title: HeLa HSV1 8h rep1

city: Kuopio

first: Henri

last: Niskanen

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

description: Library name: HeLa_HSV1_8h_rep1

data_processing:
Reads were trimmed using HOMER 4.3 software to remove poly-A tails and reads shorter than 25 nt were discarded. Quality control using FastQC tool, bases with poor quality were trimmed using FastX toolkit so that minimum 97 % of all bases in one read have to have a minimum phred quality score of 10. Alignments to ChlSab1.1 genome were done using bowtie-0.12.7 allowing up to two mismatches and up to three locations per read and the best alignment was reported. Differentially expressed genes were detected using ChlSab1.1.95.gtf coordinates, analyzeRNA.pl workflow of HOMER 4.3 and edgeR v3.2.2.
Assembly: hg19
Supplementary files format and content: Gene RPKM and fold change information
Library strategy: GRO-Seq

source_name: Uterus, Cervix

growth_protocol: Hela cells (ATCC CCL-2) were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, L-glutamine, and penicillin-streptomycin maintained at 37°C with 5% CO2.

extract_protocol:
Both infected and noninfected samples of HeLa cells (ATCC CCL-2) were prepared as two biological replicates. Cell nuclei were extracted post-infection at the indicated times. Cells were washed with PBS and scraped into swelling buffer containing 10 mM Tris-HCl (pH 7.5), 2 mM MgCl2, 3 mM CaCl2, 1 U/ml SUPERase-In and 1 U/ml RNAsin plus in ultrapure water (Gibco 15564-027, Invitrogen AM9530G, Sigma-Aldrich 21115-100ml, Invitrogen 10977-035, Invitrogen AM2694, Promega N2611). Cells were centrifuged at 400 x g for 10 minutes. Formed cell pellet was resuspended into swelling buffer containing 10 % glycerol and 4 U/ml SUPERase-In (ACROS ORGANICS 327255000, Invitrogen AM2694). Nuclei were extracted by incubating the cells in swelling buffer supplemented 10 % glycerol and 1% Igepal (Igepal®CA-630 I8896-50ml) for 5 minutes. Lysis buffer composted of swelling buffer, 0.5 % Igepal, 10% glycerol, 1 U/ml SUPERase-In and 1 U/ml RNAsin plus was added to the extracted nuclei. Nuclei were washed once with lysis buffer. Isolated nuclei were resuspended into freezing buffer containing 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 50 mM Tris-HCl (pH 8.3) and 2 U/ml SUPERase-In (Invitrogen AM9260G, Gibco 15564-027 Invitrogen 15568-025) and frozen.
Nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNAseH treated, circularized, linearized, amplified for 11-14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.

treatment_protocol: Infected sample replicates were inoculated independently with the multiplicity of infection (MOI) 5. Cells were incubated with the virus for two hours, after which the medium as changed.

value: Uterus, Cervix

value: HeLa

value: epithelial cell

value: wt

value: HSV1 infection, 8h pi


title: MDA-MB-231, siYTHDC1, rep1

status: Public on Jan 28 2026

type: SRA

city: guangzhou

first: zhenghao

last: Lai

address: yanjiang road

country: China

institute: sun yat-san memorial hospital

description: Library name: 231-siYTHDC1-1

library_source: transcriptomic

data_processing:
Qubit 3.0
Using Qubit 3.0 to initially quantify concentrations, the Agilent 2100 system initially assessed library fragment size.
After meeting expectations,the effective concentration of the library was accurately quantified using the Bio-RAD CFX 96 Fluorescent Quantitative PCR Instrument.

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer

growth_protocol: MDA-MB-231 and Hs578T cells were cultured in DMEM (Gibco) supplemented with 10% FBS (Shanghai ExCell Biology Inc.) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
RNA was harvested using Trizol. The Nanodrop2000 microspectrophotometer detects sample purity and concentration;
(1) Total RNA samples were tested and then enriched for eukaryotic mRNA by Oligo(dT) magnetic beads; (2) Add Fragmentation Buffer for mRNA fragmentation; (3) One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification; (4) Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp; (5) PCR enrichment was performed to obtain cDNA libraries.

tag: tissue

value: breast cancer

tag: cell line

tag: cell type

tag: treatment


title: HeLa HSV1 8h rep2

description: Library name: HeLa_HSV1_8h_rep2

library_source: other

molecule: other

tag: genotype

tag: batch


title: HeLa HSV1 4h rep2

description: Library name: HeLa_HSV1_4h_rep2

value: HSV1 infection, 4h pi


title: Hs578T, siYTHDC1, rep3

description: Library name: Hs578T-siYTHDC1-3


title: C5_Discovery_158

type: genomic

city: Potsdam

first: Amandeep

last: Singh

state: Brandenburg

address: Arthur-Scheunert-Allee 114-116

department: EOD

country: Germany

institute: German Institute of Human Nutrition

hyb_protocol: The bisulfite treatment and hybridisation was carried out by Life & Brain GmbH

scan_protocol: iscan, carried out by Life & Brain GmbH

data_processing: ChAMP package in R environment

label: other

molecule: genomic DNA

source_name: Blood cells

label_protocol: Labeling was carried out by Life & Brain GmbH

extract_protocol: precipitation with sodium acetate

treatment_protocol: Genomic DNA was extracted from blood cells.

tag: Sex

value: M

value: Blood cells


title: C6_Discovery_160

value: F


title: SPF SI DC2

city: Suwon

first: Jaeu

last: Yi

state: Gyeonggi-do

address: 206, World cup-ro

department: Department of Biological Science

country: South Korea

institute: Ajou University

description: Library name: SPF2

data_processing:
Illumina Casava1.8 software used for basecalling.
Assembly: RNA-seq reads were aligned to mouse reference transcriptome build mm10 (M10, GRCm38.p4) from GENCODE (http://www.gencodegenes.org/mouse_releases/10.html)
Supplementary files format and content: Fragments Per Kilobase Million (FPKM) were calculated by RSEM with default parameters.
Supplementary files format and content: Differentially expressed genes were identified by edgeR-3.16.5 [49] given absolute fold change > 2 and FDR < 10-3

organism: Mus musculus

source_name: small intestinal lamina propria

extract_protocol:
DCs were purified with flow cytometory sorting and RNA was harvested with trizol. Illumina TruSeq RNA sample prep kit was used with 1ug of total RNA for the construction of sequencing libararies.
RNA libraries were prepared for sequencing using standard Illumina protocol

value: small intestinal lamina propria

value: dendritic cells

value: SILP DC


title: MDA-MB-231, siNC, rep2

description: Library name: 231-siNC-2

value: siNC


title: C3_Discovery_157


title: CD1 mouse, sham, male, biol rep 4

city: Saint Louis

first: Shuhua

last: Fu

state: MO

address: 660 S. Euclid Avenue Campus Box 8103

country: USA

institute: Washington University in St. Louis

description: Library name: lib119

library_source: genomic

data_processing:
Raw ATAC-seq reads were aligned to the human (hg38) or mouse (mm10) reference genome and processed using AIAP, which includes four key steps: data processing, quality control, integrative analysis, and data visualization.
To generate a unified peak set, narrow peak files from all ATAC-seq libraries were merged using the merge function in the BEDTools suite.
Read counts for each ATAC-seq peak were quantified using the BEDTools coverage command.
To correct batch effects in read counts, RUVr normalization (RUVSeq R package, k = 2) was applied.
Assembly: hg38 and mm10
Supplementary files format and content: bigWig: dense, continuous data used in genome browser track
Supplementary files format and content: txt: normalized read counts of OCRs

source_name: Left Ventricle

growth_protocol: iCell Cardiomyocytes^2 were maintained per the manufacturer's instructions.  GCaMP6 hiPSC-CMs were differentiated into cardiomyocytes via GSK-3 inhibition/Wnt activation followed by TNKS inhibition/Wnt inhibition, followed by purification via lactate-mediated metabolic selection, and were then maintained in RPMI 1640 + 2% B-27 Supplement at 37 C with 5% CO2.

extract_protocol:
Cell preparation, antibody binding, tagmentation, and DNA extraction and purification were performed using the Active Motif CUT&Tag kit (Active Motif, 53171) according to the manufacturer’s instructions. The following antibodies were used: H3K27me3 (Active Motif, 39155), H3K27ac (Active Motif, 39685), H3K4me3 (Active Motif, 39159), H3K4me1 (Cell Signaling Technology, 5326), or IgG isotype control (Cell Signaling Technology, 66362S).
cDNA libraries were constructed using the Active Motif CUT&Tag kit with Nextera primers per manufacturer's instructions.

treatment_protocol: IR treatment was performed using the small animal radiation research platform (SARRP, Xstrahl Inc.). hiPSC-CMs received 25 Gy to the entire cell culture surface area. Radiation was delivered at a 3.9 Gy/min dose rate in a single fraction of 25 Gy.

value: Left Ventricle

value: PCM1+ cardiomyocyte nuclei

value: WT

value: Sham


title: CD1 mouse, sham, male, biol rep 5

description: Library name: lib121


title: C6_Discovery_155


title: GF SI DC1

description: Library name: GF1


title: CD1 mouse, ir6wk, male, biol rep 4

description: Library name: lib122

value: 25 Gy IR


title: CD1 mouse, sham, male, biol rep 3

description: Library name: lib117


title: QMJ-R248Q

city: Shanghai

first: lianghua

last: shen

state: Shanghai

address: Wujin Road No.85

institute: Shanghai General Hospital

description:
Library name: QMJ-R248Q
scRNAseq

library_source: transcriptomic single cell

data_processing:
The single-cell RNA sequencing data were processed as follows: Raw sequencing reads (FASTQ files) were aligned to the reference genome (GRCh38) and quantified using Cell Ranger (v7.1.0). The resulting gene-cell count matrix was imported into Seurat (v5.0.1) for downstream analysis. Cells with low quality (fewer than 200 detected genes or over 10% mitochondrial reads) were filtered out. Counts were normalized using the LogNormalize method. Highly variable genes were selected for principal component analysis (PCA). Dimensionality reduction was performed using UMAP. Cells were clustered via the Louvain algorithm on a shared nearest neighbor graph and were subsequently annotated into distinct cell types based on canonical marker genes. The final output is a processed count matrix with cell type annotations.
perform cell segmentation, remove PCR duplicates, and identify cell types.
Assembly: mm10
Supplementary files format and content: The processed data files consist of two key components: Gene-Cell Count Matrix: The primary processed data is provided as a sparse matrix in the Matrix Market Exchange format (.mtx), accompanied by complementary TSV files for cell barcodes (barcodes.tsv) and gene identifiers (features.tsv). This is the standard output format of Cell Ranger and represents the filtered, unfiltered, or normalized UMI count data.  Cell Metadata File: A comma-separated values (.csv) file containing essential per-cell annotations. This includes the sample origin, numerically encoded cluster identities, manually annotated cell types (e.g., T cells, B cells, Macrophages), and quality control metrics (number of genes, UMI counts, percent mitochondrial reads).  These files collectively contain the quantified gene expression data and the associated cellular metadata required to reproduce the downstream analyses described in the accompanying study. A plain-text, tab-separated matrix is also provided for broader accessibility.
Supplementary files format and content: Including all barcode labels, gene names, and expression matrices，expression matrices

source_name: PBMC

growth_protocol: First, we selected healthy donors with the appropriate HLA subtypes and isolated monocytes and Naive T lymphocytes from the peripheral blood of healthy donors using CD14+ and Naive CD8+ T cell sorting kits. CD14+ monocytes were used for the differentiation of moDCs, and Naive T lymphocytes were used for the screening of TP53 mutant-specific T lymphocytes. The expansion and screening strategy was as follows: the mutant antigen peptide (5 μg/mL) was rotationally incubated with moDCs (2×106/mL) for 3 h at 37°C in a cell culture incubator, and then the moDCs-loaded-peptide was irradiated (40 Gy) and co-cultivated with Naive CD8+ T lymphocytes from the same donor in a ratio of DC:T=1:2.5 to activate TP53 antigen-specific T lymphocytes, and 30 ng/mL of IL-21 (Peprotech, USA) was added. On day 2, the culture was continued by replacing 1640 medium containing IL-2 (25 U/mL), IL-7 (10 ng/mL), and IL-15 (10 ng/mL) (Peprotech, USA), and subsequent half-exchanges were performed every 3 days, and the culture was supplemented with fresh IL-2, IL-7, and IL-15 cytokines. On day 14, fresh, irradiated-treated moDCs loaded with mutant antigen peptides were reprepared for a second round of stimulation of TP53 antigen-specific T cells. At day 24, a third round of stimulation of TP53 antigen-specific T cells was performed. At day 25 of co-culture, TP53 mutation-specific T cells were detected after staining using CD8 antibody and HLA-A*11:01-TP53R248Q-Tetramer.

extract_protocol:
FACS-sorted CD8+/Tetramer+ cells were harvested, final cell concentration was determined by cell count on a hemocytometer, and the cell concentration was adjusted to approximately 1,000 cells per microliter with a cell viability greater than 98%. Prepare sorted CD8+/Tetramer+ T cells for 10× Genomics single-cell sequencing of rearranged VDJ according to manufacturer’s instructions. Detailed quality control metrics were generated and evaluated using single-cell analysis packages from Bioconductor, including DropletUtils, scater and scran. Genes detected in fewer than three cells and cells where fewer than 200 genes had non-zero counts were filtered out and excluded from subsequent analysis. Low-quality cells with more than 15% of the read counts derived from the mitochondrial genome were also discarded. After single-cell sequencing and analysis, the TCR sequences were evaluated using the Loupe VDJ browser (Cell Ranger, 10× Genomics), and the top ten rankings were performed according to the frequency of TCRs, and the top three ranked human TCR sequences were selected for subsequent functional experiments.
Detailed quality control metrics were generated and evaluated using single-cell analysis packages from Bioconductor, including DropletUtils, scater and scran. Genes detected in fewer than three cells and cells where fewer than 200 genes had non-zero counts were filtered out and excluded from subsequent analysis. Low-quality cells with more than 15% of the read counts derived from the mitochondrial genome were also discarded. After single-cell sequencing and analysis, the TCR sequences were evaluated using the Loupe VDJ browser (Cell Ranger, 10× Genomics), and the top ten rankings were performed according to the frequency of TCRs, and the top three ranked human TCR sequences were selected for subsequent functional experiments.

value: PBMC

value: CD8+ T

value: DC-loanding pR248 stimulation


title: C3_Discovery_154


title: HeLa HSV1 4h rep1

description: Library name: HeLa_HSV1_4h_rep1

value: Uterus, Cervix

value: HeLa

value: epithelial cell

value: wt


title: QMJ-R248Q-TC

description:
Library name: QMJ-R248Q-T
scRNAseq-TCR

data_processing:
The single-cell RNA sequencing data were processed as follows: Raw sequencing reads (FASTQ files) were aligned to the reference genome (GRCh38) and quantified using Cell Ranger (v7.1.0). The resulting gene-cell count matrix was imported into Seurat (v5.0.1) for downstream analysis. Cells with low quality (fewer than 200 detected genes or over 10% mitochondrial reads) were filtered out. Counts were normalized using the LogNormalize method. Highly variable genes were selected for principal component analysis (PCA). Dimensionality reduction was performed using UMAP. Cells were clustered via the Louvain algorithm on a shared nearest neighbor graph and were subsequently annotated into distinct cell types based on canonical marker genes. The final output is a processed count matrix with cell type annotations.
perform cell segmentation, remove PCR duplicates, and identify cell types.
Assembly: mm10
Supplementary files format and content: The processed data files consist of two key components: Gene-Cell Count Matrix: The primary processed data is provided as a sparse matrix in the Matrix Market Exchange format (.mtx), accompanied by complementary TSV files for cell barcodes (barcodes.tsv) and gene identifiers (features.tsv). This is the standard output format of Cell Ranger and represents the filtered, unfiltered, or normalized UMI count data.  Cell Metadata File: A comma-separated values (.csv) file containing essential per-cell annotations. This includes the sample origin, numerically encoded cluster identities, manually annotated cell types (e.g., T cells, B cells, Macrophages), and quality control metrics (number of genes, UMI counts, percent mitochondrial reads).  These files collectively contain the quantified gene expression data and the associated cellular metadata required to reproduce the downstream analyses described in the accompanying study. A plain-text, tab-separated matrix is also provided for broader accessibility.
Supplementary files format and content: Including all barcode labels, gene names, and expression matrices，expression matrices
Library strategy: TCR-Seq


title: CD1 mouse, sham, male, biol rep 1

description: Library name: lib075


title: CD1 mouse, ir6wk, male, biol rep 1

description: Library name: lib116


title: HeLa mock rep2

description: Library name: HeLa_mock_rep2

value: noninfected


title: CD1 mouse, ir6wk, male, biol rep 5

description: Library name: lib124


title: CD1 mouse, ir2day, male, biol rep 4

description: Library name: lib080


title: 15 day old Islet-1+ CSC clone

city: Loma Linda

first: Lorelei

last: Hughes

state: CA

address: 11021 Campus

department: Pathology and Human Anatomy

institute: Loma Linda University

data_processing:
Samples were run on an Ion Proton sequencer using an Ion torrent RNAseq run plan
Raw sequence files were aligned to the human genome (Hg19) reference sequence by the alignment plugin tool in Ion Torrent Suite software using the default parameters
Quality control was assessed by the Strand NGS program, aligned reads were then filtered based on alignment score (≥90), match count (≤1) and reads that failed vendors QC were removed
Aligned reads were normalized and quantified using the DEseq algorithm by the StrandNGS program
Assembly: Hg19
Supplementary files format and content: xlsx files with relative gene expression for all three neonatal Islet-1+ CSCs

source_name: Cardiac Stem Cell

growth_protocol: CSC clones were cultured using media generated with 66% M199, 22% EGM2, 10% GenClone Fetal Bovine Serum, 1% PEN/STREP (100X), and 1% MEM NEAA (100X) in an incubator at 37C with 5% CO2

extract_protocol:
Total RNA was harvested using miRNeasy Mini Plus Kit (QIAGEN), roughly 1μg of RNA was used to generate libraries
RNA libraries were initially constructed using an Ion Total RNA-Seq Kit v2 (Cat# 4479789) following manufacturer's protocols

value: Cardiac Stem Cell


title: 1 month old Islet-1+ CSC clone


title: CD1 mouse, ir2day, male, biol rep 2

description: Library name: lib076


title: GF SI DC2

description: Library name: GF2

value: small intestinal lamina propria

value: dendritic cells


title: AF SI DC1

description: Library name: AF1

value: SILP DC


title: HeLa mock rep1

description: Library name: HeLa_mock_rep1


title: C5_Discovery_153

value: F

value: Blood cells


title: SPF SI DC1

description: Library name: SPF1


title: AKO-DSS-3

city: Suzhou

first: Xinyue

last: Lv

address: 199 Ren'ai Road

institute: Soochow university

description: Library name: sample12

data_processing:
Filtering of Clean Reads:Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Alignment with Ribosome RNA (rRNA):Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
Alignment with Reference Genome:An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
Quantification of Gene Abundance:The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Relationship analysis of samples:Correlation analysis was performed by R. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability.The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1, the better the repeatability between two parallel experiments.
Assembly: GRCm39
Supplementary files format and content: genes.expression.xls includes raw counts for each Sample

source_name: colon

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).

value: colon

value: colon tissue


title: Macrophages, rmMETRNL-3

city: ChongQing

first: Jiayu

last: Liu

address: No. 1 Yi xue yuan Road, Yuzhong  District，ChongQing

department: School of Medical Laboratory

institute: Chongqing Medical University

description: Library name: Sample 6

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencellow-quality seguence using CLc genomic benchwork (parameter- Quality limit. 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using ClC genomic benchwork (parameters- mismath cost:. 2 insertion cost. 3deletion cost: 3 lencth fraction: 0.8 similarity faction. 0.8).
Read count extraction and normalization were perommed usina CLc aenomic benchwork.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample.

source_name: Primary macrophage

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizolreagent. llumina TruSeg RNA Sample Prep Kit wasused with 1 ug of total RNA for theconstruction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: After rmMETRNL treatment in vitro for 6 hours, primary macrophages were challenged with candida albicans for 6 hours.

value: Primary macrophage

value: WT

value: rmMETRNL treatment and challenged with Candida albicans

tag: time

value: 6 hours


title: 8 day old Islet-1+ CSC clone


title: C6_Discovery_156

value: M


title: AKO-Con-1

description: Library name: sample7


title: WT-DSS-3

description: Library name: sample6


title: Macrophages, vehicle-3

description: Library name: Sample 3

value: vehicle treatment and challenged with Candida albicans


title: Macrophages, rmMETRNL-1

description: Library name: Sample 4


title: AKO-Con-3

description: Library name: sample9


title: C5_Discovery_148


title: C3_Discovery_152


title: WT-DSS-2

description: Library name: sample5


title: WT-Con-3

description: Library name: sample3


title: C5_Discovery_151


title: Macrophages, vehicle-2

description: Library name: Sample 2


title: AKO-DSS-1

description: Library name: sample10


title: WT-Con-2

description: Library name: sample2


title: Macrophages, rmMETRNL-2

description: Library name: Sample 5


title: Macrophages, METRNL-/- -2

description: Library name: Sample5

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit. 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 lencth fraction: 0.8 similarity faction. 0.8).
Read count extraction and normalization were perommed usina CLc aenomic benchwork.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample.

source_name: Primary macrophages from  METRNL KO mice

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizolreagent. lllumina TruSeg RNA Sample Prep Kit was used with 1 ug of total RNA for theconstruction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: METRNL+/+ macrophages and  METRNL-/- macrophages were isolated form WT and METRNL KO mice, respectively. After cultured,  METRNL+/+ macrophages and  METRNL-/- macrophages were challenged  with candida albicans for 6 hours in vitro.

value: Primary macrophages from  METRNL KO mice

value: METRNL KO

value: challenged  with Candida albicans in vitro


title: Macrophages, vehicle-1

description: Library name: Sample 1


title: AKO-Con-2

description: Library name: sample8


title: Macrophages, METRNL-/- -3

description: Library name: Sample6


title: C3_Discovery_149


title: WT-Con-1

description: Library name: sample1


title: AKO-DSS-2

description: Library name: sample11


title: C3_Discovery_147


title: C3_Discovery_142


title: C3_Discovery_143


title: Targeted gene expression of patient ID020 at BL

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

country: France

institute: Centre Léon Bérard

description:
Library name: 164-ID020_BL
column name in htg_raw_ano.xlsx164-ID020_BL

data_processing:
Illumina bcl2fastq is used for generation of FASTQ files
HTG EdgeSeq Parser software (version 5.1) is used for alignment to a priori defined target sequences.  Requirements include %Q30 >= 85%, %PF >= 75%, and 180 < CD < 290
Post-sequencing quality control using three quality control metrics: 1) Percent of reads allocated to the Positive control probe must not exceed 15%, 2) Total aligned reads must exceed 1,500,000, and 3) Relative Standard Deviaion (CV) of counts within a sample must exceed 0.1 (CV is calculated after removal of counts from ANT and POS control probes and log2 transformation after addition of 2 to avoid taking the log of 0). A log2 CPM normalization is then processed.
Assembly: hg38
Supplementary files format and content: Excel (xlsx) file includes raw counts for each content
Supplementary files format and content: Excel (xlsx) file includes normalized (log2 cpm) counts for each content

source_name: Tumor

extract_protocol:
10mm2 of 5 micrometer FFPE tumour macrodissection tissue were lysed using HTG Lysis Buffer, followed by proteinase K digestion, and then transferred to an HTG EdgeSeq platform according to manufacturer protocols (HTG Molecular Diagnostics, Inc., Tucson, AZ).
The Oncology Biomarker Panel was used to  capture RNA expression levels of gene targets  on the HTG EdgeSeq platform according to manufacturer protocols (HTG Molecular Diagnostics, Inc., Tucson, AZ). The resulting DNA probes were quantitatively amplified with polymerase chain reaction adding extended primers ,including sequencing primer and sample barcode sequences. Library samples were cleaned up to remove excess primers, quantitated, pooled and sequenced using Illumina NextSeq500 sequencer using 50-cycles single end ((Illumina, Inc.).

value: Tumor

tag: patient id

tag: sample timepoint

value: baseline

tag: figo

value: I

tag: recist within 1week before rct

value: SD

tag: recist 4 weeks after rct

value: CR

tag: recist end of treatment visit

tag: hot score (gsva)

tag: hot status

value: HOT


title: C3_Discovery_146

value: Blood cells


title: Macrophages, METRNL+/+ -2

description: Library name: Sample2

source_name: Primary macrophages from WT mice

value: Primary macrophages from WT mice


title: C5_Discovery_150

value: F


title: Targeted gene expression of patient ID019 at 4WRCT

description:
Library name: 164-ID019_4WRCT
column name in htg_raw_ano.xlsx164-ID019_4WRCT

value: 4 weeks after RCT

value: III

value: PR


title: GBM8

city: Seattle

first: Bahar

last: Tercan

state: WA

address: 401 Terry Ave. N.

institute: Institute for Systems Biology

description:
Library name: GBM8
10X Genomics

data_processing:
Raw base call (BCL) files were demultiplexed into fastq files then count matrix-mapped to the hg19 reference genome using Cell Ranger using an ‘expected cell number’ = 20,000 to identify gene-specific expression per cell.
Assembly: Homo sapiens hg19
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Brain

extract_protocol:
Aliquots of 20,000 cells per sample were taken on Day 0 of the time course sampling experiment (baseline). RNA extraction and cDNA preparation was performed using the 10X Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 and protocol according to the manufacturer’s instructions.
cDNA was captured and sequenced as described above, using a standard 10X sequencing protocol (10X Genomics, Pleasanton, CA) without further enrichment on an Illumina NextSeq sequencer (Version 500).

value: Brain

value: glioblastoma-derived stem cell


title: WT-DSS-1

description: Library name: sample4

value: colon

value: colon tissue


title: Macrophages, METRNL-/- -1

description: Library name: Sample4

value: Primary macrophages from  METRNL KO mice

value: METRNL KO

value: challenged  with Candida albicans in vitro

value: 6 hours


title: C6_Discovery_144

value: M


title: GBM4

description:
Library name: GBM4
10X Genomics


title: Targeted gene expression of patient ID017 at 4WRCT

description:
Library name: 164-ID017_4WRCT
column name in htg_raw_ano.xlsx164-ID017_4WRCT

value: Tumor

value: SD

value: CR

value: COLD


title: PBMC, Infected3

description: Library name: Sample6

source_name: peripheral blood mononuclear cells (PBMC) from  systemic candida albicans infected mice

extract_protocol:
RNA was harvested using Trizolreagent. lllumina TruSeg RNA Sample Prep Kit was used with 1 ug of total RNA for theconstruction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Peripheral blood mononuclear cells were isolated from control mice and systemic candida albicans-infected  mice(infected for 7 days) with Ficoll.

value: WT

value: candida albicans infected

value: 7 days


title: PBMC, Infected2

description: Library name: Sample5

value: peripheral blood mononuclear cells (PBMC)


title: C5_Discovery_138

value: F

value: Blood cells


title: Targeted gene expression of patient ID021 at BL

description:
Library name: 164-ID021_BL
column name in htg_raw_ano.xlsx164-ID021_BL

value: baseline

value: II


title: C3_Discovery_137


title: 0131

description:
Library name: 0131
10X Genomics

value: Brain

value: glioblastoma-derived stem cell


title: Targeted gene expression of patient ID019 at BL

description:
Library name: 164-ID019_BL
column name in htg_raw_ano.xlsx164-ID019_BL

value: III

value: PR

value: HOT


title: C3_Discovery_145


title: Macrophages, METRNL+/+ -3

description: Library name: Sample3

value: Primary macrophages from WT mice

value: challenged  with Candida albicans in vitro

value: 6 hours


title: 0827

description:
Library name: 0827
10X Genomics


title: Targeted gene expression of patient ID020 at BEFRCT

description:
Library name: 164-ID020_BEFRCT
column name in htg_raw_ano.xlsx164-ID020_BEFRCT

value: Tumor

value: before RCT

value: I

value: SD

value: CR


title: C3_Discovery_141

value: M


title: Targeted gene expression of patient ID015 at BEFRCT

description:
Library name: 164-ID015_BEFRCT
column name in htg_raw_ano.xlsx164-ID015_BEFRCT


title: Targeted gene expression of patient ID015 at BL

description:
Library name: 164-ID015_BL
column name in htg_raw_ano.xlsx164-ID015_BL


title: Targeted gene expression of patient ID019 at BEFRCT

description:
Library name: 164-ID019_BEFRCT
column name in htg_raw_ano.xlsx164-ID019_BEFRCT


title: Targeted gene expression of patient ID020 at 4WRCT

description:
Library name: 164-ID020_4WRCT
column name in htg_raw_ano.xlsx164-ID020_4WRCT

value: 4 weeks after RCT


title: PMBC, Control1

description: Library name: Sample1

source_name: peripheral blood mononuclear cells (PBMC) from uninfected mice

value: WT

value: uninfected

value: 0 day


title: Macrophages, METRNL+/+ -1

description: Library name: Sample1

value: challenged with Candida albicans in vitro


title: Targeted gene expression of patient ID018 at BL

description:
Library name: 164-ID018_BL
column name in htg_raw_ano.xlsx164-ID018_BL

value: baseline

value: III

value: COLD


title: Targeted gene expression of patient ID018 at BEFRCT

description:
Library name: 164-ID018_BEFRCT
column name in htg_raw_ano.xlsx164-ID018_BEFRCT


title: C5_Discovery_140

value: F

value: Blood cells


title: C5_Discovery_133


title: Targeted gene expression of patient ID013 at BEFRCT

description:
Library name: 164-ID013_BEFRCT
column name in htg_raw_ano.xlsx164-ID013_BEFRCT

value: PR


title: Targeted gene expression of patient ID017 at BEFRCT

description:
Library name: 164-ID017_BEFRCT
column name in htg_raw_ano.xlsx164-ID017_BEFRCT

value: Tumor

value: HOT


title: Targeted gene expression of patient ID016 at 4WRCT

description:
Library name: 164-ID016_4WRCT
column name in htg_raw_ano.xlsx164-ID016_4WRCT

value: II


title: Targeted gene expression of patient ID017 at BL

description:
Library name: 164-ID017_BL
column name in htg_raw_ano.xlsx164-ID017_BL

value: SD


title: F123 mESC, T7 in situ transcription, "12Mb" clonal line, rep1

city: Stanford

first: Joo

last: Lee

address: 279 Campus Dr

department: Developmental Biology

institute: Stanford University

description: Library name: 12Mb

data_processing:
Raw reads were quality checked with FastQC
In situ transcripts were selected by filtering for raw reads that align to full 3' sleeping beauty ITR sequence using BWA
Filtered in situ transcript reads were then aligned to the mouse genome (mm10) using BWA
Assembly: mm10
Supplementary files format and content: BigWig(.bw) files were generated with deepTools (bamCoverage) on filtered and mapped reads
Supplementary files format and content: bed(.bed) files were generated with custom python script that takes in the filtered and mapped reads and returns exact coordinates of ITR-genome junctions along with the strandedness and read counts.

growth_protocol: Mouse embryonic stem cells (CastX129 hybrid F123 mESCs) were cultured in nDiff227 (Takara, Y40002) serum-free media supplemented with 2i/LIF (1μM PD0325901 (Stemcell Technologies, 72184), 3 μM CHIR99021 (Stemcell Technologies, 72054)), and 1000U/ml ESGRO mouse LIF (Sigma, ESG1107)). mESCs were cultured in 6-well plates pre-coated with 0.0015% poly-L-Ornithine (Sigma-Aldrich, A-004-C) and 10 µg/mL Laminin (Thermo-Fisher, 23017015). mESCs were fed daily by replacing with fresh media and passaged every two days with 0.25% Trypsin-EDTA (Gibco, 25300062).

extract_protocol:
In situ transcripts were purified using RNeasy Plus Micro Kit (Qiagen, 74034) following manufacturer’s protocols.
RNA-seq libraries of in situ transcripts were prepared using Stranded Total RNA Prep kit (Illumina, 2004052s5) following manufacturer’s protocols.

treatment_protocol: Genomic DNA for ~500k cells were purified using Quick-DNA Microprep Kit (Zymo Research, D3020) following manufacturer’s protocols with >500,000 input cells and 11μl elution volume. Each in situ transcription reaction was prepared as follows: 10 μl purified genomic DNA, 2μl T7 RNA Polymerase Mix (NEB, E2050S), 1μl murine RNAse inhibitor (NEB, M0314L), and 7μl milli-Q water were mixed and incubated at 37°C overnight.

value: Embryonic stem cells

value: T7 in situ transcription


title: PMBC, Control3

description: Library name: Sample3

value: peripheral blood mononuclear cells (PBMC)


title: PBMC, Infected1

description: Library name: Sample4

value: WT

value: candida albicans infected

value: 7 days


title: C5_Discovery_131


title: PMBC, Control2

description: Library name: Sample2

value: uninfected

value: 0 day


title: C3_Discovery_136

value: M


title: C5_Discovery_139


title: F123 mESC, T7 in situ transcription, "260kb" clonal line, rep1

description: Library name: 260kb


title: Targeted gene expression of patient ID015 at 4WRCT

description:
Library name: 164-ID015_4WRCT
column name in htg_raw_ano.xlsx164-ID015_4WRCT

value: 4 weeks after RCT

value: CR

value: COLD


title: Targeted gene expression of patient ID016 at BL

description:
Library name: 164-ID016_BL
column name in htg_raw_ano.xlsx164-ID016_BL

value: baseline

value: PR


title: C5_Discovery_130

value: Blood cells


title: C5_Discovery_135

value: F


title: F123 mESC, T7 in situ transcription, "134kb" clonal line, rep1

description: Library name: 134kb


title: Targeted gene expression of patient ID009 at BEFRCT

description:
Library name: 164-ID009_BEFRCT
column name in htg_raw_ano.xlsx164-ID009_BEFRCT

value: Tumor

value: before RCT

value: II

value: SD


title: C5_Discovery_134


title: C6_Discovery_128


title: F123 mESC, T7 in situ transcription, "55kb" clonal line, rep1

description: Library name: 55kb

value: Embryonic stem cells

value: T7 in situ transcription


title: Targeted gene expression of patient ID014 at 4WRCT

description:
Library name: 164-ID014_4WRCT
column name in htg_raw_ano.xlsx164-ID014_4WRCT

value: HOT


title: Targeted gene expression of patient ID014 at BEFRCT

description:
Library name: 164-ID014_BEFRCT
column name in htg_raw_ano.xlsx164-ID014_BEFRCT


title: C2_Discovery_127


title: Targeted gene expression of patient ID014 at BL

description:
Library name: 164-ID014_BL
column name in htg_raw_ano.xlsx164-ID014_BL


title: Targeted gene expression of patient ID016 at BEFRCT

description:
Library name: 164-ID016_BEFRCT
column name in htg_raw_ano.xlsx164-ID016_BEFRCT


title: F123 mESC, T7 in situ transcription, "20kb" clonal line, rep1

description: Library name: 20kb


title: F123 mESC, T7 in situ transcription, "73Mb" clonal line, rep1

description: Library name: 73Mb


title: colon tissue ATAC, segment 6

city: Cambridge

first: Surya

last: Nagaraja

state: MA

address: 7 Divinity Ave, Bauer 2nd Floor 208

department: HSCRB

institute: Harvard University

description: Library name: colon_reg_06

data_processing:
Adaptors were trimmed using in-house scripts before alignment to the mm10 genome using bowtie2, exlcuding fragments larger than 2 kb.
Duplicates were removed using PicardTools. Reads were then filtered to exclude reads on chrM and chrY
Bigwigs were generated using fragsToBigWig, scaling to total number of reads overlapping promoters.
Peaks were called across all samples using macs2 without a shifting model and fixed lambda across all regions.
Assembly: mm10
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
Bulk ATAC-seq was performed as described in SHARE-seq (Ma et al. 2020) using Tagify Tn5 enzyme from SeqWell. Genomic DNA was extracted following ATAC-seq using a Qiagen MinElute Kit.
Purified DNA was PCR amplified using NEBNext 2X MasterMix with a unique i5 and i7 index pairing per sample. Final libraries were purified using Zymo DNA Clean & Concetrator Kit.

treatment_protocol: Colon tissue was dissected between the cecum and rectum was dissected and divided into six segments of equal length (segment 1 being closest to cecum). Each segment was placed in a solution of 4 mM EDTA/10% FBS/PBS and incubated prior to scraping of colonic mucosa. Tissue was then further disgested with collagenase and dispase to single cells.

value: colon

value: colonic epithelium

value: WT

value: segment 6 (1 = adjacent to cecum, 6 = adjacent to rectum)

value: RegionalATAC


title: Targeted gene expression of patient ID011 at BEFRCT

description:
Library name: 164-ID011_BEFRCT
column name in htg_raw_ano.xlsx164-ID011_BEFRCT

value: IV

value: CR

value: COLD


title: colon tissue ATAC, segment 4

description: Library name: colon_reg_04

value: segment 4 (1 = adjacent to cecum, 6 = adjacent to rectum)


title: Targeted gene expression of patient ID011 at 4WRCT

description:
Library name: 164-ID011_4WRCT
column name in htg_raw_ano.xlsx164-ID011_4WRCT

value: 4 weeks after RCT


title: C2_Discovery_125

value: F

value: Blood cells


title: C5_Discovery_132


title: C3_Discovery_129


title: Targeted gene expression of patient ID012 at BEFRCT

description:
Library name: 164-ID012_BEFRCT
column name in htg_raw_ano.xlsx164-ID012_BEFRCT

value: Tumor

value: before RCT

value: III


title: colon tissue ATAC, segment 2

description: Library name: colon_reg_02

value: segment 2 (1 = adjacent to cecum, 6 = adjacent to rectum)


title: F123 mESC, T7 in situ transcription, TRACK-IT post-remobilization, rep1

description: Library name: post

value: Embryonic stem cells

value: wild type

value: T7 in situ transcription


title: Targeted gene expression of patient ID006 at BEFRCT

description:
Library name: 164-ID006_BEFRCT
column name in htg_raw_ano.xlsx164-ID006_BEFRCT

value: II

value: SD

value: PR


title: C6_Discovery_122

value: M


title: F123 mESC, T7 in situ transcription, TRACK-IT parental line, rep1

description: Library name: pre


title: colon tissue ATAC, segment 1

description: Library name: colon_reg_01

value: colon

value: colonic epithelium

value: WT

value: segment 1 (1 = adjacent to cecum, 6 = adjacent to rectum)

value: RegionalATAC


title: Targeted gene expression of patient ID013 at BL

description:
Library name: 164-ID013_BL
column name in htg_raw_ano.xlsx164-ID013_BL

value: baseline

value: CR

value: COLD


title: F123 mESC, T7 in situ transcription, "2Mb" clonal line, rep1

description: Library name: 2Mb


title: JUN alone

description: Library name: JUN

data_processing:
Adaptors were trimmed using in-house scripts before alignment to the mm10 genome using bowtie2, exlcuding fragments larger than 2 kb.
Duplicates were removed using PicardTools. Reads were then filtered to exclude reads on chrM and chrY
All conditions were downsampled to an equivalent number of insertions in selected regions. Multiscale footprinting was performed (Hu et al 2025) using a one-sided binomial test relative to Control_2, testing for depletion of insertions in center vs flanking windows of varying radius lengths (2-99). To test for depletion and account for intrinsic Tn5 sequence preferences, expected insertions in center and flanking windows were calculated using observed frequencies in a naked (no TF) control condition.
Bigwigs were constructed using the python package pyBigWig; footprint scores were calculated as -log(p-value) of depletion and scores from the 14 bp radius were inserted at their genomic coordinates in the mm10 genome
Assembly: mm10
Supplementary files format and content: bigwig

source_name: colon epithelium

extract_protocol:
Tn5 enzyme was added to the reaction and incubated at 37C for 30 min before purification with Qiagen MinElute Kit
Purified DNA was PCR amplified using NEBNext 2X MasterMix with a unique i5 and i7 index pairing per sample. Final libraries were purified using Zymo DNA Clean & Concetrator Kit.

treatment_protocol: Purified proteins were mixed in the combnations above with naked DNA of 63 loci cloned from mouse colonic epithelium.

value: colon epithelium

value: JUN alone

value: IVFP


title: Targeted gene expression of patient ID012 at BL

description:
Library name: 164-ID012_BL
column name in htg_raw_ano.xlsx164-ID012_BL

value: Tumor

value: III


title: F123 mESC, T7 in situ transcription, no transposons, rep1

description: Library name: ctrl

value: Embryonic stem cells

value: wild type

value: T7 in situ transcription


title: C6_Discovery_126

value: M

value: Blood cells


title: Targeted gene expression of patient ID009 at 4WRCT

description:
Library name: 164-ID009_4WRCT
column name in htg_raw_ano.xlsx164-ID009_4WRCT

value: 4 weeks after RCT

value: II

value: SD

value: HOT


title: Targeted gene expression of patient ID005 at 4WRCT

description:
Library name: 164-ID005_4WRCT
column name in htg_raw_ano.xlsx164-ID005_4WRCT

value: PR

value: PD


title: F123 mESC, T7 in situ transcription, "5kb" clonal line, rep1

description: Library name: 5kb


title: Targeted gene expression of patient ID008 at 4WRCT

description:
Library name: 164-ID008_4WRCT
column name in htg_raw_ano.xlsx164-ID008_4WRCT

value: CR


title: Targeted gene expression of patient ID008 at BEFRCT

description:
Library name: 164-ID008_BEFRCT
column name in htg_raw_ano.xlsx164-ID008_BEFRCT

value: before RCT

value: COLD


title: colon tissue ATAC, segment 3

description: Library name: colon_reg_03

value: colon

value: colonic epithelium

value: WT

value: segment 3 (1 = adjacent to cecum, 6 = adjacent to rectum)

value: RegionalATAC


title: C6_Discovery_120


title: F123 mESC, T7 in situ transcription, "70kb" clonal line, rep1

description: Library name: 70kb

value: Embryonic stem cells

value: T7 in situ transcription


title: C6_Discovery_124

value: M

value: Blood cells


title: C6_Discovery_119


title: JUN and FOXA1 combination

description: Library name: JUNFOXA1

value: colon epithelium

value: JUN and FOXA1 combination

value: IVFP


title: Targeted gene expression of patient ID009 at BL

description:
Library name: 164-ID009_BL
column name in htg_raw_ano.xlsx164-ID009_BL

value: Tumor

value: baseline

value: II

value: SD


title: Targeted gene expression of patient ID008 at BL

description:
Library name: 164-ID008_BL
column name in htg_raw_ano.xlsx164-ID008_BL

value: III

value: PR

value: CR

value: HOT


title: Targeted gene expression of patient ID005 at BL

description:
Library name: 164-ID005_BL
column name in htg_raw_ano.xlsx164-ID005_BL

value: PD

value: COLD


title: Targeted gene expression of patient ID011 at BL

description:
Library name: 164-ID011_BL
column name in htg_raw_ano.xlsx164-ID011_BL

value: IV


title: Targeted gene expression of patient ID005 at BEFRCT

description:
Library name: 164-ID005_BEFRCT
column name in htg_raw_ano.xlsx164-ID005_BEFRCT

value: before RCT


title: JUN, FOS, FOXP1 combination

description: Library name: JUNFOSFOXP1

value: JUN, FOS, FOXP1 combination


title: C6_Discovery_117

value: F

value: Blood cells


title: Targeted gene expression of patient ID004 at BEFRCT

description:
Library name: 164-ID004_BEFRCT
column name in htg_raw_ano.xlsx164-ID004_BEFRCT


title: Liver CD45+ cells enriched with F4/80+ cells, STAT1 KO, PBS, ADT

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

description:
Library name: Sample1_ADT
ADT library, 10x Genomics

data_processing:
Demultiplexed data was processed using Cellranger 6.0.0
Assembly: GRCm38.99 (GRCm38.p6)
Supplementary files format and content: Matrices (.h5 files)
Supplementary files format and content: feature_reference.csv containing all antibodies
Library strategy: CITE-seq

molecule: protein

source_name: Liver

extract_protocol:
Liver tissue was mechanically fragmented and enzymatically digested with Collagenase D and DNAse I. Liver leukocytes were isolated via density centrifugation with 37.5 % Percoll.
Cells were stained with fluoresence-activated cell sorting (FACS) antibodies and CITE-seq antibodies. Sorted CD45+ liver cells were enriched with CD3-CD19-CD45+F4/80+ cells. Cellular suspensions were loaded on a Chromium Single Cell 5′ GEM, Library & Gel Bead Kit (5' (v2) Dual index, 10X Genomics) according to the manufacturer’s instructions.

treatment_protocol: To induce MAS, mice were 5 times injected with CpG on day 0, 2, 4, 7 and 9. Control mice were 5 times injected with PBS on day 0, 2, 4, 7 and 9. At day 10, mice were sacraficed.

value: Liver

value: CD45+ cells enriched with F4/80+ cells

value: STAT1 KO

tag: age

value: 8-10 weeks old

value: PBS

value: pooled male and female

tag: library type

value: ADT

tag: adt

value: Panel of 199 antibodies, list provided in feature_reference.csv

tag: processed file


title: Liver CD45+ cells enriched with F4/80+ cells, WT, CpG, GEX

description:
Library name: Sample4_GEX
GEX library, 10x Genomics

molecule: polyA RNA

tag: tissue

tag: cell type

value: WT

tag: treatment

value: CpG

value: mRNA


title: Targeted gene expression of patient ID007 at BEFRCT

description:
Library name: 164-ID007_BEFRCT
column name in htg_raw_ano.xlsx164-ID007_BEFRCT

value: Tumor

value: III

value: SD

value: PR

value: HOT


title: colon tissue ATAC, segment 5

description: Library name: colon_reg_05

value: colon

value: colonic epithelium

tag: genotype

value: segment 5 (1 = adjacent to cecum, 6 = adjacent to rectum)

tag: batch

value: RegionalATAC


title: C2_Discovery_118

tag: Sex

value: F

value: Blood cells


title: Targeted gene expression of patient ID003 at BEFRCT

description:
Library name: 164-ID003_BEFRCT
column name in htg_raw_ano.xlsx164-ID003_BEFRCT

tag: patient id

tag: sample timepoint

value: before RCT

value: II

value: PD

value: CR

value: COLD


title: F123 mESC, T7 in situ transcription, TRACK-IT random plasmid remobilization, rep1

description: Library name: rnd

tag: cell line

value: Embryonic stem cells

value: wild type

value: T7 in situ transcription


title: JUN, FOS, FOXA1 combination

description: Library name: JUNFOSFOXA1

value: colon epithelium

value: JUN, FOS, FOXA1 combination

value: IVFP


title: C6_Discovery_123

value: M


title: Liver CD45+ cells enriched with F4/80+ cells, WT, CpG, ADT

description:
Library name: Sample4_ADT
ADT library, 10x Genomics

value: Liver

value: CD45+ cells enriched with F4/80+ cells

value: WT

value: 8-10 weeks old

value: CpG

value: pooled male and female

value: ADT

value: Panel of 199 antibodies, list provided in feature_reference.csv


title: Targeted gene expression of patient ID007 at BL

description:
Library name: 164-ID007_BL
column name in htg_raw_ano.xlsx164-ID007_BL

value: Tumor

value: baseline

tag: figo

value: III

tag: recist within 1week before rct

value: SD

tag: recist 4 weeks after rct

value: PR


title: JUN and FOXP1 combination

description: Library name: JUNFOXP1

value: colon epithelium

value: JUN and FOXP1 combination


title: C6_Discovery_121

value: Blood cells


title: Targeted gene expression of patient ID002 at BL

description:
Library name: 164-ID002_BL
column name in htg_raw_ano.xlsx164-ID002_BL

value: II

value: CR

tag: recist end of treatment visit

tag: hot score (gsva)

tag: hot status

value: COLD


title: C2_Discovery_112

value: F


title: FOXP1 alone

description: Library name: FOXP1

value: FOXP1 alone

value: IVFP


title: Targeted gene expression of patient ID004 at BL

description:
Library name: 164-ID004_BL
column name in htg_raw_ano.xlsx164-ID004_BL

value: PD


title: C6_Discovery_116


title: Liver CD45+ cells enriched with F4/80+ cells, STAT1 KO, CpG, ADT

description:
Library name: Sample2_ADT
ADT library, 10x Genomics

value: Liver

value: CD45+ cells enriched with F4/80+ cells

value: STAT1 KO

tag: age

value: 8-10 weeks old

value: CpG

value: pooled male and female

tag: library type

value: ADT

tag: adt


title: C6_Discovery_114

value: M

tag: tissue


title: C3_Discovery_111


title: RNAseq,shNT,rep2

first: wenchen

last: luo

address: Dongan Road

institute: Fudan University

description:
Library name: Sample6
NT-2

data_processing:
Raw FASTQ reads were trimmed using Trim Galore and transcript quantification was performed using Salmon in the quasi-mapping mode.
Assembly: hg38
Supplementary files format and content: RNA count matrix at the gene level.

source_name: control

extract_protocol:
For RNA-seq,total RNA was extracted using the RNAprep Pure Cell/Bacteria Kit (TIANGEN; DP430) following the manufacturer’s protocol.
For RNA-seq, the extracted RNA was utilized for library construction with the Illumina TruSeq Stranded Total RNA Library Prep Kit. The library was sequenced using paired-end 150-bp reads.

tag: cell type

value: cell line

tag: treatment

value: shNT


title: JUN and FOS combination

description: Library name: JUNFOS

value: colon epithelium

value: JUN and FOS combination

tag: batch


title: Targeted gene expression of patient ID003 at BL

description:
Library name: 164-ID003_BL
column name in htg_raw_ano.xlsx164-ID003_BL

value: Tumor

value: baseline

value: II

value: CR

value: COLD


title: Liver CD45+ cells enriched with F4/80+ cells, WT, PBS, GEX

description:
Library name: Sample3_GEX
GEX library, 10x Genomics

value: Liver

tag: genotype

value: WT

value: PBS

tag: Sex

value: mRNA


title: RNAseq,shNT,rep1

description:
Library name: Sample5
NT-1


title: Targeted gene expression of patient ID006 at BL

description:
Library name: 164-ID006_BL
column name in htg_raw_ano.xlsx164-ID006_BL

tag: patient id

tag: sample timepoint

value: SD

value: PR


title: FOXA1 alone

description: Library name: FOXA1

value: FOXA1 alone

value: IVFP


title: Targeted gene expression of patient ID002 at BEFRCT

description:
Library name: 164-ID002_BEFRCT
column name in htg_raw_ano.xlsx164-ID002_BEFRCT

value: before RCT

tag: figo

value: HOT


title: Liver CD45+ cells enriched with F4/80+ cells, WT, PBS, ADT

description:
Library name: Sample3_ADT
ADT library, 10x Genomics

value: CD45+ cells enriched with F4/80+ cells

value: 8-10 weeks old

value: pooled male and female

value: ADT

value: Panel of 199 antibodies, list provided in feature_reference.csv

tag: processed file


title: C2_Discovery_110

value: M

value: Blood cells


title: Liver CD45+ cells enriched with F4/80+ cells, STAT1 KO, CpG, GEX

description:
Library name: Sample2_GEX
GEX library, 10x Genomics

value: Liver

value: STAT1 KO

value: CpG


title: FOS alone

description: Library name: FOS

value: colon epithelium

value: FOS alone


title: C2_Discovery_109


title: Targeted gene expression of patient ID010 at BL

description:
Library name: 164-ID010_BL
column name in htg_raw_ano.xlsx164-ID010_BL

value: Tumor

value: baseline

value: III

tag: recist within 1week before rct

value: SD

tag: recist 4 weeks after rct

value: PR

value: CR

value: COLD


title: C2_Discovery_115

value: F


title: RNAseq,shNT,rep3

description:
Library name: Sample7
NT-3

tag: cell line

value: cell line

value: shNT


title: RNAseq,shDpep2.968,rep2

description:
Library name: Sample2
shD1-2

source_name: Dpep2 knockdown


title: FOS and FOXA1 combination

description: Library name: FOSFOXA1

value: FOS and FOXA1 combination

value: IVFP


title: C2_Discovery_108

source_name: Blood cells

value: M

value: Blood cells


title: Liver CD45+ cells enriched with F4/80+ cells, STAT1 KO, PBS, GEX

description:
Library name: Sample1_GEX
GEX library, 10x Genomics

value: Liver

value: CD45+ cells enriched with F4/80+ cells

value: STAT1 KO

value: 8-10 weeks old

value: PBS

value: pooled male and female

value: mRNA


title: RNAseq,shDpep2.968,rep1

description:
Library name: Sample1
shD1-1


title: C6_Discovery_113


title: C2_Discovery_106


title: FOS and FOXP1

description: Library name: FOSFOXP1

value: colon epithelium

value: FOS and FOXP1


title: no transcription factor control, rep 1

description: Library name: Control_1

value: no transcription factor control


title: no transcription factor control, rep 2

description: Library name: Control_2


title: Targeted gene expression of patient ID001 at BEFRCT

description:
Library name: 164-ID001_BEFRCT
column name in htg_raw_ano.xlsx164-ID001_BEFRCT

value: Tumor

value: before RCT

value: III

value: PR

value: CR

tag: recist end of treatment visit

tag: hot score (gsva)

tag: hot status

value: HOT


title: colonic epithelial tissue, healthy controls, rep 1

description: Library name: DSS21_M10_Fos_CT

data_processing:
Adaptors were trimmed using in-house scripts before alignment to the mm10 genome using bowtie2, exlcuding fragments larger than 2 kb.
Duplicates were removed using PicardTools. Reads were then filtered to exclude reads on chrM and chrY
Bigwigs were generated using fragsToBigWig, scaling to total number of reads overlapping promoters.
Peaks were called across all samples using macs2 without a shifting model and fixed lambda across all regions.
Assembly: mm10
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&Tag

extract_protocol:
Colonic tissue was lysted using 0.1% Triton-X 100 and 20% glycerol and bound nuclei were bound to Concavalin-A beads prior to incubation with anti-Fos antibody (courtesy of M. Greenberg) overnight. Nuclei were washed. Incubated with secondary antibody, washed again and incubated with pAG-Tn5. Nuclei were then lysed with 0.1% SDS then quenched with 0.5% Triton-X 100.
Purified DNA was PCR amplified using NEBNext 2X MasterMix with a unique i5 and i7 index pairing per sample. Final libraries were purified using Zymo DNA Clean & Concetrator Kit.

treatment_protocol: Colitis mice were treated with 1-1.5% DSS in drinking water for 3 cycles of 7 days on/10 days off. Animals were sacrificed 22 days following last cycle of DSS. Colons were incubated in 4 mM EDTA/10% FBS/PBS for 30 min then colonic mucosa was scraped.

value: colon

value: colonic epithelium

value: WT

value: control


title: control organoids, T5224 treated, 24 h, rep1

description: Library name: DSS33_M5_T5224

growth_protocol: Colon organoids were grown in WENR media: 50% ENR (Crypt Basal with 50 ng/mL EGF, 100 ng/mL Noggin, 1:100 Rspondin conditioned media) and 50% Wnt conditioned media. Organoids were passaged every 7 to 10 days by mild dissociation in TrypLE.

treatment_protocol: Mouse colonic organoids were treated with AP-1 inhbitor T-5224 at 10 uM for 24 hours before being viably frozen. Cells were later thawed and nuclei extracted using 0.1% NP-40 before performing bulk ATAC-seq.

value: control, 10 uM T-5224, 24 hours


title: Targeted gene expression of patient ID035 at BEFRCT

description:
Library name: 164-ID035_BEFRCT
column name in htg_raw_ano.xlsx164-ID035_BEFRCT

value: COLD


title: Targeted gene expression of patient ID038 at 4WRCT

description:
Library name: 164-ID038_4WRCT
column name in htg_raw_ano.xlsx164-ID038_4WRCT

value: 4 weeks after RCT

value: II

value: SD


title: Targeted gene expression of patient ID035 at BL

description:
Library name: 164-ID035_BL
column name in htg_raw_ano.xlsx164-ID035_BL

value: baseline


title: RNAseq,shDpep2.759,rep2

description:
Library name: Sample4
shD2-2

value: cell line


title: control organoids, DMSO treated, 24 h, rep1

description: Library name: DSS33_M5_DMSO

value: control, 0.1% DMSO, 24 hours


title: ileum muscle, female GFPpos, rep1

city: Boston

first: Meenakshi

last: Rao

address: 300 Longwood Ave

department: Pediatrics-Division of Gastroenterology

institute: Boston Children's Hospital

data_processing:
Paired end sequencing was then performed using Novaseq 6000 with an average read count of ~50-75 million reads per sample and an average of 90% mapped reads to the genome and minimum ~50% reads aligned to exons as determined using Qualimap
Fastq files were converted into BAM files and aligned to the genome using STAR 2.5.2 through Harvard Medical School
Samtools flagstats was used to compute alignment efficiency of reads.
Count files were generated using Subread 2.0.0 package  and FeatureCounts for all samples.
Count matrix generation, normalization, differential analyses, and visualization of sequencing data were performed using R 4.3.1 DESeq2
Assembly: mm10
Supplementary files format and content: comma separated values file with raw gene counts for each sample per column

source_name: ileum

extract_protocol:
RNA was extracted using RNAeasy Micro kit (Quiagen) as per manufacturer's protocol.
RNA libraries were generated using Takara SMARTseq v4 kit per manufacturer's protocol.

value: ileum

tag: age

value: 8-12 weeks

value: Plp1pos glia

value: muscularis

value: GFPpos

value: female


title: ileum mucosa, female GFPneg, rep3

tag: tissue

value: Plp1neg non-glia

value: mucosa

value: GFPneg


title: RNAseq,shDpep2.759,rep1

description:
Library name: Sample3
shD2-1

tag: cell type


title: C2_Discovery_104

data_processing: ChAMP package in R environment

extract_protocol: precipitation with sodium acetate

value: M

value: Blood cells


title: colonic epithelial tissue, colitis recovered, rep 1

description: Library name: DSS21_M4_Fos_CT

value: colon

value: colonic epithelium

value: WT

tag: treatment

value: colitis recovered, 22 days following cessation of DSS


title: ileum muscle, female GFPpos, rep2


title: colonic epithelial tissue, healthy controls, rep 2

description: Library name: DSS21_M11_Fos_CT

value: control

tag: batch


title: colonic epithelial tissue, colitis recovered, rep 2

description: Library name: DSS21_M5_Fos_CT

tag: genotype


title: C2_Discovery_105

tag: Sex

value: F


title: ileum mucosa, male GFPneg, rep3

value: ileum

value: male


title: Targeted gene expression of patient ID038 at BEFRCT

description:
Library name: 164-ID038_BEFRCT
column name in htg_raw_ano.xlsx164-ID038_BEFRCT

value: Tumor

tag: patient id

value: before RCT

value: II

value: SD

value: PR

value: CR

value: HOT


title: C2_Discovery_102

value: M


title: Targeted gene expression of patient ID038 at BL

description:
Library name: 164-ID038_BL
column name in htg_raw_ano.xlsx164-ID038_BL

tag: sample timepoint

value: baseline

value: COLD


title: ileum mucosa, female GFPpos, rep3

value: 8-12 weeks

value: Plp1pos glia

value: mucosa

value: GFPpos

value: female


title: C2_Discovery_101

value: F

value: Blood cells


title: Targeted gene expression of patient ID036 at 4WRCT

description:
Library name: 164-ID036_4WRCT
column name in htg_raw_ano.xlsx164-ID036_4WRCT

value: Tumor

value: 4 weeks after RCT

tag: figo

value: III


title: Targeted gene expression of patient ID037 at BL

description:
Library name: 164-ID037_BL
column name in htg_raw_ano.xlsx164-ID037_BL

value: II

value: SD


title: Targeted gene expression of patient ID036 at BL

description:
Library name: 164-ID036_BL
column name in htg_raw_ano.xlsx164-ID036_BL

value: CR


title: C2_Discovery_103


title: Targeted gene expression of patient ID037 at 4WRCT

description:
Library name: 164-ID037_4WRCT
column name in htg_raw_ano.xlsx164-ID037_4WRCT

value: PR

value: HOT


title: ileum mucosa, male GFPneg, rep2

value: ileum

value: Plp1neg non-glia

value: GFPneg

value: male


title: (AT)34 chr10

city: New York

first: Bertrand

last: Theulot

state: NY

address: 100 WASHINGTON SQ E, Attn: Duncan Smith

institute: NYU

description: Library name: 2258

data_processing:
Reads were aligned to the Saccharomyces cerevisiae S288C reference genome (R64-5-1-20240529) using BWA-MEM (v0.7.17). Alignments were converted to BAM, filtered with SAMtools (v1.19) to retain reads with mapping quality ≥30 and to remove secondary and supplementary alignments (-q 30 -F 2304), then sorted and indexed. Strand-specific coverage was computed by extracting reverse-strand reads (flags 0x50 and 0x90) and plus-strand reads (flags 0x40 and 0x80 with 0x10 excluded), and running samtools depth -aa to include all genomic positions, including zero-coverage bases. Plus- and reverse-strand coverage files were merged position-by-position with awk.
Assembly: S288C_reference_sequence_R64-5-1_20240529
Supplementary files format and content: Coverage of okazaki fragments per strand at each position on the genone (chrom,pos,cov_plus _strand, cov_minus_strand)

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to mid-log phase in YPD at 30C before treatment

extract_protocol:
Okazaki fragments were enriched and purified as described previously (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).
Libraries were generated as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).

treatment_protocol: Cells carrying a doxycycline-repressible CDC9 gene were grown to mid-log phase before addition of 40 mg/L doxycycline for 2 hrs before harvest. Cells subjected to anchor-away depletion of Cdc9 were grown to mid-log phase and then treated with rapamycin (final, 1 µg/mL) for 1 h. Genomic DNA was extracted from spheroplasts, and Okazaki fragments were isolated, end-labeled, and deep-sequenced as previously described (Smith and Whitehouse, 2012).

value: haploid yeast cells

value: MAT ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+, AT34 2 kb downstream ARS1019 cdc9::tetO7-CDC9 cmv_Laci-NAT

value: 40 mg/L doxycycline for 2 hrs


title: Targeted gene expression of patient ID034 at BEFRCT

description:
Library name: 164-ID034_BEFRCT
column name in htg_raw_ano.xlsx164-ID034_BEFRCT

value: before RCT

value: COLD


title: C2_Discovery_98

value: M

value: Blood cells


title: Targeted gene expression of patient ID034 at BL

description:
Library name: 164-ID034_BL
column name in htg_raw_ano.xlsx164-ID034_BL

value: Tumor

value: baseline


title: No Repeat control chr10

description: Library name: 2092

value: MAT ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+, Flex1 Control 2 kb downstream ARS1019, cdc9::tetO7-CDC9 cmv_Laci-NAT


title: C2_Discovery_107

value: F


title: ileum mucosa, female GFPpos, rep2

value: 8-12 weeks

value: Plp1pos glia

value: mucosa

value: GFPpos

value: female


title: ileum mucosa, female GFPneg, rep2

value: ileum

value: Plp1neg non-glia

value: GFPneg


title: (AT)34 chr6

description: Library name: 2441

value: haploid yeast cells

value: MAT ade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3-1, tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1 CDC9-FRB::KanMX ,AT-34-HPH cassette at Chr6int2 Locus

value: rapamycin (final, 1 µg/mL) for 1 h


title: Targeted gene expression of patient ID033 at 4WRCT

description:
Library name: 164-ID033_4WRCT
column name in htg_raw_ano.xlsx164-ID033_4WRCT

value: 4 weeks after RCT

value: II

value: SD

value: PR

value: HOT


title: C2_Discovery_96

value: M

value: Blood cells


title: Targeted gene expression of patient ID036 at BEFRCT

description:
Library name: 164-ID036_BEFRCT
column name in htg_raw_ano.xlsx164-ID036_BEFRCT

value: Tumor

value: before RCT

value: III

value: CR


title: ileum muscle, male GFPpos, rep3

value: ileum

value: 8-12 weeks

value: Plp1pos glia

value: muscularis

value: GFPpos

value: male


title: Targeted gene expression of patient ID037 at BEFRCT

description:
Library name: 164-ID037_BEFRCT
column name in htg_raw_ano.xlsx164-ID037_BEFRCT


title: Targeted gene expression of patient ID033 at BEFRCT

description:
Library name: 164-ID033_BEFRCT
column name in htg_raw_ano.xlsx164-ID033_BEFRCT

value: COLD


title: ileum mucosa, female GFPpos, rep1

value: mucosa

value: female


title: ileum muscle, male GFPneg, rep2

value: Plp1neg non-glia

value: GFPneg


title: rad52delta (AT)34 chr10

description: Library name: 2297

value: haploid yeast cells

value: MAT ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+, AT34 2 kb downstream ARS1019 cdc9::tetO7-CDC9 cmv_Laci-NAT Rad52::KanMX

value: 40 mg/L doxycycline for 2 hrs


title: eIF3g/i

city: Kumamoto

first: Shingo

last: Usuki

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics (IMEG)

country: Japan

institute: Kumamoto University

description: Library name: Sample 2

data_processing:
Adaptor trimming and QC were done using Trim galore (v0.6.6)
Desired sequences were extracted using seqkit (v2.4.0)
Motif counts were performed using R
Assembly: UCSC sacCer3
Supplementary files format and content: tab-delimited text file includes motif counts for each sample.

source_name: Yeast strains

extract_protocol:
SELEX was performed for 12 rounds in each experiment, as described  in 5, with 18 base-long randomized ribonucleotide sequence flanked by primer binding sites designed for cDNA synthesis, PCR and RNA synthesis by T7 RNA polymerase. For these experiments we used His6-tagged eIF3g/Tif35p or its complex with (untagged) eIF3i/Tif34p. The DNA fragments encoding them were amplified by PCR using budding yeast Saccharomyces cerevisiae genomic DNA and then cloned into pET28b (with hexa-histidine tag fused to its N-terminus, in the case of eIF3g) and were co-expressed in E. coli strain BL21-CodonPlus (DE3)-RILP (Stratagene).  The expressed protein(s) was purified by Ni-NTA (Qiagen) and Q-sepharose (Cytiva).
SELEX output RNAs were ligated to adaptor sequences and made into cDNA, which was then sequenced by generating RNAseq library

value: Yeast strains


title: Targeted gene expression of patient ID032 at 4WRCT

description:
Library name: 164-ID032_4WRCT
column name in htg_raw_ano.xlsx164-ID032_4WRCT

value: Tumor

value: 4 weeks after RCT

value: III

value: PR


title: Targeted gene expression of patient ID032 at BEFRCT

description:
Library name: 164-ID032_BEFRCT
column name in htg_raw_ano.xlsx164-ID032_BEFRCT

value: before RCT

value: CR

value: HOT


title: Targeted gene expression of patient ID033 at BL

description:
Library name: 164-ID033_BL
column name in htg_raw_ano.xlsx164-ID033_BL

value: baseline

value: II

value: SD


title: colitis organoids, T5224 treated, 24 h, rep1

description: Library name: DSS33_M4_T5224

value: colon

value: colonic epithelium

value: WT

value: colitis, 10 uM T-5224, 24 hours


title: colitis organoids, DMSO treated, 24 h, rep1

description: Library name: DSS33_M4_DMSO

value: coltiis, 0.1% DMSO, 24 hours


title: Targeted gene expression of patient ID032 at BL

description:
Library name: 164-ID032_BL
column name in htg_raw_ano.xlsx164-ID032_BL


title: C2_Discovery_99

value: F

value: Blood cells


title: C2_Discovery_100

value: M


title: C2_Discovery_95


title: ileum mucosa, male GFPpos, rep2

value: ileum

value: 8-12 weeks

value: Plp1pos glia

value: mucosa

value: GFPpos

value: male


title: C2_Discovery_92


title: No Repeat Control chr6

description: Library name: 2442

value: haploid yeast cells

value: MAT ade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3-1, tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1 CDC9-FRB::KanMX, Flex1Control-HPH cassette at Chr6int2 Locus

value: rapamycin (final, 1 µg/mL) for 1 h


title: C2_Discovery_97


title: ileum muscle, male GFPpos, rep1

value: muscularis


title: ileum mucosa, male GFPpos, rep1


title: C2_Discovery_88


title: C2_Discovery_93


title: C5_Discovery_89


title: Targeted gene expression of patient ID031 at BL

description:
Library name: 164-ID031_BL
column name in htg_raw_ano.xlsx164-ID031_BL

value: Tumor

value: baseline

value: III

value: SD

value: CR

value: COLD


title: ileum muscle, male GFPpos, rep2

value: muscle


title: ileum mucosa, male GFPneg, rep1

value: ileum

value: Plp1neg non-glia

value: GFPneg


title: C2_Discovery_94

value: F

value: Blood cells


title: Purified HSCs, CD99 KO, rep 3

city: Dallas

first: Stephen

middle: Shiu-wah

last: Chung

state: TX

address: 6001 Forest Park Road

department: Internal Medicine

institute: University of Texas Southwetsern

data_processing:
RNA-seq data was aligned by STAR (Dobin et al., 2013) to human genome hg37
Reads for each gene were counted by HTSeq (Anders et al., 2015)
Gene expression was calculated (rsem-calculate-expression)
Supplementary files format and content: tab-delimited text file includes TPM and FPKM values for each sample
Supplementary files format and content: tab-delimited text file includes TPM, FPKM, and Isoform Percentage values for each sample

source_name: blood

growth_protocol: CD99 KO and WT littermate control mice on a C57Bl/6 background were aged to 10-12 weeks of age.

extract_protocol:
Purified cells were lysed in Trizol LS, and RNA was extracted using manufacturer's protocols.
Libraries for RNA-seq were prepared using SMARTer mRNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Hematopoietic stem cells (lineage- c-kit+ sca-1+ CD150+ CD34-) and granulocyte macrophage progenitors (lineage- c-kit+ sca-1- CD16/32+ CD34+) were purified using flow cytometry from freshly isolated bone marrow from CD99 KO and WT mice

value: blood

value: hematopoietic stem cells

value: CD99 KO


title: ileum muscle, male GFPneg, rep1

value: 8-12 weeks

value: male


title: Purified HSCs, CD99 KO, rep 4


title: C2_Discovery_90

first: Amandeep

last: Singh

address: Arthur-Scheunert-Allee 114-116

institute: German Institute of Human Nutrition


title: C2_Discovery_87


title: APOE & FHRE 2xKO Rep3

city: Jena

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

institute: Leibniz Institute for Natural Product Research and Infection Biology

data_processing:
Read quality was first assessed with FastQC (v0.12.1)
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic (v.0.36)
trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner (v.2.5.2b)
Unique gene hit counts were calculated by using featureCounts from the Subread package (v.1.5.2)
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file with raw counts for each sample
Supplementary files format and content: Tab-delimited text file with TPM normalised counts for each sample

source_name: liver

growth_protocol: Mice were housed in the FSU animal facility at 24°C. Mice were exposed to a 12-hour light/12-hour dark cycle with free access to normal chow food diet and water.

extract_protocol:
RNA seq via poly A selection; mRNA from liver samples from 3 animals of each genotype were purified using the total RNA purification kit (Norgen SKU 17200)
Illumina NovaSeq, PE 2x150, mRNA Enrichment, RNA, Fragmentation and Random priming, First and second strand cDNA synthesis, end repair, 5'phosphorylation and dA-tailing, adaptor ligation PCR enrichment and sequencing

treatment_protocol: FHRE+/- and ApoE+/- mice were breed together to generate the FHRE+/+ApoE+/+ (WT), FHRE+/+ApoE-/- (ApoE KO), FHRE-/- ApoE+/+ (FHRE KO) and FHRE-/-;ApoE-/- (FHRE/ApoE KO) mice.

value: liver

value: APOE & FHRE 2xKO


title: ileum muscle, female GFPneg, rep1

value: female


title: rad52delta (AT)34 chr6

description: Library name: 2439

value: haploid yeast cells

value: MAT ade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3-1, tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1 CDC9-FRB::KanMX, rad52::LEU,AT-34-HPH cassette at Chr6int2 Locus

value: rapamycin (final, 1 µg/mL) for 1 h


title: Targeted gene expression of patient ID030 at BL

description:
Library name: 164-ID030_BL
column name in htg_raw_ano.xlsx164-ID030_BL

value: Tumor

value: baseline

value: II

value: SD

value: CR

value: COLD


title: C2_Discovery_86

city: Potsdam

value: F

value: Blood cells


title: Targeted gene expression of patient ID031 at BEFRCT

description:
Library name: 164-ID031_BEFRCT
column name in htg_raw_ano.xlsx164-ID031_BEFRCT

value: before RCT

value: III

value: HOT


title: Purified GMPs, CD99 KO, rep 3

value: blood

value: granulocyte macrophage progenitors

value: CD99 KO


title: C2_Discovery_85


title: Purified HSCs, CD99 KO, rep 2

value: hematopoietic stem cells


title: eIF3g

description: Library name: Sample 1

value: Yeast strains


title: C2_Discovery_91


title: Purified GMPs, CD99 KO, rep 2


title: C2_Discovery_84


title: Targeted gene expression of patient ID030 at 4WRCT

description:
Library name: 164-ID030_4WRCT
column name in htg_raw_ano.xlsx164-ID030_4WRCT

value: 4 weeks after RCT


title: Targeted gene expression of patient ID029 at BL

description:
Library name: 164-ID029_BL
column name in htg_raw_ano.xlsx164-ID029_BL

value: Tumor

value: IV


title: ileum mucosa, female GFPneg, rep1

value: ileum

value: 8-12 weeks

value: Plp1neg non-glia

value: mucosa

value: GFPneg

value: female


title: Purified HSCs, CD99 WT, rep 3

value: WT


title: Purified HSCs, CD99 WT, rep 1


title: C2_Discovery_82

value: F

value: Blood cells


title: Targeted gene expression of patient ID029 at BEFRCT

description:
Library name: 164-ID029_BEFRCT
column name in htg_raw_ano.xlsx164-ID029_BEFRCT

value: before RCT

value: SD

value: CR

value: COLD


title: APOE & FHRE 2xKO Rep2

value: liver

value: APOE & FHRE 2xKO


title: Purified HSCs, CD99 WT, rep 2

value: blood

value: hematopoietic stem cells


title: Targeted gene expression of patient ID030 at BEFRCT

description:
Library name: 164-ID030_BEFRCT
column name in htg_raw_ano.xlsx164-ID030_BEFRCT

value: Tumor

value: II

value: HOT


title: APOE KO Rep3

value: APOE KO


title: Targeted gene expression of patient ID028 at 4WRCT

description:
Library name: 164-ID028_4WRCT
column name in htg_raw_ano.xlsx164-ID028_4WRCT

value: 4 weeks after RCT


title: APOE & FHRE 2xKO Rep1


title: Targeted gene expression of patient ID031 at 4WRCT

description:
Library name: 164-ID031_4WRCT
column name in htg_raw_ano.xlsx164-ID031_4WRCT

value: III


title: C2_Discovery_83


title: Targeted gene expression of patient ID029 at 4WRCT

description:
Library name: 164-ID029_4WRCT
column name in htg_raw_ano.xlsx164-ID029_4WRCT

value: IV


title: Targeted gene expression of patient ID027 at 4WRCT

description:
Library name: 164-ID027_4WRCT
column name in htg_raw_ano.xlsx164-ID027_4WRCT

value: PD


title: FHRE KO Rep1

description: RNAFHREkoLuce

value: FHRE KO


title: C2_Discovery_81

value: F

value: Blood cells


title: Purified GMPs, CD99 WT, rep 2

value: granulocyte macrophage progenitors

value: WT


title: C2_Discovery_79

value: M


title: Targeted gene expression of patient ID027 at BL

description:
Library name: 164-ID027_BL
column name in htg_raw_ano.xlsx164-ID027_BL

value: baseline

value: SD

value: CR

value: COLD


title: APOE KO Rep1

value: liver


title: WT mouse Rep2

value: WT mouse


title: FHRE KO Rep2


title: Purified HSCs, CD99 KO, rep 1

value: blood

value: hematopoietic stem cells

value: CD99 KO


title: WT mouse Rep1


title: WT mouse Rep3


title: AF cells, Young, id22349

city: Nantes

first: Romain

last: Guiho

address: 1 place Alexis Ricordeau

institute: Inserm UMRS 1229-RMeS Regenerative Medicine & Skeleton

description: Library name: Sample 16

data_processing:
Quality control was peformed using fastQC ( v0.11.8)
Reads are filtered and trimmed with fastp
Sequencing data was then aligned with STAR 2.7.10b
Reads in features were counted with HTSeq 2.0.3
Assembly: Ovis_aries_rambouillet.ARS-UI_Ramb_v2.0.111 genome
Supplementary files format and content: csv matrix including raw counts for each sample

organism: Ovis aries

source_name: Intervertebral disc

growth_protocol: Cells are maintaiedn in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S)

extract_protocol:
Total RNA was extracted from AF and NP cells at passage 1 (P1) of lamb and sheep was extracted using NucleoSpin RNA XS kit (Macherey-Nagel, 740902).
Library preparation was performed with Illumina® Stranded mRNA Prep kit.

value: Intervertebral disc

value: Young

value: AF cells

tag: animal id


title: C3_Discovery_77


title: AF cells, Young, id22362

description: Library name: Sample 15


title: C2_Discovery_76

value: F


title: FHRE KO Rep3

value: FHRE KO


title: Purified GMPs, CD99 KO, rep 1

value: granulocyte macrophage progenitors


title: C2_Discovery_78

value: Blood cells


title: Targeted gene expression of patient ID028 at BEFRCT

description:
Library name: 164-ID028_BEFRCT
column name in htg_raw_ano.xlsx164-ID028_BEFRCT

value: Tumor

value: before RCT

value: II

tag: recist within 1week before rct

value: HOT


title: hILC3 PCHi-C replicate 2

city: London

first: Mikhail

last: Spivakov

address: Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: Promoter Capture Hi-C library

data_processing:
library strategy: PCHi-C (Promoter Capture Hi-C)
Sequencing data from three ILC3 PCHi-C biological replicates were aligned to hg38 genome assembly using Bowtie2 and quality-controlled using HiCUP (Wingett et al., F1000Res 2015).
Significant interactions were then detected across the replicates by CHiCAGO (Cairns et al., Genome Biol 2016) as previously described (https://doi.org/10.1038/s41596-021-00567-5) at single DpnII fragment resolution and in bins of fragments approximately 5kb in length, with the baited promoter fragments left solitary (unbinned).
Assembly: GRCh38
Supplementary files format and content: The CHiCAGO objects (.Rds files) provide interaction data for all three replicates at DpnII fragment level (hILC3_all_merged_PCHiC_fragRes.Rds) and 5kb binned with solitary promoter baits (hILCs_all_merged_PCHiC_5kb.Rds) resolution.

source_name: Tonsil

extract_protocol:
Human tonsil tissue was processed by mincing with scissors followed by transfer of up to 4g of tissue to a gentleMACS C tube (Miltenyi Biotec) containing 8 mL of phosphate-buffered saline (PBS) with 0.5 mg/mL collagenase D and 3000 U/mL DNaseI, then dissociated on a GentleMACS Octo Dissociator (Miltenyi Biotec) using “program C (Spleen program 2 followed by spleen program 3).” Tissue homogenates were incubated in a 37°C water bath for 15 minutes, then dissociated again using “program C” and transferred through a 100 μm cell strainer into 20mL RPMI containing 10% human AB serum (Sigma Aldrich). Next, cell suspension was overlaid on 10mL of Ficoll-Paque PLUS (GE Healthcare) and subjected to density-gradient separation via centrifugation for 20 min at 1800rpm, 20°C, slow acceleration, no brake. Leukocytes were collected from the interphase layer and then washed with 50mL of PBS for 6 minutes at 1600rpm for 7 minutes, 20°C. Single cell suspensions of tonsil mononuclear cells were subjected to positive selection with anti-human-CD3, anti-human-CD19 and anti-human-CD14 (Miltenyi Biotec) and transferred through LD columns (Miltenyi Biotec) according to the manufacturer guidelines. The depleted cell suspension flowthrough was collected into 15mL conical and then centrifuged for 5 minutes at 1200rpm, 20°C. Subsequently, cells were labeled with LIVE/DEAD™ Fixable Near-IR dead cell stain kit (Invitrogen). Next, cells were labeled with sorting antibody cocktail which contained  negative linage (Lin-) CD19 Brilliant Violet (BV)421 (HIB19), CD14-BV421 (63D3) and CD3-BV421 (OKT3), and the following antibodies: CD45- FITC, (HI30), CD94-PerCP-Cy5.5 (DX22), CD127-PE-Cy7 (A019D5), cKit-BV510 (104D2) and NKp44-Alexa Fluor (AF)647 (P44-8) all purchased from Biolegend (San Diego, CA), CRTH2-PE (301109, R&D). ILC3 cells were sorted based on the expression of CD45+Lin-CD127+CD94-CRTH2-cKit+NKp44+, similarly to Bar-Ephraim et al. Cell sorting was performed using a FACSAria II sorter (BD Biosciences, Mountain View, CA, USA). Post sorting sorted ILC3 cells were washed with PBS for 5 minutes at 1200rpm, 20°C and then incubated in 100L of 2% formaldehyde (in PBS) for 10 minutes, followed by an addition of 0.125M glycine. Next, cells were centrifuged at 400g for 5 minutes at 4°C, resuspended with cold PBS and centrifuged again at 400g for 5 minutes at 4°C, supernatant was discarded, and cells were snap frozen in liquid nitrogen and then stored and -80°C prior to PCHi-C analysis.
Promoter Capture Hi-C was performed as previously described (doi: 10.1016/j.cell.2021.03.051). Cells were fixed in 2% PFA for 10 minutes, lysed in a lysis buffer (30 minutes on ice), and digested with DpnII (NEB) overnight at 37C rotating (950rpm). Restriction overhangs were filled-in with Klenow (NEB) using biotin-14-dATP (Jena Bioscience), and ligation was performed in the ligation buffer for 4 hours at 16C (T4 DNA ligase; Life Technologies). After overnight decrosslinking at 65C, the ligated DNA was tagmented to produce fragments of 300-700 bp range. Ligation products were isolated using MyOne C1 streptavidin beads (Life Technologies), followed by washing with Wash&Binding buffer and nuclease-free water. Isolated Hi-C ligation products on the beads were then used directly for PCR amplification, and the final Hi-C library was purified with AMPure XP beads (Beckman Coulter). Promoter Capture Hi-C was performed using a custom-design Agilent SureSelect system following the manufacturer’s protocol.

value: Tonsil

tag: restriction enzyme

value: DpnII

tag: molecule type

value: PCHi-C DNA


title: Purified GMPs, CD99 WT, rep 1

value: blood

value: WT


title: AF cells, Old, id61458

description: Library name: Sample 14

value: Old


title: NP cells, Young, id22362

description: Library name: Sample 13

value: Intervertebral disc

value: NP cells


title: Targeted gene expression of patient ID026 at BL

description:
Library name: 164-ID026_BL
column name in htg_raw_ano.xlsx164-ID026_BL

extract_protocol:
10mm2 of 5 micrometer FFPE tumour macrodissection tissue were lysed using HTG Lysis Buffer, followed by proteinase K digestion, and then transferred to an HTG EdgeSeq platform according to manufacturer protocols (HTG Molecular Diagnostics, Inc., Tucson, AZ).
The Oncology Biomarker Panel was used to  capture RNA expression levels of gene targets  on the HTG EdgeSeq platform according to manufacturer protocols (HTG Molecular Diagnostics, Inc., Tucson, AZ). The resulting DNA probes were quantitatively amplified with polymerase chain reaction adding extended primers ,including sequencing primer and sample barcode sequences. Library samples were cleaned up to remove excess primers, quantitated, pooled and sequenced using Illumina NextSeq500 sequencer using 50-cycles single end ((Illumina, Inc.).

value: baseline

value: SD

tag: recist 4 weeks after rct

value: PR

tag: recist end of treatment visit

value: COLD


title: Targeted gene expression of patient ID027 at BEFRCT

description:
Library name: 164-ID027_BEFRCT
column name in htg_raw_ano.xlsx164-ID027_BEFRCT

value: CR

value: PD

tag: hot score (gsva)

tag: hot status


title: Targeted gene expression of patient ID025 at BEFRCT

description:
Library name: 164-ID025_BEFRCT
column name in htg_raw_ano.xlsx164-ID025_BEFRCT

tag: tissue

value: Tumor

value: before RCT

value: IV


title: Fecal bacterial DNA, MET, rep5

city: Nam-gu, Pohang-si

first: Haeun

last: Ko

state: Gyeongsangbuk-do

address: 77, Cheongam-ro

department: Life Science

institute: POSTECH

description: Library name: HE_MET_5

data_processing:
QIIME2 (v2023.02) was used to process and analyze 16S rRNA gene amplicon sequencing data
Paired-end sequences were merged and quality-filtered using Deblur.
The resulting amplicon sequence variants (ASVs) were used for downstream analyses.
Assembly: SILVA
Supplementary files format and content: Read counts are shown in 16S rRNA read count file.

organism: feces metagenome

source_name: Mus musculus feces

extract_protocol:
Fecal DNA DNA was extracted using the NucleoSpin DNA Stool Kit (MACHEREY-NAGEL) following the manufacturer’s protocol.
Metagenomic sequencing was performed on an Illumina MiSeq platform (Illumina), targeting the V3 and V4 regions of the 16S rRNA gene according to the manufacturer's instructions. 16S rRNA gene amplicon sequencing

value: Feces


title: NP cells, Young, id22361

description: Library name: Sample 11

tag: age

value: Young

tag: cell type


title: hILC3 PCHi-C replicate 3

description: Promoter Capture Hi-C library

value: Tonsil

value: DpnII

value: PCHi-C DNA


title: AF cells, Old, id50052

description: Library name: Sample 12

value: Old

value: AF cells


title: Targeted gene expression of patient ID025 at BL

description:
Library name: 164-ID025_BL
column name in htg_raw_ano.xlsx164-ID025_BL

data_processing:
Illumina bcl2fastq is used for generation of FASTQ files
HTG EdgeSeq Parser software (version 5.1) is used for alignment to a priori defined target sequences.  Requirements include %Q30 >= 85%, %PF >= 75%, and 180 < CD < 290
Post-sequencing quality control using three quality control metrics: 1) Percent of reads allocated to the Positive control probe must not exceed 15%, 2) Total aligned reads must exceed 1,500,000, and 3) Relative Standard Deviaion (CV) of counts within a sample must exceed 0.1 (CV is calculated after removal of counts from ANT and POS control probes and log2 transformation after addition of 2 to avoid taking the log of 0). A log2 CPM normalization is then processed.
Assembly: hg38
Supplementary files format and content: Excel (xlsx) file includes raw counts for each content
Supplementary files format and content: Excel (xlsx) file includes normalized (log2 cpm) counts for each content

source_name: Tumor


title: C5_Discovery_73

value: M

value: Blood cells


title: APOE KO Rep2

value: liver

value: APOE KO


title: Targeted gene expression of patient ID026 at 4WRCT

description:
Library name: 164-ID026_4WRCT
column name in htg_raw_ano.xlsx164-ID026_4WRCT

value: 4 weeks after RCT

value: II

value: SD

value: PR

value: HOT


title: Targeted gene expression of patient ID024 at 4WRCT

description:
Library name: 164-ID024_4WRCT
column name in htg_raw_ano.xlsx164-ID024_4WRCT

value: Tumor

value: III

value: CR

value: COLD


title: hILC3 PCHi-C replicate 1

description: Promoter Capture Hi-C library

value: Tonsil

value: DpnII


title: Fecal bacterial DNA, MET, rep2

description: Library name: HE_MET_2

value: Feces


title: Targeted gene expression of patient ID026 at BEFRCT

description:
Library name: 164-ID026_BEFRCT
column name in htg_raw_ano.xlsx164-ID026_BEFRCT

value: before RCT


title: Purified GMPs, CD99 WT, rep 3

value: blood

value: granulocyte macrophage progenitors

value: WT

tag: treatment


title: Fecal bacterial DNA, MET, rep6

description: Library name: HE_MET_6


title: AF cells, Young, id22337

description: Library name: Sample 9

value: Intervertebral disc

value: Young

value: AF cells


title: C5_Discovery_75

value: M

value: Blood cells


title: C5_Discovery_69

value: F


title: C2_Discovery_80


title: NP cells, Old, id50052

description: Library name: Sample 10

value: Old

value: NP cells


title: Targeted gene expression of patient ID023 at BEFRCT

description:
Library name: 164-ID023_BEFRCT
column name in htg_raw_ano.xlsx164-ID023_BEFRCT

value: Tumor

value: IV

value: SD

value: PR

value: CR

value: HOT


title: Fecal bacterial DNA, NEO, rep4

description: Library name: HE_NEO_4

value: Feces


title: Targeted gene expression of patient ID028 at BL

description:
Library name: 164-ID028_BL
column name in htg_raw_ano.xlsx164-ID028_BL

value: baseline

value: II

value: COLD


title: C5_Discovery_67


title: Fecal bacterial DNA, MET, rep1

description: Library name: HE_MET_1


title: C5_Discovery_65


title: C5_Discovery_66


title: Fecal bacterial DNA, MET, rep3

description: Library name: HE_MET_3


title: C5_Discovery_68


title: Fecal bacterial DNA, MET, rep4

description: Library name: HE_MET_4


title: NP cells, Young, id22349

description: Library name: Sample 5

value: Intervertebral disc

value: Young


title: C5_Discovery_71

value: M


title: C5_Discovery_72

value: Blood cells


title: Targeted gene expression of patient ID022 at BL

description:
Library name: 164-ID022_BL
column name in htg_raw_ano.xlsx164-ID022_BL


title: C5_Discovery_70

value: F


title: NP cells, Young, id22337

description: Library name: Sample 8


title: AF cells, Old, id61248

description: Library name: Sample 2

value: Old

value: AF cells


title: GSC-0827_2_RNA1_Lib2

city: Manhasset

first: Nyasha

last: Chambwe

address: 350 Community Drive

department: Institute of Molecular Medicine

institute: Feinstein Institutes for Medical Research

description:
Library name: GSC-0827-Rep5
GSC-0827 Replicate 5

data_processing:
Raw (FASTQ) output RNAseq files were analyzed using the nextflow (ver 22.04.3) pipeline nf-core/rnaseq (version 3.7). Read quality control analysis were performed using FastQC, with filtering of ribosomal RNA reads by SortMeRNA. Genomic contaminants were removed by BBSplit prior to read quality assessment and adapter trimming using Trim Galore. STAR was used to align filtered reads to the human reference genome GRCh37. We used SAMtools to sort and index alignments, and Picard to mark duplicate reads. Expression was quantified using RSEM.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes gene-level raw counts across all samples

source_name: brain

extract_protocol:
Total RNA was extracted and purified using the miRNeasy micro kit (Qiagen)
Total RNA was isolated from cells using the miRNeasy micro kit (Qiagen). Library preparation was performed using the rRNA depletion KAPA RNA HyperPrep Kit with RiboErase (HMR)(Roche Sequencing and Life Science).

value: brain

tag: cell line

value: cancer stem cell line

value: glioma stem cell culture

tag: batch


title: NP cells, Old, id61248

description: Library name: Sample 6

value: NP cells


title: C5_Discovery_62

tag: Sex


title: Fecal bacterial DNA, NEO, rep3

description: Library name: HE_NEO_3


title: Targeted gene expression of patient ID024 at BL

description:
Library name: 164-ID024_BL
column name in htg_raw_ano.xlsx164-ID024_BL

value: Tumor

tag: patient id

tag: sample timepoint

value: III

value: SD

value: CR


title: C5_Discovery_61


title: Fecal bacterial DNA, NEO, rep2

description: Library name: HE_NEO_2

value: Feces


title: NP cells, Old, id61227

description: Library name: Sample 1

tag: animal id


title: GSC-0827_1_RNA1_Lib2

description:
Library name: GSC-0827-Rep4
GSC-0827 Replicate 4


title: Fecal bacterial DNA, NEO, rep6

description: Library name: HE_NEO_6


title: Targeted gene expression of patient ID022 at 4WRCT

description:
Library name: 164-ID022_4WRCT
column name in htg_raw_ano.xlsx164-ID022_4WRCT

value: 4 weeks after RCT

tag: figo

value: II

tag: recist within 1week before rct

value: COLD


title: Targeted gene expression of patient ID022 at BEFRCT

description:
Library name: 164-ID022_BEFRCT
column name in htg_raw_ano.xlsx164-ID022_BEFRCT

value: before RCT

value: HOT


title: C5_Discovery_63

value: F

value: Blood cells


title: C5_Discovery_74


title: Targeted gene expression of patient ID024 at BEFRCT

description:
Library name: 164-ID024_BEFRCT
column name in htg_raw_ano.xlsx164-ID024_BEFRCT


title: Fecal bacterial DNA, AMP, rep3

description: Library name: HE_AMP_3


title: Fecal bacterial DNA, NEO, rep5

description: Library name: HE_NEO_5


title: NP cells, Old, id61458

description: Library name: Sample 3

value: Intervertebral disc

value: Old


title: whole colonic tissue, healthy control, T5224-treated, rep 2

description: Library name: DSS41prim_M11

data_processing:
EM-seq data were processed and aligned to the mm10 reference genome using the nf-core/methylseq pipeline with GPU-enabled bwa-meth.
Methylation calls were obtained with MethylDackel.
bigWig tracks were generated from per-CpG bedGraph outputs of the nf-core/methylseq pipeline by calculating per-CpG methylation fractions (methylated reads / total coverage) using custom scripts and UCSC bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: bigwig of methylation fraction at CpGs
Library strategy: EM-seq

source_name: colon

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Blood & Tissue Kit from OCT sections.
For each sample, 200 ng of DNA was resuspended in water to 48 uL, mixed with control DNA from the NEBNext Enzymatic Methyl-seq V2 Kit total and sonicated on a Covaris S220 to 200 and 600 bp. Sonicated DNA was then processed per EM-seq V2 protocol

treatment_protocol: Colitis mice were treated with 1-1.5% DSS in drinking water for 3 cycles of 7 days on/10 days off. Starting 20 days after DSS cessation, T-5224, or equivalent volume DMSO, was administered at 100 mg/kg p.o. once daily for three days. Animals were sacrificed 24 hours following final dose and colon tissue was embedded as a swiss roll in OCT.

value: colon

value: colonic epithelium

tag: genotype

value: WT

value: healthy control, 100 mg/kg T-5224 p.o.


title: whole colonic tissue, healthy control, T5224-treated, rep 1

description: Library name: DSS41prim_M10


title: GSC-0131_1_RNA1_Lib2

description:
Library name: GSC-0131-Rep4
GSC-0131 Replicate 4

value: brain

value: cancer stem cell line

value: glioma stem cell culture


title: C5_Discovery_64

value: M


title: Fecal bacterial DNA, AMP, rep2

description: Library name: HE_AMP_2

value: Feces


title: GSC-0131_2_RNA1_Lib2

description:
Library name: GSC-0131-Rep5
GSC-0131 Replicate 5


title: C2_Discovery_57


title: Fecal bacterial DNA, AMP, rep1

description: Library name: HE_AMP_1


title: Targeted gene expression of patient ID021 at BEFRCT

description:
Library name: 164-ID021_BEFRCT
column name in htg_raw_ano.xlsx164-ID021_BEFRCT

value: Tumor

value: II

value: SD

tag: recist 4 weeks after rct

value: CR


title: AF cells, Old, id61227

description: Library name: Sample 4

value: AF cells


title: GSC-0827_3_RNA1_Lib1

description:
Library name: GSC-0827-Rep3
GSC-0827 Replicate 3


title: Fecal bacterial DNA, AMP, rep5

description: Library name: HE_AMP_5


title: Fecal bacterial DNA, NEO, rep1

description: Library name: HE_NEO_1


title: whole colonic tissue, healthy control, DMSO-treated, rep 2

description: Library name: DSS41prim_M8

value: healthy control, DMSO treated


title: Fecal bacterial DNA, VAN, rep5

description: Library name: HE_VAN_5


title: Fecal bacterial DNA, AMP, rep6

description: Library name: HE_AMP_6


title: whole colonic tissue, healthy control, DMSO-treated, rep 3

description: Library name: DSS41prim_M9


title: GSC-0827_3_RNA1_Lib2

description:
Library name: GSC-0827-Rep6
GSC-0827 Replicate 6


title: GSC-0131_3_RNA1_Lib1

description:
Library name: GSC-0131-Rep3
GSC-0131 Replicate 3