title: Bone Marrow HTO library

first: Dr. Shruti

last: Naik

address: 1425 Madison Ave

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

description: Library name: BoneMarrow_HTO_S18

data_processing:
The output raw fastq files were processed through standard cell ranger pipeline from 10x genomics.
The Cell Ranger pipeline was used to process the sequencing data, generating a feature-barcode matrix that included both gene expression and HTO counts. The HTO counts were then utilized to demultiplex the pooled cells based on their unique hashtags.
Assembly: mm10
Supplementary files format and content: feature-barcode matrix files that include both gene expression and HTO counts, stored in cellranger output folder.
Supplementary files format and content: HTO information: Hashtag 1 - Petroleum Jelly, 1 week Western Diet, Hashtag 2 - Imiquimod recovery, 1 week Western Diet, Hashtag 3 -Petroleum Jelly, 4 weeks Western Diet, and Hashtag 4 - Imiquimod recovery, 4 weeks Western Diet

source_name: Bone Marrow

extract_protocol:
Bone marrow was harvested from femurs and tibias, and LSK cells were isolated using fluorescence-activated cell sorting (FACS) based on the Lin⁻Sca-1⁺c-Kit⁺ phenotype.
After sorting, the LSK cells are incubated with Hash-Tagging Oligonucleotides (HTOs). These HTOs contain a cell-specific barcode, allowing for multiplexing of samples. The cells are then pooled together.The sorted cells were then sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: 8-week old female mice were treated topically with Imiquimod or control cream (petroleum jelly) for 7 days, then rested for 23 days. Mice were then placed on a igh-fat diet for 1 or 4 weeks prior to harvest of bone marrow and sorting of LSK cells.

value: Bone Marrow

value: LSK

value: Ldlr-/-

value: various


title: Bone Marrow Gene Expression library

status: Public on Aug 13 2025

type: SRA

city: New York

state: NY

country: USA

description: Library name: BoneMarrow_S14

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: hASCs cells, Not Passed_1, control

city: London

first: Arghya

last: Paul

state: Ontario

address: Thompson Engineering Building

department: Chemical Engineering

country: Canada

institute: The University of Western Ontario

library_source: transcriptomic

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's NCS 1.0.2 and RFV 1.0.2 software with default parameter settings. Sequencer .cbcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2 2.19.0 script configureBclToFastq.pl. Sequenced reads were trimmed for adaptor sequence and aligned by STAR aligner Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons (excluding 5UTR and 3UTR) of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library (only reads mapping to annotated regions of the genome were used for the total libraray size).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples

molecule: total RNA

organism: Homo sapiens

source_name: hASCs

growth_protocol: hASCs were cultured under media conditions consisting of α-minimal essential media (alpha-MEM, Thermo Fisher Scientific) with 10% fetal bovine serum (Thermo Fisher Scientific) supplemented with 1 % penicillin/streptomycin. After every 2-3 days, culture media was exchanged for fresh media. Cells were passaged with 0.5% trypsin-EDTA upon reaching confluency of 70% to 80%. All experiments were completed with cell populations under P2-5.

extract_protocol:
After the neutralization and removal of trypsin, the cell pellet was resuspended in 𝛼-MEM and subdivided into aliquots containing 0.5 × 106 cells. Cells were passed through the microfluidic chip and collected at the outlet. After squeezing, hASCs were left for 5 min at room temperature. Then, RNA was extracted from the cells using an RNeasy Mini Kit (Qiagen) and quantified using a NanoDrop spectrophotometer. Next, the mRNA samples were converted to cDNA using the High-Capacity cDNA Conversion Kit (Applied Biosystems,USA).
RNA libraries for Rna-seq were prepared using SMARTER RNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: hASCs pellets resuspended in α-MEM was used as the control, whereas hASCs resuspended in α-MEM and passed through the microfluidic chip was used as the experimentalgroup.

tag: cell line

value: hASCs

value: Passed through


title: SW480_normoxia-1_input

city: Taipei

first: Che-Kun James

last: Shen

address: No. 128號, Section 2, Academia Rd, Nangang District

country: Taiwan

institute: Institute of Molecular Biology, Academia Sinica

library_source: genomic

data_processing:
we initially utilized BWA MEM (version 0.7.17) (Li and Durbin 2010) for read mapping to the human genome (GRCh38).
Subsequently, we filtered out read alignments with multiple hits or mapping quality less than 30 or without paired alignment.
Then we utilized MACS2 (Zhang, Liu et al. 2008) to perform peak calling. MACS2 takes the alignment file (in BAM format) of ChIP-seq reads as input and a control file helps in accounting for background noise and biases.
MACS2 is run with parameter "--nomodel --extsize 147 --keep-dup all -q 0.05" to identify narrow peaks. We retained only those peaks with a q-value cutoff of 0.05.
We used DeepTools (version 3.5.4) to perform read depth normalization and signal subtraction. The bamCoverage module within DeepTools was utilized to generate coverage tracks after normalizing to a depth of 1× (reads per genome coverage).
To obtain the ChIP-seq signal, the 'bigwigCompare' function of the DeepTools software was employed, with the input signal subtracted from the ChIP-seq signal.
Assembly: GRCh38
Supplementary files format and content: bigWig file for each sample
Supplementary files format and content: narrowPeak file for each IP and input pair

molecule: genomic DNA

source_name: Large intestine; Colon

growth_protocol: The colon cancer cell line SW480 was cultured under 5% CO2 at 37 °C in DMEM (Invitrogen) supplemented with 10% FBS (v/v) (Biological Industries) and 1% (v/v) penicillin-streptomycin (Invitrogen)

extract_protocol:
Cell were fixed with 1% Formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a S220 focused-ultrasonicator (Covaris).
The DNA libraries were prepared using KAPA HyperPrep library preparation kit (Roche) following standard protocols.

treatment_protocol: To induce hypoxia, the cells were transferred from a normoxic incubator (5% CO2 and 20% O2) to a hypoxic incubator (5% CO2 and 1% O2) for 24 hr. Increased levels of HIF-1α, as assayed by Western blotting, were used to assess induction of hypoxia.

value: Large intestine; Colon

value: Colorectal carcinoma

value: Wild type

tag: rep

value: Normoxia


title: stomach sample from fin clipped but not fed fish 2 h post infection, biological rep4

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Data was processed within OmicsBox v3.3.2
Quality control was performed on raw reads using Trimmomatic v0.39
Quality reads were aligned to the channel catfish Coco_2.0 genome using the STAR aligner v2.7.8a (parameters – 2-pass mapping=true; overhang=149; feature=exon)
Read counts were extracted from BAM files using HTseq v2.0.5 ‘count’ feature (parameters – Quantification Level=exon; Group by=parent; Overlap Mode=union; stranded=strand specific reverse)
Assembly: Coco_2.0 (GCF_001660625.3)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Ictalurus punctatus

source_name: stomach

extract_protocol:
Total RNA was extracted from tissues using the Rneasy Plus Mini Kit (Qiagen) per the manufacturer’s protocol. 250 ng of total RNA from each sample was used for library construction.
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Ligation Kit per the manufacturer’s protocol.

value: stomach

tag: disease state

value: infected

tag: time

value: 2 h

tag: feeding state

value: not fed

value: fin clipped


title: stomach sample from fin clipped but not fed fish 2 h post infection, biological rep2


title: AA_4

city: Jinan

first: Yang

last: Zhang

state: Shandong

address: 247 Beiyuan Street

department: Pharmacy

country: China

institute: The Second Hospital, Cheeloo College of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome mm10 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: renal cortex

growth_protocol: Human tubule epithelial cells (HK-2 cells) were  cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 5% fetal bovine serum (FBS).

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In vitro, HK-2 cells were serum-starved for 12 h and then treated with 5 μg/ml aristolochic acid for 48 h. Overexpression of MYDGF by a MYDGF-adenovirus transfection (vectors GV314 harboring MYDGF) were produced by GeneChem Co., Ltd (Shanghai, China).

value: renal cortex

value: human papillomavirus 16 transformed

value: overexpression of MYDGF

value: HK-4 cells with overexpression of MYDGF and aristolochic acid treatment


title: hASCs cells, Not Passed_2, control


title: AA_3

value: HK-3 cells with overexpression of MYDGF and aristolochic acid treatment


title: stomach sample from fed and fin clipped fish 8 h post infection, biological rep6

value: 8 h

value: fed


title: stomach sample from fed and fin clipped fish 8 h post infection, biological rep4


title: SW480_normoxia-2_input


title: SW480_normoxia-2_DNMT3A_ip


title: stomach sample from fed and fin clipped fish 8 h post infection, biological rep5


title: stomach sample from fed and fin clipped fish 8 h post infection, biological rep3


title: stomach sample from fed and fin clipped fish 8 h post infection, biological rep2


title: SW480-Hypoxia1-run1

data_processing:
DNA methylation analysis from the WGBS raw data were conducted by using default parameters via BatMeth2.
The complete data processing, including alignment with the human genome (GRCh38.p13; GCF_000001405.39), calculation of DNA methylation levels of CpG sites using the function "Calmeth", and identification of differentially methylated cytosine (DMC) and differentially methylated regions (DMR) using the function "batDMR".
The methylated levels of each sample from two sequencing run were summed.
Assembly: GRCh38
Supplementary files format and content: tab-separated text files include read depth and methylation level for each CpG site

source_name: Colon

growth_protocol: The colon cancer cell line SW480, breast cancer cell line MCF-7 and hepatocellular carcinoma cell line HepG2 were cultured under 5% CO2 at 37 °C in DMEM (Invitrogen) supplemented with 10% FBS (v/v) (Biological Industries) and 1% (v/v) penicillin-streptomycin (Invitrogen)

extract_protocol:
Genomic DNA was isolated from the cultured SW480 cells using QIAamp DNA mini kit (QIAGEN).
The bisulfite-converted DNA was processed for generating WGBS libraries using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences).

value: Colon

value: Colorectal carcinoma cell line

value: WT

value: Hypoxia

tag: run


title: WTMI7d2

city: Shanghai

first: Xiangdong

last: Yang

address: Xietu Road

institute: Zhongshan Hospital Affiliated to Fudan University

description: Library name: Sample8

data_processing:
Sequencing read quality was initially assessed with FastQC (version 0.11.9) following preliminary quality control (version 0.20.1). Gene expression was quantified by aligning reads to the reference genome using HISAT2 (version 2.1.0) and counting with HTSeq-count (version 0.11.2). Expression values were normalized to FPKM to account for gene length and sequencing depth.
Assembly: GRCm39
Supplementary files format and content: a csv file contains fpkm and annotation of genes

source_name: Heart

extract_protocol:
The total RNA of hearts 1 and 7 days after surgery from WT and Hdc-/- mice was extracted using TRIzol reagent (Takara) for RNA-seq analysis.
RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Heart

tag: time point

value: 7 days

value: AMI


title: WTMI1d2

description: Library name: Sample5

value: 1 day


title: WTMI7d3

description: Library name: Sample9


title: AA_1

value: HK-2 cells with overexpression of MYDGF and aristolochic acid treatment


title: SW480-Normoxia1-run1

value: Normoxia


title: WTMI1d1

description: Library name: Sample4


title: SW480_normoxia-1_DNMT3A_ip

value: Large intestine; Colon

value: Colorectal carcinoma

value: Wild type


title: SW480-Hypoxia2-run1


title: NA_6

value: renal cortex

value: human papillomavirus 16 transformed

value: HK-2 cells with aristolochic acid treatment


title: GES1_39s_shTGFBR2

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Read were aligned with TopHat v1.3.2. Command line options for Tophat were '-r 100' for RNA-Seq.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.0.2. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: GES1, shTGFBR2

growth_protocol: GES1 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: GES1 cells were transfected with pLKO lentivirus vectors for non-target, TP53, and TGFBR2 using Lipofectamine 3000, and they were exposed to puromycin for 4 days for selection.

value: Immortalized non-neoplastic gastric epithelial cells, GES1

tag: vector

tag: selective drug

value: puromycin


title: WT_Con3

description: Library name: Sample3

value: Sham


title: WTMI7d1

description: Library name: Sample7


title: WTMI1d3

description: Library name: Sample6


title: stomach sample from fed and fin clipped fish 4 h post infection, biological rep4

value: stomach

value: infected

value: 4 h

value: fed

value: fin clipped


title: SW480-Normoxia2-run1

value: Colon

value: Colorectal carcinoma cell line

value: WT


title: NC_3

value: HK-4 cells without aristolochic acid treatment


title: NC_1

value: HK-2 cells without aristolochic acid treatment


title: stomach sample from fin clipped but not fed fish 2 h post infection, biological rep1

value: 2 h

value: not fed


title: GES1_39s_shTP53

source_name: GES1, shTP53


title: stomach sample from fed and fin clipped fish 4 h post infection, biological rep5


title: hKPA, Replicate 2 d25, GEX Library

city: Los Angeles

first: Zhongwei

last: Li

state: CA

address: 1425 San Pablo St

department: Keck medicine

institute: University of Southern California

description:
library name: GEX_hKPA2
10X Chromium multiome ATAC + gene expression kit

data_processing:
Sequencing reads were aligned to the human genome (GRCh38.p14) with the Cell Ranger ARC software (version 2.0.2) using STAR aligner on the University of Southern California High Performance Cluster.
Assembly: arc-GRCm39-2024-A-v7.2.0
Supplementary files format and content: atac_fragaments_tsv.gz, Tab-separated file containing fragment information
Supplementary files format and content: atac_fragaments_tsv.gz.tbi, Index of the tab-separated file
Supplementary files format and content: H5 file containing the filtered gene by cell gene expression and peak by cell matrices
Library strategy: snRNA-seq + snATAC-seq

source_name: Human Kidney progenitor assembloid (KPA)

growth_protocol: Synthetic kidneys were cultured with Stage III medium, 37C, 5% CO2

extract_protocol:
Synthetic kidneys were miccrodissected and digested in CAP digestion solution (10mg/ml Cold Active Protease+ 2.5 mg/ml Collagenase type 4 + 0.125U/ul Dnase1)  at 12°C for 30 mins. Cells were then spun down at 350G for 5 mins and resuspended in cold autoMACS Running Buffer. Cell viablity was accessed (99% Live) and cells spun down again. 10X genomics Demonstarated Proocol CG000365 (REV C) was then used to isolate nuclei with 5 min lysis time. The single nuclei suspension was than transposed and run through a microfuidic chip (Chip J) for barcoding.
10X Chromium Single Cell Multiome + Gene Expression protocol (CG000338 Rev E)

value: Kidney cells

value: SIX2-GFP; PAX2-RFP

value: hKPAs were cultured with Stage III medium


title: NA_4

value: renal cortex

value: human papillomavirus 16 transformed

value: HK-2 cells with aristolochic acid treatment


title: stomach sample from fed and fin clipped fish 8 h post infection, biological rep1

value: stomach

value: infected

value: 8 h


title: stomach sample from fed and fin clipped fish 4 h post infection, biological rep3

value: 4 h

value: fed

value: fin clipped


title: NA_1

value: WT


title: R6 Treated Sample late timepoint BR4

city: Minneapolis

first: Hannah

last: Lembke

state: MN

address: 207 Pleasant St SE

institute: University of Minnesota

description:
Library name: R6_2_E
R6L.xlsx

data_processing:
Sequencing was completed with the Illumina NovaSeq platform SP 50PE with ~15.6M reads/sample. Quality control, data alignment and gene quantification was analyzed using the CHURP pipeline44 at the University of Minnesota Supercomputing Institute (MSI). 2 x 50bp FASTQ paired-end reads for 24 samples (13.4 million reads average per sample) were trimmed using Trimmomatic (v0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. Quality control on raw sequence data for each sample was performed with FastQC.
Assembly: Read mapping was performed via HISAT2(v2.1.0) using the Pseudomonas aeruginosa genome (ASM1462v1) as a reference. Gene quantification was performed via Feature Counts for raw read counts. Using raw read counts, differentially expressed genes were identified using the edgeR (negative binomial, R programming) feature in CLCGWB (Qiagen, Redwood City, CA). We filtered the generated list based on a minimum 2X absolute fold change, and FDR corrected p < 0.05.
Supplementary files format and content: excel sheets with calculated read differences, fold changes and p-values for each gene under each sample condition

organism: Pseudomonas aeruginosa

source_name: UCBPP PA14

growth_protocol: The WT PA14, PA14 efflux pump deletions, and lacZ fusions were streaked onto Lennox Broth (LB) agar plates from a frozen glycerol stock and grown overnight at 37 °C. From these plates, a single colony was inoculated into fresh LB media (1 mL) and grown overnight at 37 °C, shaking at 220 RPM. A 1:100 dilution of the overnight culture was performed in fresh LB media and grown until desired OD600 (Genesys 30 Visible Spectrophotometer). Cells were then treated in accordance with each assay.

extract_protocol:
RNeasy Mini Kit (Qiagen) was utilized to extract RNA according to the manufacturer’s protocol combined with an additional off-column DNase treatment (Turbo DNase, Invitrogen).
Prepared 24 unique dual-indexed Illumina stranded total RNA RiboZero Plus Ligation libraries

treatment_protocol: PA14 diluted from overnight cultures were diluted into fresh LB media containing DMSO, R-2 or R-6 (200 M) and grown to OD600 ~0.9 or ~1.2. Four biological replicates were grown for every treatment condition. For each sample, 2X volume of RNA protect reagent (Qiagen) was added, cells vortexed and incubated at room temperature for 10 min. Following incubation, 1 mL aliquots of treated cells were spun down (10 min, 5000g), supernatant decanted and cell pellet snap frozen at -80 °C.

value: UCBPP PA14

value: R-6, late


title: NC_2

value: HK-3 cells without aristolochic acid treatment


title: WT_Con1

description: Library name: Sample1

value: Heart

value: Sham


title: stomach sample from fed and fin clipped fish 4 h post infection, biological rep1


title: R6 Treated Sample late timepoint BR3

description:
Library name: R6_2_D
R6L.xlsx


title: hKPA, Replicate 2 d25, ATAC Library

description:
library name: ATAC_hKPA2
10X Chromium multiome ATAC + gene expression kit

treatment_protocol: Synthetic kidneys were cultured with Stage III medium, 37C, 5% CO2

value: Human Kidney progenitor assembloid (KPA)

value: Kidney cells

value: SIX2-GFP; PAX2-RFP


title: stomach sample from fed and fin clipped fish 4 h post infection, biological rep2


title: stomach sample from fed and fin clipped fish 4 h post infection, biological rep6


title: hKPA, Replicate 1 d25, GEX Library

description:
library name: GEX_hKPA1
10X Chromium multiome ATAC + gene expression kit

value: hKPAs were cultured with Stage III medium


title: R6 Treated Sample late timepoint BR2

description:
Library name: R6_2_C
R6L.xlsx


title: WT_Con2

description: Library name: Sample2


title: stomach sample from fed and fin clipped fish 2 h post infection, biological rep6

value: 2 h


title: LLC AM + LPS 1

city: 安徽省

first: Liqin Ma

middle: Liqin

last: Ma

state: 合肥市

address: 安徽省合肥市蜀山区宿松路与观海路交口西北角

institute: 合肥综合性国家科学中心大健康研究院

description: Library name: Sample 9

data_processing:
The fragments were mapped to the ensemble mouse reference genome GRCm39 (version 2020) using the STAR aligner.
Differential expression analysis (DESeq2) identified significant genes (fold change > 2 or < -2, p < 0.05).
Assembly: genome GRCm39 (version 2020)
Supplementary files format and content: LLC_AMs_RNAseq.xlsx.gz
Supplementary files format and content: Exel file including raw counts for each Sample

source_name: Alveolar macrophages

extract_protocol:
The cells were lysed in 1 mL of TRIzol and total RNA was extracted with a miRNeasy Micro Kit (Qiagen).
Total RNA (more than 100 ng) was used for the subsequent library preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit (Illumina). Poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using random primers. First-strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and dA-tailing was added in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA clean beads. Each sample was then amplified by PCR using P5 and P7 primers, and the PCR products were validated.

treatment_protocol: AMs were stimulated for 4 hours with DMEM medium containing 400 ng/mL lipopolysaccharide (LPS) from E. coli 055:B5 (InvivoGen, tlrl-b5lps) or in LPS-free medium (as control) for 4 hours.

value: Alveolar macrophages

value: with LPS


title: LLC AM + LPS 3

address: 安徽省合肥市蜀山区宿松路与观海路交口西北角

institute: 合肥综合性国家科学中心大健康研究院

description: Library name: Sample 11


title: GES1_39s_shNON

source_name: GES1, shNON

value: Immortalized non-neoplastic gastric epithelial cells, GES1

value: shNON

value: puromycin


title: hKPA, Replicate 1 d25, ATAC Library

description:
library name: ATAC_hKPA1
10X Chromium multiome ATAC + gene expression kit


title: R6 Treated Sample late timepoint BR1

description:
Library name: R6_2_B
R6L.xlsx


title: Ctrl AM + LPS 3

address: 安徽省合肥市蜀山区宿松路与观海路交口西北角

institute: 合肥综合性国家科学中心大健康研究院

description: Library name: Sample 8


title: Ctrl AM + LPS 2

address: 安徽省合肥市蜀山区宿松路与观海路交口西北角

institute: 合肥综合性国家科学中心大健康研究院

description: Library name: Sample 7


title: HTLV-1-infected SLB1 cell line

city: Namur

first: Damien

last: Coupeau

address: Rue de Bruxelles, 61

department: Namur Research Institute for Life Sciences

country: Belgium

institute: University of Namur

data_processing:
Viral reads recovery (alignment using BWA mem -a -T15) (BWA v0.7.11)
Adapter trimming (Trimmomatic v0.39. Included the trimming of the adapters, quality trimming (Sliding Window 4:15), and a minimal length filter of 70 nucleotides
PCR duplicates removal (dedupe.sh (BBMap v1.0))
vCircTrappist v1.0 pipeline for circRNA-originating reads identification (including Samtools v1.10 and BWA v0.7.11)
Assembly: KX905135.1 ; KT122858.1 ; AC_000008.1 ; NC_001436.1 ; EF523390.1
Supplementary files format and content: tab-delimited text file including raw circRNA-derived reads count, circularization sites sequences, splicing pattern, strandness of the reads, 5' and 3' positions of the circularization sites, max size of the circRNAs, colocalized genes, common k-mers between circularization sites, viral segment, read identifiers

extract_protocol:
RNA was extracted using TRI-reagent (Thermofisher) and 4ug were sent to sequencing (Novogene).
1µg of total RNA was sent to Novogene for the library preparation and sequencing. Library preparation include : ribosomal depletion, linear RNA degradation, RNA fragmentation, reverse transcription, second strand synthesis (using dUTPs), end-repair, A-tailing, adapter ligation, enzyme digestion to remove dUTPs-containing second strand cDNAs, size selection, PCR amplification


title: stomach sample from fed and fin clipped fish 2 h post infection, biological rep5

value: stomach

value: infected

value: fed

value: fin clipped


title: R6 Treated Sample early timepoint BR4

description:
Library name: R6_1_D
R6E.xlsx

value: UCBPP PA14

value: WT

value: R-6, early


title: R6 Treated Sample early timepoint BR3

description:
Library name: R6_1_C
R6E.xlsx


title: stomach sample from fed and fin clipped fish 2 h post infection, biological rep3


title: LLC AM 3

address: 安徽省合肥市蜀山区宿松路与观海路交口西北角

institute: 合肥综合性国家科学中心大健康研究院

description: Library name: Sample 5

value: without LPS


title: stomach sample from fed and fin clipped fish 2 h post infection, biological rep4


title: LLC AM + LPS 2

address: 安徽省合肥市蜀山区宿松路与观海路交口西北角

institute: 合肥综合性国家科学中心大健康研究院

description: Library name: Sample 10


title: hAdV-C5-infected A549, 24h of infection


title: Ctrl AM + LPS 1

address: 安徽省合肥市蜀山区宿松路与观海路交口西北角

institute: 合肥综合性国家科学中心大健康研究院

description: Library name: Sample 6


title: stomach sample from fed and fin clipped fish 2 h post infection, biological rep2


title: R6 Treated Sample early timepoint BR1

description:
Library name: R6_1_A
R6E.xlsx


title: R6 Treated Sample early timepoint BR2

description:
Library name: R6_1_B
R6E.xlsx


title: LLC AM 2

address: 安徽省合肥市蜀山区宿松路与观海路交口西北角

institute: 合肥综合性国家科学中心大健康研究院

description: Library name: Sample 4


title: stomach sample from fed and fin clipped fish 2 h post infection, biological rep1


title: hAdV-C5-infected A549, 12h of infection


title: R2 Treated Sample late timepoint BR4

description:
Library name: R2_2_E
R2L.xlsx

value: R-2, late


title: R2 Treated Sample late timepoint BR3

description:
Library name: R2_2_C
R2L.xlsx


title: hAdV-C5-infected A549, 18h of infection


title: stomach sample from fin clipped control fish, biological rep5

value: mock

value: 0 h


title: BLV-infected HEK293T

value: BLV-infected


title: LLC AM 1

address: 安徽省合肥市蜀山区宿松路与观海路交口西北角

institute: 合肥综合性国家科学中心大健康研究院

description: Library name: Sample 3

value: Alveolar macrophages


title: stomach sample from fin clipped control fish, biological rep6


title: R2 Treated Sample late timepoint BR2

description:
Library name: R2_2_B
R2L.xlsx


title: HTLV-1-infected HUT102 cell line


title: 3D, Medulla, SF, tech rep 2, patient3

city: Solna

first: Tianyi

address: Bioclinicum NKS J5:20, Solnavägen 30

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
Fastq files were mapped to human genome GRCh38 using STAR (version 2.7.10b)
subread package (version 2.0.1) was used to align the bam files using featureCount function
After import the raw data matrix into Rstudio, technical replicates were collapsed using DESeq2 collapseReplicates function
Assembly: GRCh38 (Homo_sapiens.GRCh38.108.chr.gtf)
Supplementary files format and content: RawCounts.txt

source_name: Ovary

extract_protocol:
RNA extraction of tissues and 2D cultured cells was performed using RNeasy Mini Kit (Qiagen, Germany). Total RNA of Silk-Ovarioids samples was extracted using RNeasy Micro Kit (Qiagen, Germany)
Libraries were prepared using Illumina Stranded mRNA Prep Ligation protocol (Illumina, USA) using 10 ng RNA as input.

value: Ovary

tag: tissue region

value: Medulla

tag: culture

tag: freezing

value: SF


title: Ctrl AM 2

address: 安徽省合肥市蜀山区宿松路与观海路交口西北角

institute: 合肥综合性国家科学中心大健康研究院

description: Library name: Sample 1


title: Ctrl AM 3

address: 安徽省合肥市蜀山区宿松路与观海路交口西北角

institute: 合肥综合性国家科学中心大健康研究院

description: Library name: Sample 2


title: R2 Treated Sample late timepoint BR1

description:
Library name: R2_2_A
R2L.xlsx


title: Ipsilateral primary cortex from mouse 3

city: Shatin

first: Yao

last: Zhu

address: CUHK

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
Library name: MD3R
rowname in circular_counts.csv/mRNA_counts.txt: MD3R

data_processing:
Read alignment was performed using HISAT2. The mRNA counts were obtained using featureCounts. Differential expression analysis was performed using DESeq2. The circular RNA counts were obtained using circtools. Differential expression analysis was performed using the Bioconductor package limma.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited txt file includes mRNA counts for each sample and csv file includes circular counts for each sample
Supplementary files format and content: csv files include normalized counts for each sample

source_name: mouse V1

extract_protocol:
RNA was extracted from fresh tissue. Tissue for RNA extraction was isolated from V1 contralateral and ipsilateral to the sutured eye after 3-day MD (at P28). A sterile scalpel blade and forceps were used to surgically micro-dissect the appropriate tissue section. The dissected tissue was immediately placed into a 2-mL lysing tube containing 1.4 mm spherical ceramic beads (MPBio, Lysing Matrix D, Cat. No. 116913050) and pre-filled with 1 mL of ice-cold TRIzol (Ambion, Cat. No. 15596-026) and then immediately homogenized with a bead-based homogenizer (FastPrep-24 5G, MPBio) using the preset settings for mouse brain tissue (8.0 m/sec, 30 sec). Once foaming has subsided at room temperature, the homogenate was transferred into 2 mL Phase Lock Tube (Heavy; 5Prime Bio, Cat. No. 2302830) pre-filled with 200 µL chloroform and briefly vortexed. Samples were centrifuged at 12,000 x g for 10 min at 2-4°C. The colorless upper aqueous layer was then transferred into a new 2.0 mL LoBind tube that was pre-filled with 1.5 volumes of 100% EtOH (~600 µL), then mixed thoroughly by pipetting up and down several times, and then briefly centrifuged. The sample was furthered purified using Zymo RNA Clean & Concentrator-5 (Zymo Research, R1016) according the manufacturer’s recommended protocol and always performed with the optional in-column DNase I treatment. RNA was eluted twice with ≥6 μL 1x TE buffer (pH 7.5). The approximate concentration and relative purity of RNA was determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific).
Indexed cDNA libraries were generated using the SMARTer Stranded Total RNA-Seq Kit v2 according to the manufacturer's protocol.

treatment_protocol: For monocular deprivation experiments, mice were anesthetized using 2-3% isoflurane. The top and bottom eyelid of the right eye was trimmed, and sterile nylon sutures (7-0) were used to suture the eyelid, which were further sealed with Vetbond (3M). The suture was inspected for the next 3 days post-closure to ensure that the eye did not reopen.

value: mouse V1


title: stomach sample from fin clipped control fish, biological rep4

value: stomach


title: R2 Treated Sample early timepoint BR4

description:
Library name: R2_1_D
R2E.xlsx

value: R-2, early


title: 3D, Medulla, SF, tech rep 1, patient3


title: 2D, Medulla, SF, tech rep 2, patient3


title: stomach sample from fin clipped control fish, biological rep3

value: fed


title: Ipsilateral primary cortex from mouse 2

description:
Library name: MD2R
rowname in circular_counts.csv/mRNA_counts.txt: MD2R


title: 3D, Cortex, SF, tech rep 1, patient3

value: Cortex


title: 2D, Medulla, SF, tech rep 1, patient3


title: stomach sample from fin clipped control fish, biological rep1

value: fin clipped


title: R2 Treated Sample early timepoint BR2

description:
Library name: R2_1_B
R2E.xlsx

value: UCBPP PA14

value: WT


title: stomach sample from fin clipped control fish, biological rep2


title: intestine sample from not fin clipped control fish, biological rep6

source_name: intestine

value: intestine

value: not fin clipped


title: Ipsilateral primary cortex from mouse 1

description:
Library name: MD1R
rowname in circular_counts.csv/mRNA_counts.txt: MD1R


title: Contralateral primary cortex from mouse 3

description:
Library name: MD3L
rowname in circular_counts.csv/mRNA_counts.txt: MD3L


title: 2D, Cortex, SF, tech rep 2, patient3


title: R2 Treated Sample early timepoint BR1

description:
Library name: R2_1_A
R2E.xlsx


title: 2D, Cortex, SF, tech rep 1, patient3


title: Contralateral primary cortex from mouse 1

description:
Library name: MD1L
rowname in circular_counts.csv/mRNA_counts.txt: MD1L


title: 3D, Medulla, Fresh, tech rep 3, patient5

value: Fresh


title: intestine sample from not fin clipped control fish, biological rep4

value: mock

value: 0 h


title: DMSO Control late timepoint  BR4

description: Library name: D_2_E

value: DMSO, late


title: D7-694

city: Beijing

first: Ye-Guang

last: Chen

state: China

address: Haidian  District

institute: Tsinghua University

description:
Library name: D7-694
Control colonic crypts at day 7 of DSS treatment

data_processing:
Reads were aligned to the GCRm38/mm10 genome using Bowtie 2 (v2.2.5) and sorted with samtools (v1.5).
mRNA expression analysis was performed using Hisat (version 2.1.0) and Ballgown (version 2.20.0).
Assembly: mm10
Supplementary files format and content: gene_fpkm_matrix.csv: Comma-delimited text file includes FPKM values for each sample.

source_name: Colonic crypts

extract_protocol:
Total RNA was extracted and purified by using TRIZOL reagent (Thermo Fisher Scientific). 1.5ug of total RNA was used for the construction of sequencing libraries.
RNA integrity was measured using electrophoresis. Subsequently, First-strand cDNA was generated using random hexamer primers. Then, a second-strand cDNA was synthesized. A-Tailing Mix and RNA Index Adapters followed to subjected to the end of the cDNA. The cDNA fragments were amplified by PCR and the product was qualified by Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY) and the 2100 Bioanalyzer (Agilent). After it, the products were denatured and circularized to collect the final library.

treatment_protocol: Mice are treated with 3% DSS for 5 days, followed by normal drinking water. Colonic crypts were isolated at the indicated time points for bulk RNA-seq.

value: Colonic crypts

value: Colonic epithelial cells

value: DSS


title: intestine sample from not fin clipped control fish, biological rep3


title: Contralateral primary cortex from mouse 2

description:
Library name: MD2L
rowname in circular_counts.csv/mRNA_counts.txt: MD2L

value: mouse V1


title: R2 Treated Sample early timepoint BR3

description:
Library name: R2_1_C
R2E.xlsx


title: 3D, Medulla, Fresh, tech rep 2, patient5

value: Ovary

value: Medulla


title: DMSO Control late timepoint  BR2

description: Library name: D_2_B


title: D7-692

description:
Library name: D7-692
Control colonic crypts at day 7 of DSS treatment


title: DMSO Control late timepoint  BR3

description: Library name: D_2_D


title: 3D, Medulla, Fresh, tech rep 1, patient5


title: intestine sample from not fin clipped control fish, biological rep2

value: fed


title: DMSO Control late timepoint  BR1

description: Library name: D_2_A


title: 2D, Medulla, Fresh, tech rep 2, patient5


title: intestine sample from not fin clipped control fish, biological rep1


title: DMSO Control early timepoint  BR4

description: Library name: D_1_D

value: DMSO, early


title: D5-670

description:
Library name: D5-670
Control colonic crypts at day 5 of DSS treatment


title: intestine sample from not fed nor fin clipped fish 8 h post infection, biological rep6

value: infected

value: 8 h

value: not fed


title: DMSO Control early timepoint  BR3

description: Library name: D_1_C

value: UCBPP PA14

value: WT


title: D5-167

description:
Library name: D5-167
Control colonic crypts at day 5 of DSS treatment


title: intestine sample from not fed nor fin clipped fish 8 h post infection, biological rep5

value: intestine

value: not fin clipped


title: Tissue, Medulla, Fresh, tech rep 3, patient5

value: Tissue

value: Fresh


title: intestine sample from not fin clipped control fish, biological rep5

value: mock

value: 0 h


title: D5-161

description:
Library name: D5-161
Control colonic crypts at day 5 of DSS treatment

value: Colonic crypts

value: Colonic epithelial cells

value: DSS


title: DMSO Control early timepoint  BR2

description: Library name: D_1_B


title: Tissue, Medulla, Fresh, tech rep 2, patient5

value: Ovary

value: Medulla


title: DMSO Control early timepoint  BR1

description: Library name: D_1_A

value: DMSO, early


title: D4-3

description:
Library name: D4-3
Control colonic crypts at day 4 of DSS treatment


title: ATDC5 cells, day 21 compressed, biol rep 3

city: Newcastle upon Tyne

first: Katarzyna

middle: Anna

last: Pirog

address: Biosciences Institute

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

data_processing:
Quality control (QC) was performed using FastQC (v0.11.9).
Reads were quality trimmed with Trimmomatic (0.39). Kallisto (v0.46.1)
Trimmed sequences were mapped to GRCm39/mm19
Assembly: mm19
Supplementary files format and content: raw data.txt

growth_protocol: ATDC5 cells were maintained in DMEM with 10% FCS and 1% NEAA. . To generate the agarose constructs, 2.5% w/v low gelling agarose (Sigma-Aldrich A9045) was prepared and sterilised by autoclaving. The agarose was melted in an oven set to 60oC and cooled to 39oC in a water bath before use. 10 x 106 ATDC5 cells/ml were mixed with medium and with the agarose to the final concentration of 2% w/v low gelling temperature agarose, poured into sterilised stainless-steel moulds placed in standard 12-well tissue culture plates and allowed to set for 5 minutes in a sterile laminar flow hood before chondrogenic medium was added. The tissue shapes were uniform across the experiments, standardised by ensuring the correct agar concentration, gelation time and temperature, and were consistently 3 mm in height. Medium was changed every 2 days with supplements (ITS, ascorbic acid and growth factors (10 ng/ml of BMP7 and/or 10 ng/ml TGFβ3) added freshly before use

extract_protocol:
RNA was extracted using Rneasy Mini Kit from QIAgen and DNaseI treated. 1ug of total RNA was used for the construction of sequencing librries.
Libraries were prepared using TruSeq Stranded mRNA Sequencing Library Prep kit according to manufacturer's protocol.

treatment_protocol: 30min a day daily dynamic compression at 10kPa 0.33Hz using the Flexcell FX-5000

value: chondroprogenitor

value: dynamic compression

value: day 21 compressed


title: intestine sample from not fed nor fin clipped fish 8 h post infection, biological rep3

value: infected

value: 8 h

value: not fed


title: D4-1

description:
Library name: D4-1
Control colonic crypts at day 4 of DSS treatment

value: WT


title: D4-2

description:
Library name: D4-2
Control colonic crypts at day 4 of DSS treatment


title: ATDC5 cells, day 21 compressed, biol rep 2


title: D7-3

description:
Library name: D7-3
Control colonic crypts at day 7 of DSS treatment


title: intestine sample from not fed nor fin clipped fish 8 h post infection, biological rep1

value: intestine

value: not fin clipped


title: Tissue, Medulla, Fresh, tech rep 1, patient5

value: Tissue

value: Fresh


title: 3D, Cortex, Fresh, tech rep 2, patient5

value: Cortex


title: D10-672

description:
Library name: D10-672
Control colonic crypts at day 10 of DSS treatment

value: Colonic crypts

value: Colonic epithelial cells


title: 3D, Cortex, Fresh, tech rep 1, patient5

value: Ovary


title: D10-671

description:
Library name: D10-671
Control colonic crypts at day 10 of DSS treatment

value: DSS


title: ATDC5 cells, day 21 uncompressed, biol rep 3

value: day 21 uncompressed


title: intestine sample from not fed nor fin clipped fish 8 h post infection, biological rep2


title: 2D, Medulla, Fresh, tech rep 1, patient5

value: Medulla


title: D10-166

description:
Library name: D10-166
Control colonic crypts at day 10 of DSS treatment


title: 2D, Cortex, Fresh, tech rep 2, patient5


title: ATDC5 cells, day 21 compressed, biol rep 1

value: chondroprogenitor

value: dynamic compression


title: intestine sample from not fed nor fin clipped fish 8 h post infection, biological rep4

value: infected


title: intestine sample from not fed nor fin clipped fish 4 h post infection, biological rep4

value: 4 h


title: 2D, Cortex, Fresh, tech rep 1, patient5


title: ATDC5 cells, day 21 uncompressed, biol rep 1


title: intestine sample from not fed nor fin clipped fish 4 h post infection, biological rep3

value: not fed


title: Tissue, Cortex, Fresh, tech rep 3, patient5


title: ATDC5 cells, day 14 compressed, biol rep 3

value: day 14 compressed


title: 3D, Cortex, Fresh, tech rep 3, patient5


title: intestine sample from not fed nor fin clipped fish 4 h post infection, biological rep2

value: intestine


title: CTR-725

description:
Library name: CTR-725
Control colonic crypts at day 0 of DSS treatment

value: WT


title: CTR-681

description:
Library name: CTR-681
Control colonic crypts at day 0 of DSS treatment


title: intestine sample from not fed nor fin clipped fish 4 h post infection, biological rep1

value: not fin clipped


title: intestine sample from not fed nor fin clipped fish 4 h post infection, biological rep6


title: Tissue, Cortex, Fresh, tech rep 1, patient5

value: Tissue

value: Fresh


title: ATDC5 cells, day 14 compressed, biol rep 2


title: ATDC5 cells, day 14 compressed, biol rep 1


title: intestine sample from not fed nor fin clipped fish 4 h post infection, biological rep5


title: intestine sample from not fed nor fin clipped fish 2 h post infection, biological rep6

value: 2 h


title: ATDC5 cells, day 21 uncompressed, biol rep 2


title: ATDC5 cells, day 14 uncompressed, biol rep 3

value: day 14 uncompressed


title: CTR-729

description:
Library name: CTR-729
Control colonic crypts at day 0 of DSS treatment

value: Colonic crypts

value: Colonic epithelial cells


title: 3D, Medulla, Fresh, tech rep 1, patient4

value: Ovary


title: mouse fibroblast-M11 Auto 1uM

city: Brussels

first: Marie-Isabelle

last: Garcia

address: route de lennik 808

department: IRIBHM-Jacques E. Dumont

institute: Universite Libre de Bruxelles

description:
Library name: GAG18-M11 Auto 1uM
GAG18-M11 Auto 1uM

data_processing:
Sequenced reads were trimmed for adaptor sequence (Trimmomatic-0.36)
Paired-end reads were mapped against the mouse reference genome (GRCm38.90.gtf) using the STAR_2.5.3a software to generate read alignments.
Assembly: Following transcript assembly, gene level counts were obtained using HTSeq-0.9.1
Supplementary files format and content: tab-delimited txt file includes CPM values for each sample.

growth_protocol: Mouse colon organoids were obtained from adult Vil-cre/ERT2/Apcwt/wt (colonoids) and Vil-cre/ERT2/Apcflox/flox mice after in vivo injection with tamoxifen to induce recombination of the Apc flox allele. This generated colonoids (Apc wild-type) or tumoroids (Apc floxed). Organoids were cultured as described by Sato et al (2011). Mouse colon fibroblasts from C57B/6 mice were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin, 1% amphotericin.

extract_protocol:
Total RNA from organoids was extracted using Rneasy mini kit (Qiagen) for crypts and cell lines following manufacturer’s instructions.
RNA libraries were prepared for sequencing using Ovation® SoLo RNA-Seq Library Preparation Kit (NuGEN, TECAN genomics). RNA-Seq 2x100 bases Paired-End

treatment_protocol: Organoids  were treated upon replating at day 0 for 6  days of treatment with vehicle (DMSO 0,5%), regorafenib 4 µM, regorafenib 8 µM or 5-FU 1 µM. Fibroblasts were treated upon replating at day 0 for 7 days of treatment with vehicle (DMSO 0,5%),  Regorafenib 4 µM or 10 µM, autogramin-2 1 µM or combionation of regorafenib 4 µM + autogramin-2 1 µM.

value: Colon

value: fibroblasts

value: Fibroblast

value: Wild-type

value: Autogramin-2 1uM

tag: batch

value: day 7


title: ATDC5 cells, day 14 uncompressed, biol rep 2

value: chondroprogenitor


title: intestine sample from not fed nor fin clipped fish 2 h post infection, biological rep5

tag: tissue

value: intestine

value: infected

value: not fed


title: intestine sample from not fed nor fin clipped fish 2 h post infection, biological rep4

value: not fin clipped


title: 2D, Medulla, Fresh, tech rep 2, patient4

value: Medulla

value: Fresh


title: ATDC5 cells, day 14 uncompressed, biol rep 1

tag: cell type

value: day 14 uncompressed


title: intestine sample from not fed nor fin clipped fish 2 h post infection, biological rep3

value: 2 h


title: 2D, Medulla, Fresh, tech rep 1, patient4


title: mouse fibroblast-M11 DMSO

description:
Library name: GAG16-M11 DMSO
GAG16-M11 DMSO

tag: genotype

value: DMSO


title: ATDC5 cells, day 7 compressed, biol rep 3

tag: treatment

value: dynamic compression

value: day 7 compressed


title: Tissue, Cortex, Fresh, tech rep 2, patient5

value: Ovary

value: Cortex

value: Tissue


title: mouse fibroblast-M1 (2) Rego 4+Auto 1uM

description:
Library name: GAG15-M1 (2) Rego 4+Auto 1uM
GAG15-M1 (2) Rego 4+Auto 1uM

value: Colon

tag: cell line

value: fibroblasts

value: Fibroblast

value: Wild-type

value: Rego 4uM + Auto 1uM


title: intestine sample from not fed nor fin clipped fish 2 h post infection, biological rep2

value: intestine

value: infected

value: not fed


title: Tissue, Medulla, Fresh, tech rep 3, patient4

value: Medulla

value: Fresh


title: intestine sample from not fed nor fin clipped fish 2 h post infection, biological rep1

value: 2 h

value: not fin clipped


title: Tissue, Medulla, Fresh, tech rep 2, patient4


title: ATDC5 cells, day 7 compressed, biol rep 1

value: chondroprogenitor

value: dynamic compression


title: mouse fibroblast-M1 (2) Auto 1uM

description:
Library name: GAG14-M1 (2) Auto 1uM
GAG14-M1 (2) Auto 1uM

value: Autogramin-2 1uM

value: day 7


title: mouse fibroblast-M11 Rego 4+AUTO 1 uM

description:
Library name: GAG19-M11 Rego 4+AUTO 1 uM
GAG19-M11 Rego 4+AUTO 1 uM


title: intestine sample from fed but not fin clipped fish 8 h post infection, biological rep6

value: 8 h

value: fed


title: 3D, Medulla, Fresh, tech rep 2, patient4

value: Ovary


title: ATDC5 cells, day 7 uncompressed, biol rep 3

value: day 7 uncompressed


title: Tissue, Medulla, Fresh, tech rep 1, patient4

value: Tissue


title: mouse fibroblast-M1 (2) Rego 10uM

description:
Library name: GAG13-M1 (2) Rego 10uM
GAG13-M1 (2) Rego 10uM

value: Colon

value: fibroblasts

value: Fibroblast

value: Wild-type

value: Regorafenib 10 µM


title: intestine sample from fed but not fin clipped fish 8 h post infection, biological rep5

value: intestine

value: infected


title: mouse fibroblast-M1 (2) Rego 4uM

description:
Library name: GAG12-M1 (2) Rego 4uM
GAG12-M1 (2) Rego 4uM

value: Regorafenib 4 µM


title: mouse fibroblast-M11 Rego 4uM

description:
Library name: GAG17-M11 Rego 4uM
GAG17-M11 Rego 4uM


title: ATDC5 cells, day 7 uncompressed, biol rep 2

value: chondroprogenitor


title: 3D, Cortex, Fresh, tech rep 3, patient4

value: Cortex

value: Fresh


title: mouse fibroblast-M3 (2) Rego 4+Auto 1uM

description:
Library name: GAG10-M3 (2) Rego 4+Auto 1uM
GAG10-M3 (2) Rego 4+Auto 1uM

value: Rego 4uM + Auto 1uM

value: day 7


title: 3D, Cortex, Fresh, tech rep 2, patient4


title: intestine sample from fed but not fin clipped fish 8 h post infection, biological rep4

value: 8 h

value: fed

value: not fin clipped


title: 3D, Cortex, Fresh, tech rep 1, patient4

value: Ovary


title: ATDC5 cells, day 1 control, biol rep 3

value: day 1 control


title: intestine sample from fed but not fin clipped fish 8 h post infection, biological rep2


title: 2D, Cortex, Fresh, tech rep 2, patient4


title: ATDC5 cells, day 7 compressed, biol rep 2

value: dynamic compression

value: day 7 compressed


title: ATDC5 cells, day 1 control, biol rep 2


title: mouse fibroblast-M3 (2) Rego 10uM

description:
Library name: GAG8-M3 (2) Rego 10uM
GAG8-M3 (2) Rego 10uM

value: Colon

value: fibroblasts

value: Fibroblast

value: Wild-type


title: intestine sample from fed but not fin clipped fish 8 h post infection, biological rep1

value: intestine

value: infected


title: 2D, Cortex, Fresh, tech rep 1, patient4

value: Cortex


title: Tissue, Cortex, Fresh, tech rep 3, patient4

value: Tissue

value: Fresh


title: intestine sample from fed but not fin clipped fish 4 h post infection, biological rep6

value: 4 h


title: mouse fibroblast-M3 (2) Auto 1uM

description:
Library name: GAG9-M3 (2) Auto 1uM
GAG9-M3 (2) Auto 1uM

value: Autogramin-2 1uM

value: day 7


title: mouse fibroblast-M3 (2) Rego 4uM

description:
Library name: GAG7-M3 (2) Rego 4uM
GAG7-M3 (2) Rego 4uM

value: Regorafenib 4 µM


title: ATDC5 cells, day 1 control, biol rep1

value: chondroprogenitor


title: mouse fibroblast-M3 (2) DMSO

description:
Library name: GAG6-M3 (2) DMSO
GAG6-M3 (2) DMSO

value: DMSO


title: intestine sample from fed but not fin clipped fish 4 h post infection, biological rep5

value: fed

value: not fin clipped


title: Tissue, Cortex, Fresh, tech rep 2, patient4

value: Ovary


title: D28

city: Stanford

first: Jennifer

middle: Brigitta

last: Parker

address: 257 Campus Drive

department: Surgery

institute: Stanford University

data_processing:
FASTQs were demultiplexed, and files then aligned to mm10 reference genome using Space Ranger (10x Genomics, v.2.0.1).
Downstream analyses were conducted with Seurat, applying the spatial data vignette.
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files, spatial files
Library strategy: spatial transcriptomic (10x Visium)

molecule: cytoplasmic RNA

source_name: Skin

extract_protocol:
Tissue was flashfrozen per 10x's Visium Tissue Preprataion Protocol (CG000240)
Visiun was then performed at the Stanford Genomics Facility (SGF) using the 10x Genomics Visium platform. The relevant protocols were followed per manufacturer’s guidelines.

value: Skin

value: Wildtype


title: Tissue, Cortex, Fresh, tech rep 1, patient4


title: mouse fibroblast-M1 (2) DMSO

description:
Library name: GAG11-M1 (2) DMSO
GAG11-M1 (2) DMSO

value: Colon

value: fibroblasts

value: Fibroblast

value: Wild-type


title: 3D, Medulla, Fresh, tech rep 3, patient3

value: Medulla


title: ATDC5 cells, day 7 uncompressed, biol rep 1

value: day 7 uncompressed


title: mouse fibroblast-Rego 4+Auto 1uM

description:
Library name: GAG5-M3 Rego 4+Auto 1uM
GAG5-M3 Rego 4+Auto 1uM

value: Rego 4uM + Auto 1uM


title: intestine sample from fed but not fin clipped fish 4 h post infection, biological rep3

value: intestine

value: infected

value: 4 h


title: Day21_1


title: Day12_2


title: mouse fibroblast-M3 Auto 1uM

description:
Library name: GAG4-M3 Auto 1uM
GAG4-M3 Auto 1uM

value: Autogramin-2 1uM

value: day 7


title: intestine sample from fed but not fin clipped fish 4 h post infection, biological rep4

value: fed


title: intestine sample from fed but not fin clipped fish 8 h post infection, biological rep3

value: 8 h

value: not fin clipped


title: 3D, Medulla, Fresh, tech rep 2, patient3

value: Ovary

value: Fresh


title: mouse fibroblast-M3 Rego 10uM

description:
Library name: GAG3-M3 Rego 10uM
GAG3-M3 Rego 10uM

value: Colon

value: Regorafenib 10 µM


title: mouse fibroblast-M3 Rego 4uM

description:
Library name: GAG2-M3 Rego 4uM
GAG2-M3 Rego 4uM

value: fibroblasts

value: Fibroblast

value: Regorafenib 4 µM


title: 3D, Medulla, Fresh, tech rep 1, patient3

value: Medulla


title: Day12_1

value: Skin

value: Wildtype


title: Unwounded2


title: intestine sample from fed but not fin clipped fish 2 h post infection, biological rep6

value: intestine

value: infected

value: 2 h


title: 2D, Medulla, Fresh, tech rep 2, patient3


title: mouse colonoid M14-5-FluoroUracil

description:
Library name: IGA24-KO-M14-T4-1uM-5FU.24
IGA24-KO-M14-T4-1uM-5FU.24

value: organoids Apc deficient (Floxed)

value: epithelium

value: Apc deficient (floxed)

value: 5-FU 1 µM

value: day 6


title: mouse fibroblast-M3 DMSO

description:
Library name: GAG1-M3 DMSO
GAG1-M3 DMSO

value: Wild-type

value: DMSO

value: day 7


title: Day21_2


title: intestine sample from fed but not fin clipped fish 2 h post infection, biological rep5

value: fed

value: not fin clipped


title: 2D, Medulla, Fresh, tech rep 1, patient3

value: Ovary

value: Fresh


title: Day 28 [scATAC-seq]

library_source: genomic single cell

data_processing:
Raw base call (BCL) files were demultiplexed to fastq files using the 10x Genomics Cell Ranger tool cellranger-atac mkfastq. These files were then aligned to the mouse genome (mm10) using cellranger-atac count with default parameters.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Nuclei were isolated from flash-frozen mouse skin using an adaptation of 10x's nuclei isolation (CG000365)
Library was performed according to the manufacter’s instructions (single cell ATAC v2 protocol, 10x Genomics). Briefly, nuclei suspensions are incubated in a Transposition Mix.Barcoded Gel Beads, transposed nuclei, and master mix are loaded together with partitioning oil into the chip to generate the gel bead-in-emulsion (GEM). Once gel beads are dissolved, oligonucleiotides containing 1) P5 sequence, 2) a 16 nucleotide 10x barcode, and 3) a read 1N sequence are released and form barcoded single-stranded DNA. The pooled barcoded DNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Skin

value: Day 28


title: Tissue, Medulla, Fresh, tech rep 3, patient3

value: Medulla

value: Tissue


title: intestine sample from fed but not fin clipped fish 2 h post infection, biological rep4

value: intestine

value: infected

value: 2 h


title: Unwounded1

value: Wildtype


title: Day 21 [scATAC-seq]

value: Day 21


title: mouse tumoroid M14-8 µM Regorafenib

description:
Library name: IGA23-KO-M14-T3-8uM-Rego.23
IGA23-KO-M14-T3-8uM-Rego.23

value: Colon

value: organoids Apc deficient (Floxed)

value: epithelium

value: Apc deficient (floxed)

value: Regorafenib 8 µM

value: day 6


title: mouse tumoroid M14-DMSO.1

description:
Library name: IGA21-KO-M14-T1-DMSO.21
IGA21-KO-M14-T1-DMSO.21

value: DMSO


title: intestine sample from fed but not fin clipped fish 2 h post infection, biological rep3

value: fed

value: not fin clipped


title: Tissue, Medulla, Fresh, tech rep 1, patient3

value: Ovary

value: Fresh


title: Tissue, Medulla, Fresh, tech rep 2, patient3

value: Medulla

value: Tissue


title: intestine sample from fed but not fin clipped fish 4 h post infection, biological rep2

value: intestine

value: infected

value: 4 h


title: Unwounded [scATAC-seq]

value: Skin

value: Wildtype


title: Day 12 [scATAC-seq]

value: Day 12


title: mouse colonoid M3-5-FluoroUracil

description:
Library name: IGA20-KO-M3-T4-1uM-5FU.20
IGA20-KO-M3-T4-1uM-5FU.20

value: Colon

value: organoids Apc deficient (Floxed)

value: epithelium

value: 5-FU 1 µM


title: mouse tumoroid M14-4 µM Regorafenib

description:
Library name: IGA22-KO-M14-T2-4uM-Rego.22
IGA22-KO-M14-T2-4uM-Rego.22

value: Apc deficient (floxed)

value: Regorafenib 4 µM

value: day 6


title: 3D, Cortex, Fresh, tech rep 3, patient3

value: Ovary

value: Cortex


title: intestine sample from fed but not fin clipped fish 2 h post infection, biological rep1

value: 2 h

value: fed

value: not fin clipped


title: intestine sample from fed but not fin clipped fish 2 h post infection, biological rep2

value: intestine

value: infected


title: Day 12 Treatment_3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

extract_protocol:
Skin tissue from mouse specimens was minced on ice and digested in DMEM-F12 (GIBCO®) with 0.5mg/ml LiberaseTM (Roche) for 30 minutes at 37º in an orbital shaker. The digests were quenched with quench media (DMEM-F12 with 10% Fetal Bovie Serum (FBS, Sigma)), centrifuged at 300 x G for 5 minutes at 4 deg C, resuspended in quench media, filtered through 100, 70, and 40um cell strainers (Falcon cell strainer, ThermoFisher), centrifuged once more, and resuspended in FACS buffer.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: skin

value: unsorted

value: wildtype

value: fibrosed skin treatment w/ CYP26B1 inhib

value: Day 12 Treatment


title: mouse tumoroid M3-8 µM Regorafenib

description:
Library name: IGA19-KO-M3-T3-8uM-Rego.19
IGA19-KO-M3-T3-8uM-Rego.19

value: Colon

value: organoids Apc deficient (Floxed)

value: epithelium

value: Regorafenib 8 µM


title: 3D, Cortex, Fresh, tech rep 2, patient3

value: Fresh


title: intestine sample from fed but not fin clipped fish 4 h post infection, biological rep1

data_processing:
Data was processed within OmicsBox v3.3.2
Quality control was performed on raw reads using Trimmomatic v0.39
Quality reads were aligned to the channel catfish Coco_2.0 genome using the STAR aligner v2.7.8a (parameters – 2-pass mapping=true; overhang=149; feature=exon)
Read counts were extracted from BAM files using HTseq v2.0.5 ‘count’ feature (parameters – Quantification Level=exon; Group by=parent; Overlap Mode=union; stranded=strand specific reverse)
Assembly: Coco_2.0 (GCF_001660625.3)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted from tissues using the Rneasy Plus Mini Kit (Qiagen) per the manufacturer’s protocol. 250 ng of total RNA from each sample was used for library construction.
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Ligation Kit per the manufacturer’s protocol.

value: 4 h


title: intestine sample from fin clipped but not fed fish 8 h post infection, biological rep6

value: 8 h

value: not fed

value: fin clipped


title: mouse tumoroid M3-4 µM Regorafenib

description:
Library name: IGA18-KO-M3-T2-4uM-Rego.18
IGA18-KO-M3-T2-4uM-Rego.18

value: Apc deficient (floxed)

value: Regorafenib 4 µM

value: day 6


title: intestine sample from fin clipped but not fed fish 8 h post infection, biological rep5

value: intestine

value: infected


title: 3D, Cortex, Fresh, tech rep 1, patient3

value: Ovary

value: Cortex


title: Day 12 Treatment_2

value: skin

value: unsorted

value: wildtype

value: fibrosed skin treatment w/ CYP26B1 inhib

value: Day 12 Treatment


title: intestine sample from fin clipped but not fed fish 8 h post infection, biological rep4


title: mouse colonoid F11-5-FluoroUracil

description:
Library name: IGA16-KO-F11-T1-1uM-5FU.16
IGA16-KO-F11-T1-1uM-5FU.16

value: Colon

value: organoids Apc deficient (Floxed)

value: epithelium

value: 5-FU 1 µM


title: Day 28_3

value: fibrosed skin

value: Day 28


title: mouse tumoroid M3-DMSO.1

description:
Library name: IGA17-KO-M3-T1-DMSO.17
IGA17-KO-M3-T1-DMSO.17

value: Apc deficient (floxed)

value: DMSO


title: Day 12 Treatment_1


title: intestine sample from fin clipped but not fed fish 8 h post infection, biological rep3

value: intestine

value: 8 h

value: not fed

value: fin clipped


title: 2D, Cortex, Fresh, tech rep 2, patient3

value: Ovary

value: Cortex

value: Fresh


title: 2D, Cortex, Fresh, tech rep 1, patient3


title: intestine sample from fin clipped but not fed fish 8 h post infection, biological rep2

value: infected


title: mouse tumoroid F11-8 µM Regorafenib

description:
Library name: IGA15-KO-F11-T5-8uM-Rego.15
IGA15-KO-F11-T5-8uM-Rego.15

value: Regorafenib 8 µM

value: day 6


title: Tissue, Cortex, Fresh, tech rep 3, patient3

value: Tissue


title: mouse tumoroid F11-4 µM Regorafenib

description:
Library name: IGA14-KO-F11-T3-4uM-Rego.14
IGA14-KO-F11-T3-4uM-Rego.14

value: Colon

value: organoids Apc deficient (Floxed)

value: epithelium

value: Regorafenib 4 µM


title: Tissue, Cortex, Fresh, tech rep 2, patient3


title: intestine sample from fin clipped but not fed fish 8 h post infection, biological rep1


title: Day 28_1

value: skin

value: unsorted

value: wildtype

value: fibrosed skin

value: Day 28


title: Day 28_2


title: mouse tumoroid F11-DMSO.1

description:
Library name: IGA13-KO-F11-T1-DMSO.13
IGA13-KO-F11-T1-DMSO.13

value: Apc deficient (floxed)

value: DMSO


title: Day 21

value: Day 21


title: intestine sample from fin clipped but not fed fish 4 h post infection, biological rep6

value: intestine

value: 4 h

value: not fed

value: fin clipped


title: Day 12

value: Day 12


title: mouse colonoid M1-5-FluoroUracil

description:
Library name: IGA12-WT-M1-T4-1uM-5FU.12
IGA12-WT-M1-T4-1uM-5FU.12

value: Colon

value: organoids Apc WT

value: Apc WT

value: 5-FU 1 µM

value: day 6


title: intestine sample from fin clipped but not fed fish 4 h post infection, biological rep5

value: infected


title: 3D, Medulla, Fresh, tech rep 3, patient2

value: Ovary

value: Medulla

value: Fresh


title: mouse colonoid M1-8 µM Regorafenib

description:
Library name: IGA11-WT-M1-T3-8uM-Rego.11
IGA11-WT-M1-T3-8uM-Rego.11

value: epithelium

value: Regorafenib 8 µM


title: Unwounded 3

value: skin

value: unsorted

value: wildtype

value: unwounded, normal skin

value: Unwounded


title: 3D, Medulla, Fresh, tech rep 2, patient2


title: mouse colonoid M1-4 µM Regorafenib

description:
Library name: IGA10-WT-M1-T2-4uM-Rego.10
IGA10-WT-M1-T2-4uM-Rego.10

value: Regorafenib 4 µM


title: intestine sample from fin clipped but not fed fish 4 h post infection, biological rep3

value: intestine

value: 4 h

value: not fed

value: fin clipped


title: 3D, Medulla, Fresh, tech rep 1, patient2


title: mouse colonoid M1-DMSO.1

description:
Library name: IGA9-WT-M1-T1-DMSO.9
IGA9-WT-M1-T1-DMSO.9

value: Colon

value: organoids Apc WT

value: Apc WT

value: DMSO

value: day 6


title: Unwounded 2


title: Tissue, Medulla, Fresh, tech rep 3, patient2

value: Ovary

value: Medulla

value: Tissue

value: Fresh


title: intestine sample from fin clipped but not fed fish 4 h post infection, biological rep1

value: infected


title: Unwounded 1

value: skin

value: unsorted

value: wildtype

value: unwounded, normal skin


title: Ac-HFD4, mycolic acid-specific T cells, activated by mycolic acid-pulsed hCD1Tg BMDCs for 48hrs

city: Chicago

first: Chyung-Ru

last: Wang

state: Illinois

address: 320 E Superior St

department: Microbiology and Immunology

institute: Northwestern University

data_processing:
Reads were analyzed by using STAR and HTseq for aligning and counting.
Assembly: mm10
Supplementary files format and content: tab-delimated text file includes raw counts for each sample

source_name: lymph node

extract_protocol:
RNA was extracted by using the RNeasy Micro kit (Qiagen).
Libraries were prepared by using the Ultra-Low-Input RNA-Seq Prep.

treatment_protocol: Mice were fed either NC or HFD for 10 weeks. Cells of lymph nodes from NC-fed and HFD-fed mice were activated by mycolic acid-pulsed hCD1Tg BMDCs for 48hrs. Activated mycolic acid-specific T cells were purified by cell sorting.

value: lymph node

value: mycolic acid-specific T cells

value: The mouse was fed with HFD for 10 weeks.


title: Tissue, Medulla, Fresh, tech rep 2, patient2


title: mouse colonoid M40-5-FluoroUracil

description:
Library name: IGA8-WT-M40-T4-1uM-5FU.8
IGA8-WT-M40-T4-1uM-5FU.8

value: Colon

value: epithelium

value: 5-FU 1 µM


title: mouse colonoid M40-8 µM Regorafenib

description:
Library name: IGA7-WT-M40-T3-8uM-Rego.7
IGA7-WT-M40-T3-8uM-Rego.7

value: organoids Apc WT

value: Apc WT

value: Regorafenib 8 µM


title: intestine sample from fin clipped but not fed fish 4 h post infection, biological rep2

value: intestine

value: 4 h

value: not fed

value: fin clipped


title: Tissue, Medulla, Fresh, tech rep 1, patient2

value: Ovary

value: Medulla

value: Tissue

value: Fresh


title: intestine sample from fin clipped but not fed fish 2 h post infection, biological rep6

value: infected

value: 2 h


title: Ac-HFD2, mycolic acid-specific T cells, activated by mycolic acid-pulsed hCD1Tg BMDCs for 48hrs

value: lymph node

value: mycolic acid-specific T cells

value: The mouse was fed with HFD for 10 weeks.


title: Tissue, Cortex, Fresh, tech rep 1, patient3

value: Cortex


title: Ac-HFD3, mycolic acid-specific T cells, activated by mycolic acid-pulsed hCD1Tg BMDCs for 48hrs


title: mouse colonoid M40-4 µM Regorafenib

description:
Library name: IGA6-WT-M40-T2-4uM-Rego.6
IGA6-WT-M40-T2-4uM-Rego.6

value: Colon

value: organoids Apc WT

value: epithelium

value: Regorafenib 4 µM

value: day 6


title: 3D, Cortex, Fresh, tech rep 2, patient2


title: Ac-HFD1, mycolic acid-specific T cells, activated by mycolic acid-pulsed hCD1Tg BMDCs for 48hrs


title: mouse colonoid M40-DMSO.1

description:
Library name: IGA5-WT-M40-T1-DMSO.5
IGA5-WT-M40-T1-DMSO.5

value: Apc WT

value: DMSO


title: intestine sample from fin clipped but not fed fish 2 h post infection, biological rep5

value: intestine

value: not fed

value: fin clipped


title: intestine sample from fin clipped but not fed fish 4 h post infection, biological rep4

value: 4 h


title: mouse colonoid M41-1 µM 5-FluoroUracil

description:
Library name: IGA4-WT-M41-T4-1uM-5FU.4
IGA4-WT-M41-T4-1uM-5FU.4

value: 5-FU 1 µM


title: intestine sample from fin clipped but not fed fish 2 h post infection, biological rep4

value: infected

value: 2 h


title: intestine sample from fin clipped but not fed fish 2 h post infection, biological rep3


title: Ac-NC4, mycolic acid-specific T cells, activated by mycolic acid-pulsed hCD1Tg BMDCs for 48hrs

value: lymph node

value: mycolic acid-specific T cells

value: The mouse was fed with NC for 10 weeks.


title: 3D, Cortex, Fresh, tech rep 1, patient2

value: Ovary

value: Cortex

value: Fresh


title: Ac-NC3, mycolic acid-specific T cells, activated by mycolic acid-pulsed hCD1Tg BMDCs for 48hrs


title: mouse colonoid M41-8 µM Regorafenib

description:
Library name: IGA3-WT-M41-T3-8uM-Rego.3
IGA3-WT-M41-T3-8uM-Rego.3

value: Colon

value: organoids Apc WT

value: epithelium

value: Regorafenib 8 µM


title: Ac-NC2, mycolic acid-specific T cells, activated by mycolic acid-pulsed hCD1Tg BMDCs for 48hrs


title: Tissue, Cortex, Fresh, tech rep 2, patient2

value: Tissue


title: Tissue, Cortex, Fresh, tech rep 3, patient2


title: intestine sample from fin clipped but not fed fish 2 h post infection, biological rep2

value: intestine

value: not fed


title: intestine sample from fin clipped but not fed fish 2 h post infection, biological rep1

value: fin clipped


title: mouse colonoid M41-DMSO.1

description:
Library name: IGA1-WT-M41-T1-DMSO.1
IGA1-WT-M41-T1-DMSO.1

value: Apc WT

value: DMSO

value: day 6


title: mouse colonoid M41-4 µM Regorafenib

description:
Library name: IGA2-WT-M41-T2-4uM-Rego.2
IGA2-WT-M41-T2-4uM-Rego.2

value: Regorafenib 4 µM


title: 3D, Medulla, SF, tech rep 3, patient1

value: Medulla

value: SF


title: Tissue, Cortex, Fresh, tech rep 1, patient2

value: Ovary


title: intestine sample from fed and fin clipped fish 8 h post infection, biological rep5

value: infected

value: 8 h

value: fed


title: C57BL6/J postnatal day15, biological replicate 1

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

data_processing:
Sequencing outputs were demultiplexed using cellranger (6.1.2) mkfastq
Fastq files were aligned to Mus musculus mm10 reference using cellranger (6.1.2) count or multi
Assembly: Mouse reference, mm10
Supplementary files format and content: Processed data files are gzipped cellranger count output directory (sample_feature_bc_matrix or filtered_feature_bc_matrix).

extract_protocol:
Freshly collected skins were minced using scissors, and suspended  in digestion buffer (RPMI with 5%v/v  fetal bovine serum, 0.3mg/mL Liberase TM (Merck) and 5U/mL DNase1) and incubated 37°C for 30minutes twice. The samples were resuspended in another digestion buffer (TrypLE Select Enzyme(Thermo Fisher Scientific) with 5U/mL DNase1) and incubated 37°C for 15minutes. The obtained cell suspensions were filtered through a 70µm cell strainer, washed in Minimum Essential Medium alpha (Thermo Fisher Scientific) with 2%v/v FBS.
Isolated skin cells were individually labeled using the 3' CellPlex Kit Set A (10x Genomics). SYTOX negative cells from each individual were sorted using the BD FACS Aria III system (BD Biosciences).Library preparation was performed according to the 10x Genomics protocol "Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing".

value: skin

tag: strain

value: postnatal day15


title: C57BL6/J postnatal day15, biological replicate 2


title: intestine sample from fed and fin clipped fish 8 h post infection, biological rep4

tag: disease state


title: intestine sample from fed and fin clipped fish 8 h post infection, biological rep3

tag: time


title: SmoM2-Ptenfl/fl replicate1

city: New York

first: Yinwen

last: Liang

email: liangy@mskcc.org, liangyinwen@gmail.com

state: New York

address: 1275 york avenue

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: FL_1
scRNA_seq on SmoM2-Ptenfl/fl_replicate1

data_processing:
The Cell Ranger Single Cell software suite (10x Genomics) was used to align reads, and generate feature-barcode matrices. The reference genome used was the Genome Reference Consortium Mouse Build 38 (GRCm38, Gencode annotation mm10). Raw reads were processed using the Cell Ranger count program using default parameters.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 including barcodes, feature and matrix files for replicates.

source_name: SHH-MBs

growth_protocol: SHH-MBs from P22 SmoM2 and P16 SmoM2-Ptenfl/fl mice

extract_protocol:
Tumor tissues were dissected out in ice-cold Hank's balanced salt solution (HBSS) on ice, dissociated in Papain (Worthington, LK003176) at 37°C for 30 min. Following dissociation, samples were triturated by pipetting up and down using a P1000, filtered through a 40um cell strainer (Falcon), followed by PBS wash, and then centrifuged at 500â€…g at 4°C for 5min. To obtain live cells, cell suspentions were loaded to EasySep Dead Cell Removal kit (STEMCELL technologies,17899) before pool loading to 10x Chips.
Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction.
10x library (3' scRNA-seq)

treatment_protocol: Tamoxifen injection at P0

value: SHH-MBs

value: Tamoxifen injection at P0


title: C57BL6/J postnatal day0, biological replicate 1

value: postnatal day0


title: SmoM2-Ptenfl/fl replicate2

description:
Library name: FL_2
scRNA_seq on SmoM2-Ptenfl/fl_replicate2


title: 3D, Medulla, SF, tech rep 1, patient1


title: SmoM2 replicate1

description:
Library name: WT_2
scRNA_seq on SmoM2_replicate1

value: Atoh1-FlpoER/+;  R26MASTR/LSL-SmoM2


title: 3D, Medulla, SF, tech rep 2, patient1


title: ChIP_DKO_Input_N3

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

description: 10% aliquot sheared chromatin

data_processing:
Quality was assessed using FastQC v0.11.9 & Fastq-Screen v0.15.2
Files were mapped to GRCm38 using Bowtie2 v.2.3.5.1
Duplicates were marked using samtools markduplicates v1.10
Peak calling was performed using Epic2 (FDR cutoff of 0.05. Window and gap sizes were 100 bp, 3 gaps for H3K4me3, 200 bp and 3 gaps for H3K27me3 and 50 bp, 2 gaps for Suz12)
Reads were counted in R using the Bioconductor package DiffBind (v.3.10.1) and differential enrichment was done using edgeR (v.3.42.4)
Regions were assigned to nearest genomic feature using ChIPseeker (v1.36) in R
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-deliminted text files with counts for all replicates and genotypes within each ChIP target across consensus peaks.

source_name: Hippocampus

growth_protocol: C57BL/6N background mice in standard home-cage housing (12h light/dark, ad libitum food and water, 19-22°C, 50-50% air humidity).

extract_protocol:
Tissue was homogenized and nuclei were isolated.
Nuclei were stained with anti-NeuN mouse antibody (Millipore, #mab377), an Alexa 488 secondary antibody (Life Technologies # A11001) and Vybrant DyeCycle Ruby (Life Technologies, #V102673) and nuclei were sorted using flow cytometry.
Sorted nuclei were pelleted by centrifugation at 3.200 g for 15 minutes, transferred to Bioruptor Microtubes (Diagenode, C30010016) shearing tubes and carefully re-suspended in RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS and 1x Complete EDTA free protease inhibitor cocktail (Roche, 11873580001). Samples were incubated 10 minutes at 4°C and then sheared using a Bioruptor (Diagenode) for 4 times at 5 cycles and followed by 2 cycles at 30″ ON/OFF high power. Samples were spun down in between every 5 cycles. Sheared chromatin was cleared by centrifugation at 10.000 rpm for 10 minutes and the supernatant was stored in DNA low-binding tubes (Eppendorf, 022431021).
Sheared chromatin was pre-cleared with BSA-blocked protein G magnetic beads (Dynabeads, Invitrogen, 10004D) for 1 hour at 4°C. For every ChIP-reaction the appropriate amount of chromatin, depending on the different antibodies, was used (Supplementary Table 1). ChIP-reactions were performed by overnight incubation on a rotating wheel at 4°C in ChIP buffer (50 mM Tris-HCl at pH 8.0, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 20 mM EDTA, 1x Complete EDTA free protease inhibitor cocktail). As input control a 10% aliquot of each sheared chromatin sample was saved and stored at -80°C. Subsequently, 30 μl of BSA-blocked protein G magnetic beads were added to each ChIP-reaction and the mixture was incubated on a rotator at 4°C for 4 hours. The chromatin-bead complexes were washed twice at 4°C for 5 minutes at slow rotation (15 rpm) with ChIP buffer containing 0.1% SDS, twice with wash buffer (100 mM Tris-HCl pH 8.0, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 20 mM EDTA) and twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). For reverse crosslinking, chromatin-bead complexes and 10% input controls were resuspended in 300 μl elution buffer (100 mM NaHCO3, 1% SDS) with 200 mM NaCl and incubated at 65°C overnight. On the next day, the samples were treated with 1 μl of RNAse A (Thermo Scientific, EN0531) for 1 hour at 37°C. Subsequently, 6 μl 0.5M EDTA and 1 μl Proteinase K (Roche, 3115828001) were added and the samples were incubated at 45°C for 1 hour. DNA was then purified by phenol-chloroform extraction and samples were eluted in 16 μl Tris buffer (10 mM Tris-HCl pH 8.0) in a DNA low-binding tube and stored at −80°C.
Library construction was performed by using QIAseq™ Ultralow Input Library Kits (Qiagen, 180492) according to manufacturer’s protocol and purified using AMPure XP beads (Beckman Coulter, A63880).

treatment_protocol: Animals were sacrificed by cervical dislocation at 6 months of age and hippocampi were dissected, isolated, snap-frozen in liquid nitrogen and stored at −80°C until further use.

value: NeuN + sorted nuclei

value: Hippocampus

tag: chip antibody


title: Tissue, Medulla, Fresh, tech rep 3, patient1

value: Tissue

value: Fresh


title: intestine sample from fed and fin clipped fish 8 h post infection, biological rep6

city: Auburn

first: Jason

last: Abernathy

address: 990 Wire Road

institute: USDA-ARS

value: intestine

tag: feeding state

value: fin clipped


title: Tissue, Medulla, Fresh, tech rep 1, patient1

value: Medulla


title: Ac-NC1, mycolic acid-specific T cells, activated by mycolic acid-pulsed hCD1Tg BMDCs for 48hrs

value: lymph node

value: mycolic acid-specific T cells

value: The mouse was fed with NC for 10 weeks.


title: AL3

city: Guangzhou

first: Jing

last: Ren

address: shatai road

institute: southern medical university

description: Library name: AL3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
clean reads were separately aligned to the reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie (in a reference-based approach. To identify DEGs (differential expression genes), the expression level of each gene was calculated according to the transcripts per million reads (TPM) method.
fRSEM was used to quantify gene abundances. DEGs with |log2 (foldchange)| ≥ 1 and P-adjust ≤ 0.05 were considered to be significantly different expressed genes. In addition, functional-enrichment analysis including GO and Reactome was performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at P-adjust ≤ 0.05.
Assembly: GRCm38
Supplementary files format and content: tab-delinited text file includes raw fpkm for all samples

source_name: medial prefrontal cortex

growth_protocol: Mice were housed in groups of three to five per cage under controlled temperature conditions (22-25 °C) on a 12/12-h light/dark cycle (lights on from 7:00 A.M. to 7:00 P.M.) with ad libitum access to food and water.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol Reagent according to the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (Takara). RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDrop Technologies).
The transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, the paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer (2 × 150bp read length). The raw paired-end reads were trimmed and quality was controlled by fastp with default parameters.

treatment_protocol: Mice were divided into high- and low-anxiety group based on their behaviors in EPM..

value: medial prefrontal cortex

tag: group

value: low anxiety


title: intestine sample from fed and fin clipped fish 8 h post infection, biological rep1

value: infected

value: 8 h

value: fed


title: ChIP_DKO_Input_N2

description: 10% aliquot sheared chromatin


title: AL2

description: Library name: AL2


title: AL1

description: Library name: AL1


title: intestine sample from fed and fin clipped fish 4 h post infection, biological rep5

value: 4 h


title: 3D, Cortex, SF, tech rep 2, patient1

value: Ovary

value: Cortex

value: SF


title: ChIP_DKO_Input_N1

description: 10% aliquot sheared chromatin

value: NeuN + sorted nuclei

value: Hippocampus


title: ChIP_DKO_Suz12_N3

description: Pull-down sample

value: Suz12 Rb (Cell Signaling #3737S)


title: 3D, Cortex, SF, tech rep 1, patient1


title: C57BL6/J postnatal day0, biological replicate 2

value: skin

value: postnatal day0


title: intestine sample from fed and fin clipped fish 4 h post infection, biological rep4

value: intestine

value: fin clipped


title: Tissue, Cortex, Fresh, tech rep 2, patient1

value: Tissue

value: Fresh


title: SmoM2 replicate2

description:
Library name: WT_3
scRNA_seq on SmoM2_replicate2

value: SHH-MBs

value: Atoh1-FlpoER/+;  R26MASTR/LSL-SmoM2

value: Tamoxifen injection at P0


title: AH3

description: Library name: AH3

value: medial prefrontal cortex

value: high anxiety


title: ChIP_DKO_Suz12_N2

description: Pull-down sample


title: Tissue, Cortex, Fresh, tech rep 1, patient1

value: Ovary


title: intestine sample from fed and fin clipped fish 4 h post infection, biological rep3

value: infected

value: 4 h

value: fed


title: AH1

description: Library name: AH1


title: ChIP_DKO_Suz12_N1

description: Pull-down sample

value: NeuN + sorted nuclei

value: Hippocampus


title: Tissue, Medulla, Fresh, tech rep 2, patient1

value: Medulla


title: Pancreatic Cancer Cell, iMQT_020

city: Yeonsu-gu, Incheon

first: Yulseung

last: Sung

address: Room-317-3, Veritas Hall D, Yonsei University, 85 Songdogwahak-Ro

department: College of Pharmacy

country: South Korea

institute: Yonsei University

data_processing:
StringTie program was utilized to assemble gene/trasncript according to the reference gene model
With the assembled data with the read count of known gene, we selected genes with differential expression profile. Quality check and normalization between samples were conducted to assess the statistical significance
Among the sample groups, we ignored where the gene count was 0 ( Among 46,427 genes, we ignored 25,473 genes)
In order to minimize the systemic bias, read cound data was assessed to calculate the size factor, and it was utilized for Trimmed mean of M-values normalization. (edgeR R library - calcNormFactors was applied)
Assembly: Genomic Reference (GRCh38)
Supplementary files format and content: TXT format with read counts and gene/transcript ID and names

extract_protocol:
Trizol based Total RNA extraction
Genomic Reference (GRCh38) was utilized. Bowtie2 aligner was used to map the library through HISAT2 program with sspliced read mapping strategy.

treatment_protocol: Vehicle or iMQT_020 Treated for 48 hours

value: Pancreatic Adenocarcinoma


title: AH2

description: Library name: AH2


title: ChIP_DKO_K27_N3

description: Pull-down sample

value: H3K27trime Ms (Abcam #ab6002)


title: MTE-RAS PV-10 treated tumors 3

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

description: Library name: S06_688

data_processing:
Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1).
Processed raw reads were then aligned to human genome mm10 using STAR (v2.7.7a).
Gene expression was evaluated as read count at gene level with RSEM (v1.3.0) and Gencode gene model v30.
Gene express data were then normalized and differential expression between experimental groups were evaluated using DEseq2.
Assembly: mm10
Supplementary files format and content: gene/transcript reads count file, text format

source_name: Tumor

growth_protocol: MTE-Ras cells were injected subcutaneously into the right flank of C57BL/6 mice. Total RNA was isolated from three mouse tumors each from PBS and PV-10 treated mice using the RNeasy Mini Kit (Qiagen, #74104) according to the manufacturer's protocol, followed by DNase treatment using RNase-Free DNase Set (Qiagen, #79254). The RNA extracted from tumors was quantitated with the Qubit Fluorometer (ThermoFisher Scientific, Waltham, MA) and screened for quality on the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA). The samples were then processed for RNA-sequencing using the NuGEN Universal RNA-Seq Library Preparation Kit with NuQuant (Tecan Genomics, Redwood City, CA).

extract_protocol:
Briefly, 100 ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer’s protocol. Quality control steps were performed, including TapeStation size assessment and quantification using the Kapa Library Quantification Kit (Roche, Wilmington, MA). The final libraries were normalized, denatured, and sequenced on the Illumina NovaSeq 6000 sequencer with the SP-200 cycle reagent kit to generate 100-150 million 100-base read pairs per sample (Illumina, Inc., San Diego, CA).
All work was performed by the Moffitt Cancer Center Molecular Genomics Core Facility (RRID:SCR_012333). Read adapters were detected using BBMerge (v37.02) (RRID:SCR_016970) and subsequently removed with cutadapt (v1.8.1) (RRID:SCR_011841). Processed raw reads were then aligned to mouse genome mm10 using STAR (v2.7.7a) (RRID:SCR_004463). Gene expression was evaluated as read count at the gene level using RSEM (v1.3.0) (RRID:SCR_000262) with the Gencode gene model vM21. Normalization and differential expression analysis between the experimental and control groups were performed using DESeq2 (RRID:SCR_015687) (27). Gene set enrichment analysis (GSEA) was performed on the ranked gene list, based on fold change between experimental and control groups, using the gseGO function from the cluster Profiler R package (v 4.6.2). The analysis focused on Gene Ontology (GO) terms.

value: Tumor

value: MTE-RAS

value: Mouse Tracheal Epithelial cancer cells

value: transformed oncogenic RAS mutation

value: PV-10 treatement intralesionally in tumors


title: ChIP_DKO_K27_N2

description: Pull-down sample


title: intestine sample from fed and fin clipped fish 4 h post infection, biological rep1

value: intestine

value: fin clipped


title: intestine sample from fed and fin clipped fish 4 h post infection, biological rep6


title: intestine sample from fed and fin clipped fish 2 h post infection, biological rep6

value: 2 h


title: MTE-RAS PV-10 treated tumors 2

description: Library name: S05_595


title: Pancreatic Cancer Cell, Vehicle

value: Vehicle


title: ChIP_DKO_K27_N1

description: Pull-down sample


title: MTE-RAS PV-10 treated tumors 1

description: Library name: S04_572


title: intestine sample from fed and fin clipped fish 2 h post infection, biological rep5

value: infected


title: SNU-1_shTP53_Nutlin-3_24h

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

institute: Chiba University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Read were aligned with HISAT2.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.0.2.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: Human gastric epithelial cancer cell line SNU-1

growth_protocol: SNU-719, SNU-1, AGS, MKN45, MKN7, MKN74, TMK1, KATO-III and GES1 were grown in RPMI 1640 with 10% FBS,  penicillin-streptomycin. IM95 was grown in DMEM with 10% FBS,  penicillin-streptomycin and 10 mg/L human recombinant insulin. YCCEL1, WI-38 and IMR-90 were grown in MEM with 10% FBS,  penicillin-streptomycin and Non-Essential Amino Acids .

extract_protocol:
Total RNA was collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

tag: stimulation

value: SNU-1 + shTP53


title: ChIP_DKO_K4_N3

description: Pull-down sample

value: H3K4trime Rb (Abcam #ab8580)


title: intestine sample from fed and fin clipped fish 8 h post infection, biological rep2

value: 8 h

value: fed


title: MTE-RAS control tumors 3

description: Library name: S03_581

value: PBS treatement intralesionally in tumors


title: ChIP_DKO_K4_N2

description: Pull-down sample

value: NeuN + sorted nuclei

value: Hippocampus


title: intestine sample from fed and fin clipped fish 2 h post infection, biological rep3


title: MTE-RAS control tumors 2

description: Library name: S02_569

value: Tumor


title: intestine sample from fed and fin clipped fish 4 h post infection, biological rep2

value: 4 h


title: intestine sample from fed and fin clipped fish 2 h post infection, biological rep4


title: SNU-1_shTP53_DMSO_24h

value: DMSO


title: SNU-1_shNT_RG7388_24h

value: SNU-1 + shNT


title: ChIP_DKO_K4_N1

description: Pull-down sample


title: ChIP_Ogg1_Input_N3

description: 10% aliquot sheared chromatin


title: SNU-1_shNT_Nutlin-3_24h


title: MTE-RAS control tumors 1

description: Library name: S01_564

value: MTE-RAS

value: Mouse Tracheal Epithelial cancer cells

value: transformed oncogenic RAS mutation


title: intestine sample from fed and fin clipped fish 2 h post infection, biological rep2

value: intestine

value: 2 h

value: fin clipped


title: mouse_ON_aT

city: Saint Louis

first: David

last: Gutmann

address: 660 S. Euclid Ave

institute: Washington University in St. Louis School of Medicine

description: 10x Genomics

data_processing:
chemistry: Single Cell 5' PE
The demultiplexing, barcode processing, gene couning and aggregation were made using the cellranger pipline v6.1.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
Cell quality was evaluated by number of reads, detected gene count, and percentage of mitochondrial read. Cell lowers than 200 counts and mitochondrial gene percentages greater than 5% were removed across all datasets. We analyzed our data using Seurat (v5.0.3) in R (v4.1.1). SCTransform (v2) was applied to perform data normalization with default settings, followed by PCA. Harmony was applied to perform data integration using Seurat IntegrateLayers function with ‘method = HarmonyIntegration’.  FindNeighbors with top 20 PCs followed by FindCluster function were used to cluster cells. UMAP was implemented on Harmony embeddings to visualize cell clusters.
Assembly: mm10-2020-A
Supplementary files format and content: sequences corresponding to every barcode in the matrix table
Supplementary files format and content: sequences corresponding to every feature in the matrix table
Supplementary files format and content: matrix table with the number of unique molecular identifiers for every feature by row and every barcode by column

source_name: optic nerve

extract_protocol:
Nf1-OPG optic nerves were collected from ten 12-week old mice, and pooled to prepare a single-cell suspension. Optic nerves were collected and dissociated using the neural dissociation kit (Miltenyi Biotec, 130-095-942) followed by debris (Miltenyi Biotec, 130-107-677) and myelin (Miltenyi Biotec, 130-096-733) removal. Single cell supensions from meningeal duras were prepared as described above, stained with 7-AAD, and sorted using MoFlo. Live cells were collected and sent for scRNA sequencing.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  Gene Expression libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 5’ Reagent Kit (v2 Chemistry Dual Index) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns (PN-1000263), Chromium Next GEM Chip K Single Cell Kit, 48 rxns (PN-1000286) and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library.

value: optic nerve

value: anti-TIGIT


title: SNU-1_shNT_DMSO_24h


title: ChIP_Ogg1_Input_N2

description: 10% aliquot sheared chromatin


title: intestine sample from fin clipped control fish, biological rep6

value: mock

value: 0 h


title: mouse_ON_aP

description: 10x Genomics


title: ChIP_Ogg1_Input_N1

description: 10% aliquot sheared chromatin


title: DSS_KO_516

description: HBO1 KO colonic crypts at day 3 of DSS treatment

data_processing:
Reads were aligned to the GCRm38/mm10 genome using Bowtie 2 (v2.2.5) and sorted with samtools (v1.5).
mRNA expression analysis was performed using Hisat (version 2.1.0) and Ballgown (version 2.20.0).
Assembly: mm10
Supplementary files format and content: gene_fpkm_matrix_OHRNAseq.csv and gene_fpkm_matrix_RNAseq.csv: Comma-delimited text file includes FPKM values for each sample.

treatment_protocol: For small intestinal organoids RNA-seq, Vill-creERT2;HBO1 fl/fl mice small intestianl crypts were isolated for organoids culture, the organoids were treated with 4-OH-tamoxifen(4-OHT) for HBO1 knock out. Et-OH treatment as the control. For colonic epithelial cells RNA-seq, the control and HBO1 KO mice were all fed with 3% DSS (MW; 36–50 kDa; MP Biomedicals) dissolved in drinking water, and both the control and HBO1 KO crypts were isolated at day 3.

value: Colonic crypts

value: Colonic epithelial cells

value: DSS


title: intestine sample from fin clipped control fish, biological rep4

value: fed


title: SNU-719_shTP53_DMSO_24h

source_name: Human gastric epithelial cancer cell line SNU-719

value: SNU-719 + shTP53


title: DSS_KO_515


title: ChIP_Ogg1_Suz12_N2

description: Pull-down sample

value: NeuN + sorted nuclei

value: Hippocampus

value: Suz12 Rb (Cell Signaling #3737S)


title: SNU-1_shTP53_RG7388_24h

value: SNU-1 + shTP53


title: intestine sample from fed and fin clipped fish 2 h post infection, biological rep1

value: infected


title: SNU-719_shTP53_RG7388_24h


title: DSS_WT_529

description: Control colonic crypts at day 3 of DSS treatment


title: ChIP_Ogg1_Suz12_N3

description: Pull-down sample


title: intestine sample from fin clipped control fish, biological rep5

value: intestine


title: SNU-719_shNT_RG7388_24h

value: SNU-719 + shNT


title: SNU-719_shNT_Nutlin-3_24h


title: intestine sample from fin clipped control fish, biological rep2

value: fin clipped


title: DSS_WT_509


title: intestine sample from fin clipped control fish, biological rep3


title: ChIP_Ogg1_K27_N2

description: Pull-down sample

value: H3K27trime Ms (Abcam #ab6002)


title: ChIP_Ogg1_Suz12_N1

description: Pull-down sample


title: intestine sample from fin clipped control fish, biological rep1


title: 4OH_2

description: HBO1 KO small intestinal organoids

source_name: Small intestinal epithelium

value: Small intestinal epithelium

value: Small intestinal organoids


title: SNU-719_shTP53_Nutlin-3_24h


title: 4OH_3

description: HBO1 KO small intestinal organoids


title: SNU-719_shNT_DMSO_24h

value: DMSO