d, Distal, F, M0, Rep4

description: Library name: 10015CN82_E2


title: 1yr, Middle, M, M7, Rep1

description: Library name: 10015CN91_C2


title: HepG2-CTCF_MO-ChIP-exo_rep3_239-411

description: Library name: HepG2-CTCF MO-ChIP-exo - Rep 3

value: Anti-CTCF Sigma 07-729 Lot 3905315


title: K562-IgG_ChIP-seq_control_(SPRI+TP)_rep1_105-111

description: Library name: K562-IgG ChIP-seq control (SPRI+TP) - Rep 1


title: 0d, Distal, F, M0, Rep3

description: Library name: 10015CN82_E1


title: HepG2-CTCF_MO-ChIP-exo_rep2_239-311

description: Library name: HepG2-CTCF MO-ChIP-exo - Rep 2


title: K562-USF1_MO-ChIP-exo_rep2_235-211

description: Library name: K562-USF1 MO-ChIP-exo - Rep 2

value: Anti-USF1-1B8 DSHB Lot 6/13/19


title: K562-USF1_MO-ChIP-exo_rep1_235-111

description: Library name: K562-USF1 MO-ChIP-exo - Rep 1


title: 1yr, Proximal, M, M7, Rep1

description: Library name: 10015CN91_C1


title: 0d, Distal, F, M0, Rep1

description: Library name: 10015CN82_D1


title: K562-CTCF_MO-ChIP-exo_(1_k_cells)_rep1_271-111

description: Library name: K562-CTCF MO-ChIP-exo (1 k cells) - Rep 1


title: K562-USF1_MO-ChIP-exo_(XL_in_PBS)_rep1_247-111

description: Library name: K562-USF1 MO-ChIP-exo (XL in PBS) - Rep 1


title: HepG2-CTCF_MO-ChIP-exo_rep1_239-211

description: Library name: HepG2-CTCF MO-ChIP-exo - Rep 1

value: Anti-CTCF Sigma 07-729 Lot 3858178


title: 0d, Proximal, F, M0, Rep1

description: Library name: 10015CN82_C1


title: K562-CTCF_MO-ChIP-exo_(10_k_cells)_rep1_270-111

description: Library name: K562-CTCF MO-ChIP-exo (10 k cells) - Rep 1


title: 0d, Distal, F, M0, Rep2

description: Library name: 10015CN82_D2


title: 2yr, Middle, F, M3, Rep5

description: Library name: 10015CN121_E1


title: K562-CTCF_MO-ChIP-exo_(1_M_cells)_rep2_281-211

description: Library name: K562-CTCF MO-ChIP-exo (1 M cells) - Rep 2

value: Anti-CTCF Sigma 07-729 Lot 4041658


title: K562-CTCF_MO-ChIP-exo_(100_k_cells)_rep1_269-111

description: Library name: K562-CTCF MO-ChIP-exo (100 k cells) - Rep 1


title: K562-CTCF_MO-ChIP-exo_(1_M_cells)_rep1_281-111

description: Library name: K562-CTCF MO-ChIP-exo (1 M cells) - Rep 1


title: 2yr, Middle, F, M3, Rep4

description: Library name: 10015CN121_D2


title: K562-CTCF_MO-ChIP-exo_(50_M_cells)_rep2_245-211

description: Library name: K562-CTCF MO-ChIP-exo (50 M cells) - Rep 2


title: 2yr, Middle, F, M3, Rep2

description: Library name: 10015CN121_C2


title: K562-CTCF_MO-ChIP-exo_(5_M_cells)_rep2_280-211

description: Library name: K562-CTCF MO-ChIP-exo (5 M cells) - Rep 2


title: 2yr, Middle, F, M3, Rep1

description: Library name: 10015CN121_C1


title: 1w, Distal, F, M2, Rep2

description: Library name: 10015CN120_E2


title: 2yr, Middle, F, M3, Rep3

description: Library name: 10015CN121_D1


title: K562-CTCF_MO-ChIP-exo_(5_M_cells)_rep1_280-111

description: Library name: K562-CTCF MO-ChIP-exo (5 M cells) - Rep 1


title: K562-CTCF_MO-ChIP-exo_(50_M_cells)_rep1_245-111

description: Library name: K562-CTCF MO-ChIP-exo (50 M cells) - Rep 1


title: 1w, Distal, F, M2, Rep1

description: Library name: 10015CN120_E1


title: K562-CTCF_MO-ChIP-exo_(GE)_rep2_279-211

description: Library name: K562-CTCF MO-ChIP-exo (GE) - Rep 2


title: 1w, Middle, F, M2, Rep1

description: Library name: 10015CN120_D1


title: 0d, Proximal, F, M0, Rep2

description: Library name: 10015CN82_C2


title: 1w, Middle, F, M2, Rep2

description: Library name: 10015CN120_D2


title: K562-CTCF_MO-ChIP-exo_(GE)_rep1_279-111

description: Library name: K562-CTCF MO-ChIP-exo (GE) - Rep 1


title: 1w, Proximal, F, M2, Rep2

description: Library name: 10015CN120_C2


title: 1w, Proximal, F, M2, Rep1

description: Library name: 10015CN120_C1


title: K562-CTCF_MO-ChIP-exo_(2X_Antibody)_rep2_278-211

description: Library name: K562-CTCF MO-ChIP-exo (2X Antibody) - Rep 2


title: K562-CTCF_MO-ChIP-exo_(NEB_Universal_Adapter)_rep2_103-111

description: Library name: K562-CTCF MO-ChIP-exo (NEB Universal Adapter) - Rep 2

value: Anti-CTCF Sigma 07-729 Lot 3749972


title: 1w, Middle, M, M4, Rep2

description: Library name: 10015CN119_D2

value: M


title: 2yr, Middle, F, M3, Rep6

description: Library name: 10015CN121_E2


title: K562-CTCF_MO-ChIP-exo_(NEB_Universal_Adapter)_rep1_102-111

description: Library name: K562-CTCF MO-ChIP-exo (NEB Universal Adapter) - Rep 1


title: 1w, Proximal, M, M4, Rep1

description: Library name: 10015CN119_C1

value: Proximal colon


title: 1w, Distal, M, M4, Rep1

description: Library name: 10015CN119_E1


title: K562-CTCF_MO-ChIP-exo_(4X_Dynabead)_rep2_277-211

description: Library name: K562-CTCF MO-ChIP-exo (4X Dynabead) - Rep 2


title: K562-CTCF_MO-ChIP-exo_(4X_Dynabead)_rep1_277-111

description: Library name: K562-CTCF MO-ChIP-exo (4X Dynabead) - Rep 1


title: 1w, Middle, M, M4, Rep1

description: Library name: 10015CN119_D1


title: 1w, Proximal, M, M4, Rep2

description: Library name: 10015CN119_C2


title: K562-CTCF_MO-ChIP-exo_(1st_Adapter_Ligation:_T4_Ligase)_rep4_230-111

description: Library name: K562-CTCF MO-ChIP-exo (1st Adapter Ligation: T4 Ligase) - Rep 4


title: K562-CTCF_MO-ChIP-exo_(1st_Adapter_Ligation:_T4_Ligase)_rep2_231-211

description: Library name: K562-CTCF MO-ChIP-exo (1st Adapter Ligation: T4 Ligase) - Rep 2


title: K562-CTCF_MO-ChIP-exo_(1st_Adapter_Ligation:_T4_Ligase)_rep3_231-311

description: Library name: K562-CTCF MO-ChIP-exo (1st Adapter Ligation: T4 Ligase) - Rep 3


title: K562-CTCF_MO-ChIP-exo_(2X_Antibody)_rep1_278-111

description: Library name: K562-CTCF MO-ChIP-exo (2X Antibody) - Rep 1


title: 1w, Distal, M, M6, Rep2

description: Library name: 10015CN118_E2


title: 1w, Distal, M, M6, Rep1

description: Library name: 10015CN118_E1


title: K562-CTCF_MO-ChIP-exo_(Klenow_Alternative_Fill-In)_rep3_233-311

description: Library name: K562-CTCF MO-ChIP-exo (Klenow Alternative Fill-In ) - Rep 3


title: 1w, Middle, M, M6, Rep1

description: Library name: 10015CN118_D1


title: 1w, Proximal, M, M6, Rep1

description: Library name: 10015CN118_C1


title: 1w, Proximal, M, M6, Rep2

description: Library name: 10015CN118_C2


title: K562-CTCF_MO-ChIP-exo_(11_cycles)_rep1_263-111

description: Library name: K562-CTCF MO-ChIP-exo (11 cycles ) - Rep 1


title: K562-CTCF_MO-ChIP-exo_(Klenow_Alternative_Fill-In)_rep1_233-111

description: Library name: K562-CTCF MO-ChIP-exo (Klenow Alternative Fill-In ) - Rep 1


title: 6m, Distal, F, M8, Rep1

description: Library name: 10015CN111_E1

value: F


title: K562-CTCF_MO-ChIP-exo_(10_cycles)_rep1_262-111

description: Library name: K562-CTCF MO-ChIP-exo (10 cycles ) - Rep 1


title: K562-CTCF_MO-ChIP-exo_(9_cycles)_rep1_261-111

description: Library name: K562-CTCF MO-ChIP-exo (9 cycles ) - Rep 1


title: 6m, Middle, F, M8, Rep1

description: Library name: 10015CN111_D1


title: 6m, Proximal, F, M8, Rep2

description: Library name: 10015CN111_C2


title: K562-CTCF_MO-ChIP-exo_(8_cycles)_rep1_161-111

description: Library name: K562-CTCF MO-ChIP-exo (8 cycles ) - Rep 1


title: 6m, Middle, F, M8, Rep2

description: Library name: 10015CN111_D2


title: K562-CTCF_MO-ChIP-exo_(1st_Adapter_Ligation:_T4_Ligase)_rep1_231-111

description: Library name: K562-CTCF MO-ChIP-exo (1st Adapter Ligation: T4 Ligase) - Rep 1


title: 6m, Proximal, F, M8, Rep1

description: Library name: 10015CN111_C1


title: K562-CTCF_MO-ChIP-exo_(7_cycles)_rep2_259-111

description: Library name: K562-CTCF MO-ChIP-exo (7 cycles ) - Rep 2


title: 1w, Middle, M, M6, Rep2

description: Library name: 10015CN118_D2


title: 6m, Distal, M, M4, Rep1

description: Library name: 10015CN110_E1


title: K562-CTCF_MO-ChIP-exo_(6_cycles)_rep2_258-111

description: Library name: K562-CTCF MO-ChIP-exo (6 cycles ) - Rep 2


title: 6m, Middle, M, M4, Rep2

description: Library name: 10015CN110_D2


title: K562-CTCF_MO-ChIP-exo_(Klenow_Alternative_Fill-In)_rep2_233-211

description: Library name: K562-CTCF MO-ChIP-exo (Klenow Alternative Fill-In ) - Rep 2


title: 6m, Middle, M, M4, Rep1

description: Library name: 10015CN110_D1


title: K562-CTCF_MO-ChIP-exo_(5_cycles)_rep2_257-111

description: Library name: K562-CTCF MO-ChIP-exo (5 cycles ) - Rep 2


title: K562-CTCF_MO-ChIP-exo_(5_cycles)_rep1_158-111

description: Library name: K562-CTCF MO-ChIP-exo (5 cycles ) - Rep 1


title: 6m, Proximal, M, M4, Rep1

description: Library name: 10015CN110_C1


title: 6m, Proximal, M, M4, Rep2

description: Library name: 10015CN110_C2


title: 0d, Distal, F, M1, Rep2

description: Library name: 10015CN109_E2


title: 0d, Distal, F, M1, Rep1

description: Library name: 10015CN109_E1


title: 0d, Middle, F, M1, Rep1

description: Library name: 10015CN109_D1


title: K562-CTCF_MO-ChIP-exo_(2_cycles)_rep2_255-111

description: Library name: K562-CTCF MO-ChIP-exo (2 cycles ) - Rep 2


title: K562-CTCF_MO-ChIP-exo_(3_cycles)_rep1_156-111

description: Library name: K562-CTCF MO-ChIP-exo (3 cycles ) - Rep 1


title: 0d, Proximal, F, M1, Rep2

description: Library name: 10015CN109_C2


title: K562-CTCF_MO-ChIP-exo_(8_cycles)_rep2_260-111

description: Library name: K562-CTCF MO-ChIP-exo (8 cycles ) - Rep 2


title: K562-CTCF_MO-ChIP-exo_(2_cycles)_rep1_155-111

description: Library name: K562-CTCF MO-ChIP-exo (2 cycles ) - Rep 1


title: 0d, Proximal, F, M1, Rep1

description: Library name: 10015CN109_C1


title: 6m, Distal, M, M4, Rep2

description: Library name: 10015CN110_E2


title: K562-CTCF_MO-ChIP-exo_(1_cycle)_rep1_154-111

description: Library name: K562-CTCF MO-ChIP-exo (1 cycle ) - Rep 1


title: 2yr, Middle, M, M1, Rep6

description: Library name: 10015CN105_E2


title: K562-CTCF_MO-ChIP-exo_(7_cycles)_rep1_160-111

description: Library name: K562-CTCF MO-ChIP-exo (7 cycles ) - Rep 1


title: K562-CTCF_MO-ChIP-exo_(XL_5min_in_PBS)_rep1_128-111

description: Library name: K562-CTCF MO-ChIP-exo (XL 5min in PBS) - Rep 1


title: 2yr, Middle, M, M1, Rep5

description: Library name: 10015CN105_E1


title: K562-CTCF_MO-ChIP-exo_(6_cycles)_rep1_159-111

description: Library name: K562-CTCF MO-ChIP-exo (6 cycles ) - Rep 1


title: 2yr, Middle, M, M1, Rep3

description: Library name: 10015CN105_D1


title: K562-CTCF_MO-ChIP-exo_(XL_5min_in_PBS_2X_Gly_Quench)_rep1_124-111

description: Library name: K562-CTCF MO-ChIP-exo (XL 5min in PBS, 2X Gly Quench) - Rep 1


title: K562-CTCF_MO-ChIP-exo_(XL_5min_in_PBS_1X_GlyP_Quench)_rep1_116-111

description: Library name: K562-CTCF MO-ChIP-exo (XL 5min in PBS, 1X GlyP Quench) - Rep 1


title: 2yr, Middle, M, M1, Rep2

description: Library name: 10015CN105_C2


title: 2yr, Middle, M, M1, Rep1

description: Library name: 10015CN105_C1


title: K562-CTCF_MO-ChIP-exo_(3_cycles)_rep2_156-112

description: Library name: K562-CTCF MO-ChIP-exo (3 cycles ) - Rep 2


title: K562-CTCF_MO-ChIP-exo_(3_cycles)_rep3_256-111

description: Library name: K562-CTCF MO-ChIP-exo (3 cycles ) - Rep 3


title: 2yr, Distal, M, M1, Rep5

description: Library name: 10015CN104_E1


title: K562-CTCF_MO-ChIP-exo_(0.1%_FA)_rep1_251-111

description: Library name: K562-CTCF MO-ChIP-exo (0.1p FA) - Rep 1


title: K562-CTCF_MO-ChIP-exo_(0.83%_FA)_rep1_228-111

description: Library name: K562-CTCF MO-ChIP-exo (0.83p FA) - Rep 1


title: 2yr, Distal, M, M1, Rep6

description: Library name: 10015CN104_E2


title: K562-CTCF_MO-ChIP-exo_(XL_5min_1X_GlyP_Quench)_rep2_146-112

description: Library name: K562-CTCF MO-ChIP-exo (XL 5min, 1X GlyP Quench) - Rep 2


title: 2yr, Distal, M, M1, Rep3

description: Library name: 10015CN104_D1


title: 2yr, Distal, M, M1, Rep2

description: Library name: 10015CN104_C2


title: K562-CTCF_MO-ChIP-exo_(XL_5min_1X_GlyP_Quench)_rep1_146-111

description: Library name: K562-CTCF MO-ChIP-exo (XL 5min, 1X GlyP Quench) - Rep 1


title: K562-CTCF_MO-ChIP-exo_(XL_in_PBS)_rep3_248-111

description: Library name: K562-CTCF MO-ChIP-exo (XL in PBS )- Rep 3


title: 2yr, Distal, M, M1, Rep4

description: Library name: 10015CN104_D2


title: K562-CTCF_MO-ChIP-exo_(XL_5min)_rep1_266-111

description: Library name: K562-CTCF MO-ChIP-exo (XL 5min ) - Rep 1


title: 2yr, Distal, M, M1, Rep1

description: Library name: 10015CN104_C1


title: K562-CTCF_MO-ChIP-exo_(1_cycle)_rep2_254-111

description: Library name: K562-CTCF MO-ChIP-exo (1 cycle ) - Rep 2


title: 2yr, Distal, M, M2, Rep2

description: Library name: 10015CN103_E2


title: 2yr, Middle, M, M1, Rep4

description: Library name: 10015CN105_D2


title: K562-CTCF_MO-ChIP-exo_(XL_in_PBS)_rep1_246-111

description: Library name: K562-CTCF MO-ChIP-exo (XL in PBS )- Rep 1


title: 2yr, Middle, M, M2, Rep2

description: Library name: 10015CN103_E1


title: K562-CTCF_MO-ChIP-exo_rep4_229-511

description: Library name: K562-CTCF MO-ChIP-exo - Rep 4


title: K562-CTCF_MO-ChIP-exo_rep5_157-111

description: Library name: K562-CTCF MO-ChIP-exo - Rep 5


title: K562-CTCF_MO-ChIP-exo_(XL_5min_in_PBS_1X_Gly_Quench)_rep1_120-111

description: Library name: K562-CTCF MO-ChIP-exo (XL 5min in PBS, 1X Gly Quench) - Rep 1

value: Anti-CTCF Sigma 07-729 Lot SLCB7084


title: 2yr, Proximal, M, M2, Rep2

description: Library name: 10015CN103_D1


title: K562-CTCF_MO-ChIP-exo_rep3_229-411

description: Library name: K562-CTCF MO-ChIP-exo - Rep 3


title: 2yr, Middle, M, M2, Rep1

description: Library name: 10015CN103_C2


title: 2yr, Proximal, M, M2, Rep1

description: Library name: 10015CN103_C1


title: K562-CTCF_MO-ChIP-exo_rep2_229-311

description: Library name: K562-CTCF MO-ChIP-exo - Rep 2


title: 2yr, Distal, M, M2, Rep1

description: Library name: 10015CN103_D2


title: K562-CTCF_MO-ChIP-exo_rep1_229-111

description: Library name: K562-CTCF MO-ChIP-exo - Rep 1


title: HepG2_(Frozen_Chromatin)-IgG_ChIP-exo_5.0_rep1_026-111

description: Library name: HepG2 (Frozen Chromatin)-IgG ChIP-exo 5.0 - Rep 1


title: HepG2-IgG_ChIP-exo_5.0_rep1_025-111

description: Library name: HepG2-IgG ChIP-exo 5.0 - Rep 1


title: 2yr, Proximal, M, M1, Rep4

description: Library name: 10015CN102_D2


title: HepG2_(Frozen_Chromatin)-FoxA1_ChIP-exo_5.0_rep1_024-111

description: Library name: HepG2 (Frozen Chromatin)-FoxA1 ChIP-exo 5.0 - Rep 1

value: Anti-FoxA1 Santa Cruz Biotechnology SC-101058 Lot A2721


title: 2yr, Proximal, M, M1, Rep5

description: Library name: 10015CN102_E1


title: 2yr, Proximal, M, M1, Rep3

description: Library name: 10015CN102_D1


title: 2yr, Proximal, M, M1, Rep6

description: Library name: 10015CN102_E2


title: HepG2-FoxA1_ChIP-exo_5.0_(Std_Desalting_Adapters)_rep1_023-111

description: Library name: HepG2-FoxA1 ChIP-exo 5.0 (Std Desalting Adapters)- Rep 1


title: K562-CTCF_MO-ChIP-exo_(XL_in_PBS)_rep2_246-211

description: Library name: K562-CTCF MO-ChIP-exo (XL in PBS )- Rep 2


title: 2yr, Proximal, M, M1, Rep1

description: Library name: 10015CN102_C1


title: 2yr, Proximal, M, M1, Rep2

description: Library name: 10015CN102_C2


title: 2yr, Distal, M, M3, Rep2

description: Library name: 10015CN100_E2


title: HepG2_(Frozen_Chromatin)-USF1_ChIP-exo_5.0_(SPRI_Beads)_rep1_019-111

description: Library name: HepG2 (Frozen Chromatin)-USF1 ChIP-exo 5.0 (SPRI Beads)- Rep 1


title: 2yr, Middle, M, M3, Rep1

description: Library name: 10015CN100_D1


title: HepG2-USF1_ChIP-exo_5.0_(SPRI_Beads)_rep1_016-111

description: Library name: HepG2-USF1 ChIP-exo 5.0 (SPRI Beads)- Rep 1


title: HepG2-USF1_ChIP-exo_5.0_(Std_Desalting_Adapters)_rep1_017-111

description: Library name: HepG2-USF1 ChIP-exo 5.0 (Std Desalting Adapters)- Rep 1


title: 2yr, Proximal, M, M3, Rep2

description: Library name: 10015CN100_C2


title: 2yr, Proximal, M, M3, Rep1

description: Library name: 10015CN100_C1


title: 2yr, Middle, M, M3, Rep2

description: Library name: 10015CN100_D2


title: HepG2_(Frozen_Chromatin)-USF1_ChIP-exo_5.0_rep1_018-111

description: Library name: HepG2 (Frozen Chromatin)-USF1 ChIP-exo 5.0 - Rep 1


title: HepG2-USF1_ChIP-exo_5.0_rep1_015-111

description: Library name: HepG2-USF1 ChIP-exo 5.0 - Rep 1


title: 2yr, Distal, M, M3, Rep1

description: Library name: 10015CN100_E1


title: K562_(Frozen_Chromatin)-GATA1_ChIP-exo_5.0_rep2_014-111

description: Library name: K562 (Frozen Chromatin)-GATA1 ChIP-exo 5.0 - Rep 2

value: Anti-GATA1 SC-266 Lot C0518


title: K562_(Frozen_Chromatin)-CTCF_ChIP-exo_5.0_(SPRI_Beads)_rep2_013-111

description: Library name: K562 (Frozen Chromatin)-CTCF ChIP-exo 5.0 (SPRI Beads)- Rep 2

value: Anti-CTCF Sigma 07-729 Lot 3515588


title: 1yr, Middle, F, M5, Rep1

description: Library name: 10014CN110_D1

value: Middle colon


title: 1yr, Middle, F, M5, Rep2

description: Library name: 10014CN110_D2


title: K562_(Frozen_Chromatin)-IgG_ChIP-exo_5.0_rep1_012-111

description: Library name: K562 (Frozen Chromatin)-IgG ChIP-exo 5.0 - Rep 1

value: Leukemia


title: 1yr, Proximal, F, M5, Rep2

description: Library name: 10014CN110_C2


title: 1yr, Distal, F, M5, Rep1

description: Library name: 10014CN110_E1


title: K562-IgG_ChIP-exo_5.0_rep1_011-111

description: Library name: K562-IgG ChIP-exo 5.0 - Rep 1

value: IgG Sigma i5006 Lot SLCB7084


title: HepG2-FoxA1_ChIP-exo_5.0_rep1_021-111

description: Library name: HepG2-FoxA1 ChIP-exo 5.0 - Rep 1


title: 1yr, Distal, M, M6, Rep2

description: Library name: 10014CN109_E2

value: Distal colon


title: K562-GATA1_ChIP-exo_5.0_(Std_Desalting_Adapters)_rep1_009-111

description: Library name: K562-GATA1 ChIP-exo 5.0 (Std Desalting Adapters) - Rep 1


title: 1yr, Distal, M, M6, Rep1

description: Library name: 10014CN109_E1


title: K562-GATA1_ChIP-exo_5.0_(SPRI_Beads)_rep1_008-111

description: Library name: K562-GATA1 ChIP-exo 5.0 (SPRI Beads) - Rep 1


title: K562_(Frozen_Chromatin)-GATA1_ChIP-exo_5.0_rep1_010-111

description: Library name: K562 (Frozen Chromatin)-GATA1 ChIP-exo 5.0 - Rep 1


title: HepG2_(Frozen_Chromatin)-USF1_ChIP-exo_5.0_(Std_Desalting_Adapters)_rep1_020-111

description: Library name: HepG2 (Frozen Chromatin)-USF1 ChIP-exo 5.0 (Std Desalting Adapters) - Rep 1

value: Hepatocellular carcinoma


title: HepG2-FoxA1_ChIP-exo_5.0_(SPRI_Beads)_rep1_022-111

description: Library name: HepG2-FoxA1 ChIP-exo 5.0 (SPRI Beads)- Rep 1


title: K562-GATA1_ChIP-exo_5.0_rep1_007-111

description: Library name: K562-GATA1 ChIP-exo 5.0 - Rep 1


title: 1yr, Middle, M, M6, Rep2

description: Library name: 10014CN109_D2


title: 1yr, Middle, M, M6, Rep1

description: Library name: 10014CN109_D1


title: K562_(Frozen_Chromatin)-CTCF_ChIP-exo_5.0_(Std_Desalting_Adapters)_rep1_006-111

description: Library name: K562 (Frozen Chromatin)-CTCF ChIP-exo 5.0 (Std Desalting Adapters) - Rep 1


title: K562-CTCF_ChIP-exo_5.0_(Std_Desalting_Adapters)_rep1_003-111

description: Library name: K562-CTCF ChIP-exo 5.0 (Std Desalting Adapters)- Rep 1


title: K562_(Frozen_Chromatin)-CTCF_ChIP-exo_5.0_rep1_004-111

description: Library name: K562 (Frozen Chromatin)-CTCF ChIP-exo 5.0 - Rep 1


title: K562_(Frozen_Chromatin)-CTCF_ChIP-exo_5.0_(SPRI_Beads)_rep1_005-111

description: Library name: K562 (Frozen Chromatin)-CTCF ChIP-exo 5.0 (SPRI Beads)- Rep 1


title: 1yr, Proximal, M, M6, Rep1

description: Library name: 10014CN109_C1


title: 1yr, Distal, F, M7, Rep2

description: Library name: 10014CN107_E2


title: 1yr, Distal, F, M7, Rep1

description: Library name: 10014CN107_E1


title: 1yr, Proximal, M, M6, Rep2

description: Library name: 10014CN109_C2


title: 1yr, Proximal, F, M5, Rep1

description: Library name: 10014CN110_C1


title: 1yr, Middle, F, M7, Rep1

description: Library name: 10014CN107_D1


title: 1yr, Proximal, F, M7, Rep2

description: Library name: 10014CN107_C2


title: Sample 172 low flow low pressure

city: Seattle

first: Samuel

middle: G

last: Rayner

state: WA

address: 850 Republican Street

department: Medicine

institute: University of Washington

description:
Library name: 172-LF-LP_S12
GeneCounts1.tsv

data_processing:
Raw FASTQ files were quality-checked with FastQC.
Reads were aligned to the GRCh38 human reference genome using STAR aligner.
Gene-level counts were quantified using featureCounts.
Count normalization and differential expression analysis were performed using DESeq2 in R.
Assembly: GRCh38 (GENCODE v38)
Supplementary files format and content: Gene-level counts (raw and normalized) in tab-delimited text files

source_name: Distal Pulmonary Arteries

growth_protocol: PAECs were cultured within a culture chamber in EGM-2 (Lonza) to confluence, at 37 degrees and 5% CO2

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA quality was assessed using an Agilent Bioanalyzer.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina, with polyA selection, following the manufacturer's instructions.

treatment_protocol: Cells were exposed to shear stress (0, 3, or 20 dyn/cm²) and pressure (0 or 60 mmHg) for 24 hours within a resistor-coupled microfluidic platform.

value: Distal Pulmonary Arteries

value: Primary Human Cells

value: Pulmonary artery endothelial cells

value: CHD-PAH

value: Female

tag: pressure

value: Low

tag: shear

tag: round


title: K562-CTCF_ChIP-exo_5.0_rep1_001-111

description: Library name: K562-CTCF ChIP-exo 5.0 - Rep 1


title: Sample 172 static

description:
Library name: 172-Static_S13
GeneCounts1.tsv

value: Static


title: 1yr, Proximal, F, M7, Rep1

description: Library name: 10014CN107_C1

value: Proximal colon

value: F


title: 2w, Middle, M, M3, Rep1

description: Library name: 10014CN106_C2

value: M


title: Sample 172 high flow low pressure

description:
Library name: 172-HFLP_S45
GeneCounts1.tsv

value: High


title: Sample 172 low flow high pressure

description:
Library name: 172-LF-HP_S11
GeneCounts1.tsv


title: 2w, Proximal, M, M3, Rep1

description: Library name: 10014CN106_C1


title: Sample 172 high flow high pressure

description:
Library name: 172-HF-HP_S10
GeneCounts1.tsv


title: Sample 170 static

description:
Library name: 170-Static_S29
GeneCounts1.tsv


title: Sample 170 low flow low pressure

description:
Library name: 170-LF-LP_S30
GeneCounts1.tsv


title: 6m, Distal, F, M2, Rep2

description: Library name: 10007CN72_E2


title: 6m, Distal, F, M2, Rep1

description: Library name: 10007CN72_E1


title: 1yr, Middle, F, M7, Rep2

description: Library name: 10014CN107_D2


title: 6m, Middle, F, M2, Rep1

description: Library name: 10007CN72_D1


title: Sample 170 high flow low pressure

description:
Library name: 170-HF-LP_S32
GeneCounts1.tsv


title: 6m, Proximal, F, M2, Rep2

description: Library name: 10007CN72_C2


title: K562-CTCF_ChIP-exo_5.0_(SPRI_Beads)_rep1_002-111

description: Library name: K562-CTCF ChIP-exo 5.0 (SPRI Beads)- Rep 1

value: Anti-CTCF Sigma 07-729 Lot 3515588


title: Sample 170 high flow high pressure

description:
Library name: 170-HFHP_S33
GeneCounts1.tsv


title: 6m, Middle, F, M2, Rep2

description: Library name: 10007CN72_D2

value: Middle colon


title: larva_head_33dpf_WT_rep3

city: Chicago

first: Erica

last: Davis

state: IL

address: 225 E Chicago Avenue

department: Advanced Center for Translational and Genetic Medicine (ACT-GeM)

institute: Ann & Robert H Lurie Children's Hospital of Chicago

description: Library name: WT-3

data_processing:
FASTQ read quality, was evaluated using FastQC. Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt. Trimmed reads were aligned to the Danio rerio genome (danRer11) using STAR. Read counts for each gene were calculated using htseq-count9 in conjunction with a gene annotation file for danRer11 obtained from Ensembl. Normalization and differential expression were calculated using DESeq2 that employs the Wald test. The cut-off for determining significantly differentially expressed genes was an FDR-adjusted p-value less than 0.05 using the Benjamini-Hochberg method. Pathway and process enrichment analysis was carried out with the following ontology sources: GO Biological Processes, KEGG Pathway, Reactome Gene Sets, and WikiPathways. All genes in the genome were used as the enrichment background. Ontology terms with a p-value <0.01, a minimum count of 3, and an enrichment factor >1.5 are collected and grouped into clusters based on their membership similarities. More specifically, p-values are calculated based on the cumulative hypergeometric distribution. Kappa scores are used as the similarity metric when performing hierarchical clustering on the enriched terms, and sub-trees with a similarity of  > 0.3 are considered a cluster. The most statistically significant term within a cluster is chosen to represent the cluster.
Assembly: danRer11
Supplementary files format and content: The processesd files are in Excel sheet format. The differentially expressed genes file include differential expression values (Log2Fold change) along with statistical significance. The gene ontology fole includes fold change difference.

organism: Danio rerio

growth_protocol: Embryos were obtained from natural matings of adult snapin heterozygous 9bpdel-2bpins mutants zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media (0.3 g/L NaCl, 75 mg/L CaSO4, 37.5 mg/L NaHC03, 0.003% methylene blue) at 28°C until 5 dpf. At 3 dpf, and before transfer to the aquatics system, larvae were genotyped with the ZEG (zebrafish embryo genotyper). From 5 dpf onward, larvae were transferred to the main aquatics system and fed commercially available solid particles suitable for their developmental stage.

extract_protocol:
Total RNA was extracted from zebrafish heads homogenized in Trizol (Thermo Fisher Scientific) according to manufacturer's instructions. Total RNA samples were evaluated for quality using RIN scores generated from an Agilent Bioanalyzer 2100. RNA quantity was determined with Qubit fluorometer.
The Illumina Stranded mRNA Library Preparation Kit was used to prepare sequencing libraries from 100 ng of high-quality RNA samples (RIN>9.5). The Kit procedure was performed without modifications. This procedure includes mRNA purification and fragmentation, cDNA synthesis, 3’ end adenylation, Illumina adapter ligation, library PCR amplification and validation.

tag: developmental stage

value: 33 days post-fertilization

value: wild type


title: 6m, Proximal, F, M2, Rep1

description: Library name: 10007CN72_C1


title: larva_head_33dpf_WT_rep2

description: Library name: WT-2


title: larva_head_33dpf_WT_rep1

description: Library name: WT-1


title: Sample 168 static

description:
Library name: 168-Static_S19
GeneCounts1.tsv

value: IPAH


title: larva_head_33dpf_Mutant_rep2

description: Library name: Mut-2

value: snapin 9bpdel-2bpins homozygous


title: Sample 168 low flow low pressure

description:
Library name: 168-LF-LP_S20
GeneCounts1.tsv

value: Distal Pulmonary Arteries


title: 6m, Distal, M, M2, Rep1

description: Library name: 10007CN71_E2

value: Distal colon


title: 6m, Middle, M, M2, Rep2

description: Library name: 10007CN71_D2


title: Sample 168 low flow high pressure

description:
Library name: 168-LF-HP_S21
GeneCounts1.tsv

value: Primary Human Cells

value: Pulmonary artery endothelial cells


title: larva_head_10dpf_WT_rep3

description: Library name: WT-3

growth_protocol: Embryos were obtained from natural matings of adult snapin heterozygous 9bpdel-2bpins mutants zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media (0.3 g/L NaCl, 75 mg/L CaSO4, 37.5 mg/L NaHC03, 0.003% methylene blue) at 28°C until 10 dpf. From 5-10 dpf, larvae were fed dry food 2x daily and media was changed.

value: 10 days post-fertilization


title: 6m, Middle, M, M2, Rep1

description: Library name: 10007CN71_D1


title: larva_head_33dpf_Mutant_rep4

description: Library name: Mut-4


title: larva_head_10dpf_Mutant_rep2

description: Library name: MT-2


title: larva_head_10dpf_WT_rep2

description: Library name: WT-2


title: Sample 168 high flow low pressure

description:
Library name: 168-HF-LP_S22
GeneCounts1.tsv

value: Female

value: Low


title: 6m, Proximal, M, M2, Rep2

description: Library name: 10007CN71_C2

value: Proximal colon


title: Sample 116 static

description:
Library name: 116-Static_S14
GeneCounts1.tsv

value: Control Failed Donor

value: Static


title: BMDMs, Imi, rep3

city: Chengdu

first: Hongzhi

last: He

address: No.14,3Rd Section Of Ren Min Nan Rd.

country: China

institute: West China School/Hospital of Stomatology, Sichuan University

description:
Library name: Sample 9
Column name in gene.count.matrix.annot.txt: Imi_3

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach. To identify DEGs (differential expression genes) between two different groups, the expression level of each gene was calculated according to the transcripts per million reads method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2, DEGs with |log2 (foldchange)|≥1 and P-adjust ≤0.05 were considered to be significantly different expressed genes. Differential expression and functional enrichment analyses including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted using the Majorbio Cloud Platform (www.majorbio.com).
Assembly: GRCm39
Supplementary files format and content: gene count values for each sample

source_name: bone marrow

growth_protocol: In a 12-well plate, 1.5×106 BMDMs are incubated for 24h at 37°C.

extract_protocol:
Total RNA was extracted from tissues using TRIzol® Reagent (ThermoFisher, MA, USA). according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). RNA degradation and contamination was monitored on 1% agarose gels. Then RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥8.0, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
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). The ranscriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer (2 × 150bp read length).

treatment_protocol: BMDMs are  treated with DMSO (negative control), LPS (positive control) or 1 μg/mL imiquimod in three replicate. Each group contained three independent samples.

value: bone marrow

value: primary cell

value: macrophage

value: Imi


title: Sample 168 high flow high pressure

description:
Library name: 168-HFHP_S23
GeneCounts1.tsv

value: High


title: 6m, Proximal, M, M2, Rep1

description: Library name: 10007CN71_C1

value: M


title: larva_head_10dpf_Mutant_rep3

description: Library name: MT-3

value: snapin 9bpdel-2bpins homozygous


title: 8w, Middle, F, M1, Rep1

description: Library name: 10005CN88_E1

value: Middle colon

value: F


title: 8w, Middle, F, M1, Rep2

description: Library name: 10005CN88_E2


title: BMDMs, LPS, rep2

description:
Library name: Sample 5
Column name in gene.count.matrix.annot.txt: LPS_2

value: LPS


title: BMDMs, LPS, rep3

description:
Library name: Sample 6
Column name in gene.count.matrix.annot.txt: LPS_3


title: BMDMs, Imi, rep2

description:
Library name: Sample 8
Column name in gene.count.matrix.annot.txt: Imi_2


title: Sample 170 low flow high pressure

description:
Library name: 170-LF-HP_S31
GeneCounts1.tsv

value: Distal Pulmonary Arteries

value: Primary Human Cells

value: Pulmonary artery endothelial cells

value: CHD-PAH


title: BMDMs, LPS, rep1

description:
Library name: Sample 4
Column name in gene.count.matrix.annot.txt: LPS_1


title: BMDMs, DMSO, rep3

description:
Library name: Sample 3
Column name in gene.count.matrix.annot.txt: Ctrl_3

value: DMSO


title: BMDMs, Imi, rep1

description:
Library name: Sample 7
Column name in gene.count.matrix.annot.txt: Imi_1


title: 8w, Proximal, F, M1, Rep2

description: Library name: 10005CN88_D2

value: Proximal colon


title: BMDMs, DMSO, rep1

description:
Library name: Sample 1
Column name in gene.count.matrix.annot.txt: Ctrl_1


title: enteric neural crest cells sample10 treated with FGL2 recombination protein

city: Jinan

first: Jichang

last: Han

state: Shandong

address: 107 Wenhua Xi Road

department: Department of Pediatric Surgery

institute: Qilu hospital of Shandong University

description:
Library name: Sample10
F-5

data_processing:
Raw paired-end reads were quality controlled using Fastp (v0.18.0) to remove adapter sequences, low-quality reads, and reads containing more than 10% ambiguous bases (N)
Ribosomal RNA (rRNA) sequences were removed by aligning reads to a species-specific rRNA database using Bowtie2 (v2.2.8) with no mismatches allowed
Clean reads aligned to mouse genome (GRCm39, Ensembl release 111) using HISAT2 (v2.1.0)
Transcript assembly was performed with StringTie (v1.3.4)
Gene-level expression quantification was performed using RSEM (v1.2.19), generating estimated counts for each gene in each sample
Assembly: GRCm39
Supplementary files format and content: The processed data file (FGL2_gene_estimated_counts_matrix.txt). Each value represents the RSEM-estimated number of reads assigned to the corresponding gene in the specified sample. Values are not normalized for sequencing depth or gene length

source_name: Colon

extract_protocol:
This dataset comprises bulk RNA sequencing data from primary mouse enteric neural crest cells (ENCCs) stimulated with fibrinogen-like protein 2 (FGL2) or left untreated as controls. ENCCs were isolated from embryonic day 14–15 C57BL/6J mice and cultured under defined conditions to ensure >95% expression of P75 and nestin markers. Total RNA was extracted using TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality and integrity were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and verified by RNase-free agarose gel electrophoresis.
Poly(A)+ mRNA was enriched from total RNA using Oligo(dT) beads. The enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse-transcribed into cDNA using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end-repaired, A-tailed, and ligated to Illumina sequencing adapters. Adapter-ligated fragments were purified with AMPure XP Beads (1.0×) and PCR-amplified. The final cDNA libraries were sequenced on an Illumina NovaSeq 6000 platform (paired-end, 2 × 150 bp) by Gene Denovo Biotechnology Co., Ltd. (Guangzhou, China).

value: Colon

value: enteric neural crest cells

value: FGL2 recombination protein


title: 8w, Proximal, F, M1, Rep1

description: Library name: 10005CN88_D1


title: BMDMs, DMSO, rep2

description:
Library name: Sample 2
Column name in gene.count.matrix.annot.txt: Ctrl_2

value: bone marrow

value: primary cell

value: macrophage


title: larva_head_33dpf_Mutant_rep1

description: Library name: Mut-1

value: 33 days post-fertilization


title: enteric neural crest cells sample9 treated with FGL2 recombination protein

description:
Library name: Sample9
F-4


title: Sample 116 low flow high pressure

description:
Library name: 116-LF-HP_S16
GeneCounts1.tsv

value: Control Failed Donor

value: Female

value: Low

value: High


title: Sample 116 low flow low pressure

description:
Library name: 116-LF-LP_S15
GeneCounts1.tsv

value: Distal Pulmonary Arteries


title: Sample 116 high flow low pressure

description:
Library name: 116-HF-LP_S17
GeneCounts1.tsv

value: Primary Human Cells


title: enteric neural crest cells sample8 treated with FGL2 recombination protein

description:
Library name: Sample8
F-3


title: enteric neural crest cells sample7 treated with FGL2 recombination protein

description:
Library name: Sample7
F-2


title: 8w, Distal, F, M1, Rep2

description: Library name: 10005CN88_C2

value: Distal colon

value: F


title: Sample 112 static

description:
Library name: 112-Static_S39
GeneCounts1.tsv

value: Pulmonary artery endothelial cells

value: Static


title: 8w, Distal, F, M1, Rep1

description: Library name: 10005CN88_C1


title: Sample 112 low flow low pressure

description:
Library name: 112-LF-LP_S40
GeneCounts1.tsv


title: enteric neural crest cells sample6 treated with FGL2 recombination protein

description:
Library name: Sample6
F-1

value: Colon


title: enteric neural crest cells sample5 without treatment

description:
Library name: Sample5
NC-5

value: enteric neural crest cells

value: control


title: enteric neural crest cells sample4 without treatment

description:
Library name: Sample4
NC-4


title: 3w, Distal, M, M5, Rep1

description: Library name: 10005CN85_E1

value: M


title: Sample 112 low flow high pressure

description:
Library name: 112-LF-HP_S41
GeneCounts1.tsv


title: enteric neural crest cells sample3 without treatment

description:
Library name: Sample3
NC-3


title: 3w, Distal, M, M5, Rep2

description: Library name: 10005CN85_E2


title: Sample 112 high flow low pressure

description:
Library name: 112-HF-LP_S42
GeneCounts1.tsv


title: enteric neural crest cells sample1 without treatment

description:
Library name: Sample1
NC-1


title: enteric neural crest cells sample2 without treatment

description:
Library name: Sample2
NC-2


title: Sample 116 high flow high pressure

description:
Library name: 116-HFHP_S18
GeneCounts1.tsv


title: Sample 112 high flow high pressure

description:
Library name: 112-HFHP_S43
GeneCounts1.tsv


title: 3w, Middle, M, M5, Rep2

description: Library name: 10005CN85_D2

value: Middle colon


title: Sample 107 static

description:
Library name: 107-Static_S9
GeneCounts1.tsv

value: Male


title: PBMCs from Mouse control replicate2

city: Aarhus

first: Soren

last: Paludan

address: CF Møllers Alle 6, Building 1115

department: Biomedicine

country: Denmark

institute: Aarhus university

description: Library name: Mouse_UT_2

data_processing:
To ensure high data quality, Trim Galore was used in paired-end mode to remove low-quality base pairs and adaptor sequences from the libraries. Subsequently, sequencing reads were aligned to their respective reference genomes using the STAR aligner.
Assembly: GCF_000001405.40_GRCh38, GCF_000001635.27_GRCm39, ASM359739v1 and rGopEvg1_v1.p, ASM1834038v1, and bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: Tab-separated count matrix

source_name: PBMC

extract_protocol:
RNA harvested using Rneasy mini plus kit (Qiagen) was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit

value: PBMC

value: PBMCs from Mouse control


title: 3w, Middle, M, M5, Rep1

description: Library name: 10005CN85_D1


title: PBMCs from Mouse control replicate1

description: Library name: Mouse_UT_1


title: Mouse PBMCs treated with cGAMP replicate3

description: Library name: Mouse_cGAMP_3

value: Mouse PBMCs treated with cGAMP


title: 3w, Proximal, M, M5, Rep2

description: Library name: 10005CN85_C2

value: Proximal colon


title: Mouse PBMCs treated with cGAMP replicate1

description: Library name: Mouse_cGAMP_1


title: 3w, Proximal, M, M5, Rep1

description: Library name: 10005CN85_C1


title: Sample 107 low flow high pressure

description:
Library name: 107-LF-HP_S6
GeneCounts1.tsv

value: Control Failed Donor

value: Low

value: High


title: Sample 107 low flow low pressure

description:
Library name: 107-LF-LP_S8
GeneCounts1.tsv

value: Distal Pulmonary Arteries

value: Primary Human Cells


title: 3w, Distal, F, M1, Rep2

description: Library name: 10005CN84_E2

value: Distal colon

value: F


title: Sample 107 high flow low pressure

description:
Library name: 107-HF-LP_S7
GeneCounts1.tsv

value: Pulmonary artery endothelial cells


title: 3w, Distal, F, M1, Rep1

description: Library name: 10005CN84_E1


title: Frontal cortex, batch 3, excision, sample 5

city: East victoria Park

first: Amira

last: Allahham

state: Perth, WA

address: 2/88 Dane st.

country: Australia

institute: Fiona Wood Foundation

description: Library name: E5P6

data_processing:
The RNA sequencing data was processed on an external Linux server using the sequence shown in Figure 2. Genome data was sent from AGRF, downloaded on the server and processed using MATE Terminal (Version 1.8.0), and R studio version (Version 3.6.1). Poor quality reads were checked using FastQC (Version 0.11.3) where the first 15 base pairs were trimmed using the fastp software (Chen et al., 2018). Raw RNA sequences were aligned with the reference genome Mus musculus GRCm38.102 from Ensembl (Cunningham et al., 2018) (http://asia.ensembl.org/Mus_musculus/Info/Index) using the STAR read aligner (Version 2.7) (Dobin et al., 2013) to generate BAM files to represent the aligned sequences. Rows that have little or no information about gene information were prefiltered from the dataset and a minimal filtering rule was applied where rows of the DESeqDataSet, a subclass of SummarizedExperiment used to store input values, calculations and results of an analysis of differential expression, were removed because they have no counts, or only have a single count across all samples were removed. The quality of data was assessed before the analysis where the distribution of the raw read counts was plotted using a bar plot, then it was transformed using regularised log (rlog) which transforms the count data to the log2 scale in a way that minimizes differences between samples for rows with small counts, normalising it with respect to library size. This was also plotted as box plots for better visualisation. For the analysis, Principal Component Analysis (PCA) and hierarchical clustering methods were performed to explore the similarity of samples by bringing out strong patterns in a dataset and identifying outliers. A heatmap showing the correlations in gene expression for all pairwise combinations of samples in the dataset was created. Using the package DESeq2 (Version 1.24.0) (Love et al., 2014) on R studio (Version 3.6.1), differential gene analysis was performed to quantitate changes in expression levels between the different intervention groups of the samples. The Wald test in DESeq2 was used for significance, and corrections for multiple testing was done by calculating the Benjamini-Hochberg adjusted p-values. A threshold of adjusted p-value (Padj) <0.05 and absolute log2(fold change) >1 were set to identify differentially expressed genes (DEGs). DEG results were visualised using volcano plots and heatmaps using the ggplot, ggrepel and pheatmap packages in R studio. For analysis of functions and pathways, overrepresentation analysis of the DEGS list on gene ontology (GO) terms and Kyoto Encyclopaedia of Genes and Genomes (KEGG) based pathway analysis was run using ClusterProfiler (Version 3.12.0) (Yu et al., 2012). GO pathway significance was set to p-value <0.05, and it included three types of pathways; biological functions (BP), molecular functions (MF), and cell component (CC) pathways. Batch corrections were included in the analysis by making the batch a factor and excluding its effects on the final results.
Assembly: Mus musculus GRCm38.102 from Ensembl
Supplementary files format and content: Mouse_brain_GEO_counts.csv

source_name: Brain, Piriform cortex

growth_protocol: The RNeasy mini kit (Cat No./ID: 74104, QIAGEN, Germany) was used to harvest the RNA in the brain sections. The samples were first pipetted up and down in the lysis buffer to break down the tissue, vortexed for one minute to homogenise the sample, then 350 µl of 70% ethanol was added to it. 700 µl of sample and the precipitate that formed was transferred to the RNeasy spin column placed in a 2 ml collection tube. The lid was gently closed, and the sample was centrifuged for 15 s at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane and the flow-through was discarded. For the column DNase digestion, 350 µl of Buffer RW1 was added to the RNEasy spin column and centrifuged for 15 s at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane, then the flow through was discarded, 10 µl of DNase 1 stock solution was added to 70 µl of Buffer RDD, mixed gently by inverting the tube, and centrifuged briefly to collect residual liquid. Then, 80 μl of DNase I incubation mix was added to the RNeas spin column membrane, it was incubated at room temperature for 15 mins, 350 μl of buffer RW1 was added to it and it was centrifuged at ≥8000 x g (≥10,000 rpm), then 700 μl buffer RW1 was added to it, and it was centrifuged again at the same setting and the flow-through was discarded. To wash the spin column membrane, 500 μl buffer RPE was added to the RNeasy spin column, and it was centrifuged for 15 mins at ≥8000 x g (≥10,000 rpm) and the flow through was discarded, then another 500 μl of buffer RPE were added and it was centrifuged at the same speed for 2 mins. Finally, the column was placed in a new 2 ml collection tube and centrifuged at full speed for 1 min, placed in another 1.5 ml collection tube and 30-50 μl of RNAse-free water was added directly to the spin column membrane and it was centrifuged at ≥8000 x g (≥10,000 rpm) for 1 min to elute the RNA, and it was stored at -80°C.

extract_protocol: Before analysis, RNA concentration was quantified at OD260 nm by using a NanoDrop-1000 (Thermo Fisher Scientific, USA), and quality control tests were performed on the Bioanalyzer to ensure there is enough RNA. Aliquots of 10 μg were sent for sequencing at the Australian Genome Research Facility (AGRF), where 1 μg of total RNA was used for sequencing via the Illumina Nova-Seq Control Software (Version 1.6.0.). Real Time Analysis (RTA) (Version 3.4.4) for real-time base calling was used, and it produced a 100bp single end run. The Illumina bcl2fastq (Version 2.20.0.422) pipeline was used to generate the primary sequence data.

treatment_protocol: Mice underwent isoflurane anaesthesia through inhalation of vapour liquid isoflurane 100% (v/v), which was administered at a 4 ml/min oxygen rate during the induction in a chamber, and then maintained at a 2 ml/min oxygen rate for the duration of the procedures using a mask. Analgesia of 0.1 mg/kg dose of Buprenorphine was given subcutaneously to the mice while they were under anaesthesia to minimize pain during recovery. Burn procedures were performed on the right dorsal flank, and sham and excision procedures were performed on the medial posterior dorsal side. Both locations were away from the limbs to avoid restriction of movement and discomfort during recovery. In all three groups, the injury site was shaved in preparation for the procedure. In the sham group, the skin was shaved without inducing any injury to the site, which was done to control for the effects of anaesthesia, analgesics and handling. Before the burn procedure, the injury site was cleaned with a 4% chlorhexidine scrub. A brass rod 19 mm in diameter was heated to > 90° C and then applied to the skin for 10 seconds, which created a 7-8% TBSA full thickness burn injury, damaging both skin layers and ablating nerve endings at the site of injury to minimize pain during recovery. For the excision group, the injury site was cleaned with a 4% chlorhexidine scrub and a punch biopsy 12 mm in diameter was used to score the skin and provide a template for the excision. Scissors and forceps were then used to complete the excision, which was also a full-thickness injury. As mouse skin lacks tension, the area created by the excision later expanded to be of the same size as that of the burn. After the procedures, each mouse recovered from anaesthesia in a separate cage and was then returned to its home cage. No dressing was used as it increases discomfort (Sugarbaker & Chang, 1979). Post injury, mice were given drinking water containing 1 mg/mL of Paracetamol for five days to reduce pain during recovery (Taylor et al., 2016). Paracetamol was consumed at a rate of approximately 20 mg per day.

value: Brain, Piriform cortex

value: Mixed brain tissue

value: Sham


title: Frontal cortex, batch 3, sham, sample 3

description: Library name: E5P8


title: Frontal cortex, batch 3, sham, sample 4

description: Library name: E5P9


title: Frontal cortex, batch 3, sham, sample 2

description: Library name: E5P7


title: PBMCs from Mouse control replicate3

description: Library name: Mouse_UT_3


title: Frontal cortex, batch 3, excision, sample 3

description: Library name: E5P4

value: Excision


title: 3w, Middle, F, M1, Rep2

description: Library name: 10005CN84_D2

value: Middle colon


title: Sample 107 high flow high pressure

description:
Library name: 107-HF-HP_S5
GeneCounts1.tsv

value: Male


title: Frontal cortex, batch 3, excision, sample 2

description: Library name: E5P3


title: Frontal cortex, batch 3, burn, sample 5

description: Library name: E5P15

value: Burn


title: 3w, Middle, F, M1, Rep1

description: Library name: 10005CN84_D1


title: Sample 105 static

description:
Library name: 105-Static_S24
GeneCounts1.tsv

value: IPAH

value: Female

value: Static


title: Frontal cortex, batch 3, burn, sample 4

description: Library name: E5P14


title: Frontal cortex, batch 3, burn, sample 3

description: Library name: E5P13


title: Mouse PBMCs treated with cGAMP replicate2

description: Library name: Mouse_cGAMP_2

value: PBMC

value: Mouse PBMCs treated with cGAMP


title: Sample 105 low flow low pressure

description:
Library name: 105-LF-LP_S25
GeneCounts1.tsv

value: Distal Pulmonary Arteries

value: Low


title: Sample 105 low flow high pressure

description:
Library name: 105-LF-HP_S26
GeneCounts1.tsv

value: Primary Human Cells

value: High


title: 3w, Proximal, F, M1, Rep2

description: Library name: 10005CN84_C2

value: Proximal colon

value: F


title: 3w, Proximal, F, M1, Rep1

description: Library name: 10005CN84_C1


title: Frontal cortex, batch 3, burn, sample 2

description: Library name: E5P12

value: Brain, Piriform cortex

value: Mixed brain tissue


title: Frontal cortex, batch 3, sham. sample 5

description: Library name: E5P10

value: Sham


title: Sample 105 high flow low pressure

description:
Library name: 105-HF-LP_S27
GeneCounts1.tsv

value: Pulmonary artery endothelial cells


title: Frontal cortex, batch 2, excision, sample 3

description: Library name: E3FC9

source_name: Brain, Frontal cortex

value: Brain, Frontal cortex

value: Excision


title: 3w, Distal, M, M9, Rep2

description: Library name: 10005CN46_E2

value: Distal colon

value: M


title: Sample 105 high flow high pressure

description:
Library name: 105-HFHP_S28
GeneCounts1.tsv

value: IPAH

value: Female


title: 3w, Distal, M, M9, Rep1

description: Library name: 10005CN46_E1


title: Sample 95 static

description:
Library name: 95-Static_S4
GeneCounts1.tsv

value: Male

value: Static


title: Frontal cortex, batch 3, excision, sample 4

description: Library name: E5P5


title: Frontal cortex, batch 2, burn, sample 3

description: Library name: E3FC5

value: Burn


title: Sample 95 low flow low pressure

description:
Library name: 95-LF-LP_S3
GeneCounts1.tsv

value: Distal Pulmonary Arteries

value: Primary Human Cells

value: Low


title: Frontal cortex, batch 2, burn, sample 4

description: Library name: E3FC6


title: Frontal cortex, batch 2, burn, sample 2

description: Library name: E3FC4


title: Frontal cortex, batch 2, excision, sample 1

description: Library name: E3FC7


title: Frontal cortex, batch 2, sham, sample 4

description: Library name: E3FC2


title: Frontal cortex, batch 2, sham, sample 5

description: Library name: E3FC3


title: 3w, Middle, M, M9, Rep1

description: Library name: 10005CN46_D1

value: Middle colon


title: 3w, Proximal, M, M9, Rep1

description: Library name: 10005CN46_C1

value: Proximal colon