title: 3 samplespooled-CPL scRNA seq

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:
cell plex
Ctrl1_barcodes.tsv.gz
Ctrl1_features.tsv.gz
Ctrl1_matrix.mtx.gz
Ctrl2_barcodes.tsv.gz
Ctrl2_features.tsv.gz
Ctrl2_matrix.mtx.gz
Ctrl3_barcodes.tsv.gz
Ctrl3_features.tsv.gz
Ctrl3_matrix.mtx.gz

data_processing:
The Cell Ranger Single Cell software suite (10x Genomics) was used to demultiplex samples, 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: barcodes, feature and matrix files for replicates.

source_name: mouse embryonic yolk sac

extract_protocol:
Yolk sac from E8.75 mouse embryos were dissected, disassocited into single cells and labelled with oligos (CellPlex kit) 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.  Finallibraries were sequenced on Illumina NovaSeq S4platform (R1 – 28cycles, i7 – 8cycles, R2 – 90 cycles).

value: mouse embryonic yolk sac

value: Ttr-Cre/+; R26lsl-rtTA-EGFP/+


title: INTS11 ChIP-seq, 48h, rep2, input

status: Public on Jun 25 2025

type: SRA

city: Gainesville

first: Conner

middle: Mark

last: Traugot

state: FL

address: 2033 Mowry Rd, CGRC 265

country: USA

institute: University of Florida

description:
Library name: INTS11 ChIP-seq_48h_rep2_input
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)

library_source: genomic

data_processing:
Adapter sequences were first trimmed using Trimmomatic v0.39 to remove sequencing adapters. This step also removed reads smaller than 20 bp and reads with quality lower than 20.
Forward and reverse reads were paired and combined into a single read using PEAR (v0.9.2). PCR Duplicates were collapsed using fastx-collapser from fastx_toolkit (v0.0.14) and UMIs were removed using cutadapt (v5.0).
Reads were mapped to the human and KSHV reference genomes using HISAT2 (v2.2.1) with default parameters.
ChIP-seq peaks were called using MACS2 (v2.2.7.1) and files for visualization of the data were generated using bamCoverage and computeMatrix from Deeptools2 (v3.5.2).
Assembly: Human: hg38, KSHV: GQ994935.1
Supplementary files format and content: ChIP-seq samples include bigwig visualizations of mapped reads.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: iSLK.219 cells were maintained in DMEM supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin, 250 μg/mL G418, 400 μg/mL hygromycin and 10 μg/mL puromycin. They were cultured at in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cells were crosslinked by incubating with standard growth media supplemented with 1% formaldeyde for 10 min. Crosslinking was quenched by adding glycine to a concentration of 125 mM. Cells were centrifuged and sonicated to generate cell lysate and shear DNA.
Sheared DNA samples were incubated overnight with 5 μg of INTS11 or control IgG antibody for the immunoprecipitation. The resulting DNA was extracted using phenol/chloroform/isoamyl alcohol. The libraries were generated using the Takara ThruPLEX Tag-seq Kit according the manufacturer protocols.

tag: cell line

tag: cell type

value: Human epithelial


title: Healthy CSF1R treated quadricep biological replicate 3

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

institute: University of Kentucky

library_source: transcriptomic

data_processing:
Raw FASTQ files underwent pre-alignment quality control, then were aligned using STAR aligner (reference genome: GRCm38/mm10) in Partek Flow with requrement of junction reads to match introns and strict paired-end compatibility. Quantified reads went through a noise reduction filter with maximum feature exclusion set less than or equal to 10 and were analyzed to obtain differential gene expression using DESeq2 (minimum read cutoff of 50).  Differential gene expression was calculated comparing ACLT and Control limbs for both CSF1-Ri and placebo treatment
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Skeletal muscle

extract_protocol:
Mouse quadricep RNA was isolated using TRIzol and the Zymo MicroPrep Kit and prepared for RNA-sequencing
Conducted at NovoGene

treatment_protocol: Mice received 40mg/kg of CSF1-R inhibitor or .5% sucrose in drinking water for 7 days following ACL transection

tag: tissue

value: Skeletal muscle


title: NOD-lymphnode-vehicle-mouse5rep4

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

data_processing:
Fastq files were processed to dcc files using GeoMx NGS pipeline software. Using the dcc files, spatial transcriptomics analysis was conducted in R studio v4.2.1 using the GeomxTools 3.4.0 package
The GeoMx whole mouse transcriptome atlas was used as the probe assay metadata
Sequencing quality was assessed using the default quality control (QC) parameter cut-offs, namely: minimum number of reads (1000); minimum percentage of reads trimmed (80%), stitched (80%), and aligned (80%); sequencing saturation (50%); negative control counts (10); maximum counts observed in no treatment control (NTC) well (1000); minimum number of nuclei estimated (100); and minimum segment area (5000). Any ROI that did not satisfy the above criteria was removed as part of QC filtering.
Following segment QC, probe QC was also performed to remove any outlier either globally or locally before generating gene-level count data.
The limit of quantification was determined per segment using the value recommended in the workflow, and segments with less than 1-5% of genes detected were removed. Furthermore, only genes that were detected in at least 1% of segments were retained.
The data was normalized using the quartile 3 method and log transformed.
For each organ, a linear mixed model without random slope was used to identify differentially expressed genes between vehicle and treatment groups for both the 3- and 7-day timepoints. Genes with linear scale fold change ³ 1.5 and p-value < 0.05 were considered as differentially expressed.
Assembly: GeoMx mouse whole transcriptome assay v1
Supplementary files format and content: .dcc files = Digital count conversion file (dcc file)
Supplementary files format and content: Rawcounts_LCMV.txt = raw counts for LCMV mouse dataset
Supplementary files format and content: q3 normalized counts_LCMV.txt = q3 normalized and log transformed values for LCMV mouse dataset
Supplementary files format and content: Rawcounts_NOD.txt = raw counts for NOD mouse dataset
Supplementary files format and content: q3 normalized counts_NOD.txt = q3 normalized and log transformed values for NOD mouse dataset
Library strategy: Spatial transcriptomics

source_name: lymph node

growth_protocol: RIP-LCMV-GP mice were purchased from Jackson Laboratory and bred in-house. Five-week-old female NOD/ShiLT mice were purchased from Jackson Laboratory and acclimated at the IU Laboratory Animal Research Center (LARC) for at least one week prior to treatment.

extract_protocol:
Mouse pancreas sections (5 µm) were fixed, sectioned, and mounted on positively charged slides. The slideswere deparaffinized, heated in antigen retrieval solution (Thermo Fisher Scientific) at 100 °C for 20 min, and treated with 1 µg/mL proteinase K at 37 °C for 15 min. Mouse transcriptomics was visualized using the GeoMx mouse whole transcriptome atlas (NanoString Technologies, GMX-RNA-NGS-MsWTA). An overnightin situhybridization was performed with a mouse WTA probe, and the next day, the slides were washed twice at 37 °C for 25 min with 50% formamide/2X SSC buffer to remove unbound probes. The slides were then washed twice with 2X SSC buffer for 2 minutes at RT and blocked with blocking buffer containing Buffer W (Nanostring) with 1% Fc-Receptor blocker (Milteny) and 5% Normal Donkey Serum (Jackson Laboratories) as described previously (98). The slides were incubated with guinea pig anti-insulin (Dako), 1:200 rabbit anti-CD3 (Abcam), mouse anti-CD68 (Santa Cruz).The slides were washed twice with 2xSSC and incubated with secondary antibodies (1:400 goat-anti-guinea pig Alexa-488; 1:200 goat-anti rabbit Alexa-594 and 1:200 goat-anti mouse Alexa-647) for 30 minutes. Then, the slides were washed four times with 2xSSC for 3 minutes and counter-stainedwith 1:20,000 Syto83 (Invitrogen) for 1 h at room temperature. Stained slides were loaded onto the GeoMx instrument and scanned. After visual inspection using the GeoMx Digital Spatial Profiler (DSP; NanoString Technologies), geometrical ROIs (100 μm diameter) with different histologies were selected for oligonucleotide collection. Photocleaved oligonucleotides from each spatially resolved ROI were sequenced with the Illumina NextSeq500 sequencer (Illumina).
The GeoMx libraries were prepared according to the GeoMx DSP NGS Readout User Manual. Briefly, for each plate, 4 μl of a GeoMx DSP sample was used for amplification. Each GeoMx DSP sample in a well was uniquely indexed with dual indexes. 4 μL of each resulting PCR product, including the NTC negative control, were pooled and purified with AMPure XP beads (Beckman Coulter). The final libraries were qualified and quantified using TapeStation and Qubit, respectively. The libraries were sequenced on an Illumina NextSeq 500 to generate 27 bp paired-end sequence reads.

treatment_protocol: Eight-week-old maleRIP-LCMV-GPmice werepre-treated with TYK2i (BMS-986202, 30 mg/kg) or vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse) by oral gavage two days prior to inoculation with LCMV. Mice continued to receive TYK2i treatment daily until the study endpoint. Six-week-old female NOD mice were treated with BMS-986202 (30 mg/kg) or vehicle for 6 weeks by oral gavage.Themice from each group were euthanized after 6 weeks of TYK2i treatment (12-weeks of age), and the pancreas was harvested and fixed for downstream analysis as described previously(80).

tag: mouse number

value: lymph node

tag: treatment

tag: roi

tag: strain

value: NOD/ShiLT

tag: age

value: 6-week old

tag: Sex

value: Female


title: Healthy individual 3

type: genomic

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

description: DNA extracted from peripheral blood of healthy individuals

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

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

data_processing: Data were processed in R, normalized using BMIQ normalization.

label: Cy5 and Cy3

source_name: Peripheral Blood

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA from the whole blood samples was extracted using salting out method.

value: F


title: 3 samples pooled-GEX scRNA seq

city: New York

description:
gene expression
Ctrl1_barcodes.tsv.gz
Ctrl1_features.tsv.gz
Ctrl1_matrix.mtx.gz
Ctrl2_barcodes.tsv.gz
Ctrl2_features.tsv.gz
Ctrl2_matrix.mtx.gz
Ctrl3_barcodes.tsv.gz
Ctrl3_features.tsv.gz
Ctrl3_matrix.mtx.gz

library_source: transcriptomic single cell

molecule: polyA RNA

tag: genotype


title: Healthy individual 1


title: INTS11 ChIP-seq, 48h, rep1

description:
Library name: INTS11 ChIP-seq_48h_rep1
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: ACLT CSF1R treated quadricep biological replicate 2


title: DOX_Input

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.Reads were aligned to mouse assembly mm10 using bowtie2 (v2.2.2) with default parameters.To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Assembly: mm10
Supplementary files format and content: BigWig files containing read densities normalized to 10 million reads

source_name: Mouse epiblast stem cells

growth_protocol: Epiblast stem cells were grown as previously described (Medina-Cano et al, Development 2022)

extract_protocol:
25M cells were fixed in 1% formaldehyde for 10 min, after quenching and cell lysis, chromatin was sonicated using a  E220 Focused-ultrasonicator (Covaris).
Libraries were prepared using the ThruPLEX®DNA-Seq kit (R400676, Takara) following the manufacturer’s instructions, purified with SPRIselect magnetic beads (B23318, Beckman Coulter), and quantified using a Qubit Flex fluorometer (ThermoFisher Scientific) and profiled with a TapeStation (Agilent).

treatment_protocol: Doxycycline (1ug/ml) for 24hr or untreated

value: Mouse epiblast stem cells

value: 1ug/mL Doxcycylin, 24hr

tag: chip antibody


title: Healthy CSF1R treated quadricep biological replicate 2


title: INTS11 ChIP-seq, 48h, rep1, input

description:
Library name: INTS11 ChIP-seq_48h_rep1_input
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: NOD-lymphnode-vehicle-mouse5rep3

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: NOD-lymphnode-vehicle-mouse5rep2


title: INTS11 ChIP-seq, 24h, rep2

description:
Library name: INTS11 ChIP-seq_24h_rep2
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: ACLT CSF1R treated quadricep biological replicate 1


title: INTS11 ChIP-seq, 24h, rep2, input

description:
Library name: INTS11 ChIP-seq_24h_rep2_input
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: Healthy CSF1R treated quadricep biological replicate 1


title: DOX_Flag_M2_Rep1

value: Flag


title: Healthy individual 6


title: NOD-pancreas-vehicle-mouse5rep5

source_name: pancreas

value: pancreas


title: NOD-lymphnode-vehicle-mouse5rep1


title: DOX_Flag_M2_Rep2


title: ACLT placebo treated cartilage biological replicate 2

source_name: Cartilage

extract_protocol:
Mouse cartilage RNA was isolated using TRIzol and the Zymo MicroPrep Kit and prepared for RNA-sequencing
Conducted at NovoGene

value: Cartilage


title: INTS11 ChIP-seq, 24h, rep1

description:
Library name: INTS11 ChIP-seq_24h_rep1
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: NOD-pancreas-vehicle-mouse5rep4


title: CTL_Input

value: No Doxycycline


title: INTS11 ChIP-seq, 24h, rep1, input

description:
Library name: INTS11 ChIP-seq_24h_rep1_input
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: CTL_H3K4me3_Epicypher


title: NOD-pancreas-vehicle-mouse5rep3


title: CTL_Flag_M2_Rep2


title: INTS11 ChIP-seq, 0h, rep2

description:
Library name: INTS11 ChIP-seq_0h_rep2
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: ACLT placebo treated cartilage biological replicate 1


title: CTL_Flag_M2_Rep1


title: NOD-pancreas-vehicle-mouse5rep2


title: Healthy placebo treated cartilage biological replicate 1


title: ESC, RNA, Rep4

city: Cologne

first: Robert

last: Hänsel-Hertsch

department: CMMC

country: Germany

institute: University of Cologne

description:
gsea_report_for_na_neg_1693415212828.tsv
gsea_report_for_na_pos_1693415212828.tsv

data_processing:
basecalls were performed using BaseSpace DRAGEN Analysis - Version: 1.3.0
Assembly: mm39
Supplementary files format and content: bigwig, bed (peak file), tsv (gene set enrichment analysis ouput)

source_name: Stem cells

growth_protocol: cultured on gelatine-coated (Sigma-Aldrich, ES-006-B) dishes in 2i/L medium (GMEM (Gibco, 11710035), 20 % foetal bovine serum (Merck, ES-009-C), 1X NEAA (Gibco, 11140-035), 1X L-glutamine (Gibco, 35035-038), 1000 ng/mL LIF (Gibco, A35934), 0.1 mM 2-mercaptoethanol (Gibco, 21985023), 1 mM sodium pyruvate (Gibco, 113060039), 3µM GSK3βi (AXON, 1386), 1 µM MEKi (AXON, 1408) at 37 °C with 5 % CO2 and passaged every other day.

extract_protocol:
Nuclei isolation from in vitro cultured cells. For nuclei isolation, cells were incubated in NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM Spermidine, 0.1 % Triton X-100, 20 % glycerol, 1X cOmplete Proteinase Inhibitor) for 3 min on ice. Nuclei were fixed with 0.1 % formaldehyde (Thermo Scientific, 28906) in PBS for 1 min at room temperature. Formaldehyde was quenched with 74 mM glycine and nuclei were pelleted by centrifugation at 450 xg for 3 min at 4 °C. RNA isolation and RNA-seq from in vitro cultured cells. Total RNA from cultured cells were extracted using the NucleoSpin RNA Kit (Macherey-Nagel, 740955.50) according to the manufacturer’s protocol. RNA-seq libraries were generated with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with Unique Dual Indices for Illumina (Lexogen, 115.384) and sequenced on an Illumina NovaSeq 6000 platform using NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles) (Illumina, 20028401). All RNA-seq experiments were conducted in four independent technical replicates.
10,000 nuclei were transferred into new 0.2 mL PCR tubes and incubated for 3 h at 58 °C in 50 µL Denaturation buffer (10 mM Tris pH 8.0 (HCl), 50 mM NaCl, 0.2 % (w/v) SDS, 0.5 ng/mL proteinase K). Denaturation was stopped by purification of the tagmented DNA fragments using the MinElute Reaction Cleanup Kit (QIAGEN, 28204). DNA was eluted in 23 µL EB buffer and amplified analogously to CUT&Tag (https://www.nature.com/articles/s41467-019-09982-5) for 12-20 cycles. Appropriate number of cycles can be estimated via qPCR and will depend on epitope abundancy. Amplified sequencing libraries were one-sided size-selected using first a 0.5 X SPRI beads ratio to remove large fragments followed by purification with 1.3 X SPRI beads ratio followed by elution in 26 µL EB buffer.

treatment_protocol: For epiblast-like cell differentiation, 200,000 embryonic stem cells were plated onto fibronectin-coated (Corning, 354008) in 2i/L medium and allowed to attach overnight. The next morning, medium was changed to EpiLC-Diff medium (0.5 X DMEM/F-12 (Gibco, 10565-018), 0.5 X Neurobasal Medium (Gibco, 21103049), 1 X N2 (Gibco, 17502048), 1 X B27 (Gibco, 17504044), 20 ng/mL activin A (STEMCELL, 78132.1), 12 ng/mL bFGF (STEMCELL, 78134), 1 % KSR (Gibco, 10828010), 0.1 mM 2-mercaptoethanol (Gibco, 21985023), 0.04 ng/mL bovine serum albumin (Gibco, 15260037) for 48 h.

value: Stem cells


title: INTS11 ChIP-seq, 0h, rep1

description:
Library name: INTS11 ChIP-seq_0h_rep1
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: NOD-pancreas-vehicle-mouse5rep1


title: ACLT CSF1R treated cartilage biological replicate 2


title: ESC, RNA, Rep3


title: NOD-pancreas-vehicle-mouse4rep5


title: INTS11 ChIP-seq, 0h, rep1, input

description:
Library name: INTS11 ChIP-seq_0h_rep1_input
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: Healthy CSF1R treated cartilage biological replicate 2


title: ACLT placebo treated quadricep biological replicate 4


title: INTS11 knockdown RNA-seq, KD, 72h, rep2

description:
Library name: INTS11 KD RNA-seq_72h_KD_rep2
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)

data_processing:
Adapter sequences were first trimmed using Trimmomatic v0.39 to remove sequencing adapters. This step also removed reads smaller than 20 bp and reads with quality lower than 20.
Forward and reverse reads were paired and combined into a single read using PEAR (v0.9.2). PCR Duplicates were collapsed using fastx-collapser from fastx_toolkit (v0.0.14) and UMIs were removed using cutadapt (v5.0).
Reads were mapped to the human and KSHV reference genomes using HISAT2 (v2.2.1) with default parameters. Gene counts were generated using htseq-count (v2.0.3).
From the RNA-seq samples, differential gene expression was performed using edgeR's generalized linear model approach (v4.6.2). Gene ontology results were generated using the Bioconductor clusterProfiler tool (v4.16.0).
Assembly: Human: hg38, KSHV: GQ994935.1
Supplementary files format and content: RNA-seq samples include tab-delimited text files with raw read counts

extract_protocol:
Total RNA was isolated using TRIzol according to the manufacturer's protocols.
Libraries were generated using the Takara SMARTer Stranded Total RNA-Seq Kit v3 according to the manufacturer's protocol.

treatment_protocol: RNA-seq samples were transfected with siRNA targeting INTS11 or a scramble control. After 24 hours, all samples were treated with 0.2 μg/mL doxycycline to induce the expression of RTA and reactivate the KSHV lytic cycle. The time point for each sample represents the time of collection after reactivation.


title: ESC, RNA, Rep1


title: NOD-pancreas-vehicle-mouse4rep4


title: Healthy placebo treated cartilage biological replicate 2


title: ESC, RNA, Rep2


title: INTS11 knockdown RNA-seq, KD, 72h, rep1

description:
Library name: INTS11 KD RNA-seq_72h_KD_rep1
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: Healthy CSF1R treated cartilage biological replicate 1


title: ACLT CSF1R treated cartilage biological replicate 1


title: NOD-pancreas-vehicle-mouse4rep3


title: EpiLC, RNA, Rep3

source_name: Epiblast like cells

value: Epiblast like cells


title: NOD-pancreas-vehicle-mouse4rep2


title: INTS11 knockdown RNA-seq, scramble, 72h, rep2

description:
Library name: INTS11 KD RNA-seq_72h_Scr_rep2
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)

value: Scramble shRNA


title: DBAM-8R

city: Madison

first: Michaela

middle: Elizabeth

last: Trautman

state: WI

address: 2500 Overlook Terrace

institute: University of Wisconsin Madison

description: RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

data_processing:
Analysis of significantly differentially expressed genes (DEGs) was completed in R version 3.4.3 (Team, 2017) using edgeR (Robinson et al., 2010) and limma (Ritchie et al., 2015). Gene names were converted to gene symbol and Entrez ID formats using the mygene package. Genes with too many missing values were removed, if genes were present in less than one diet/strain/sex group they were removed. To reduce the impact of external factors not of biological interest that may affect expression, data was normalized to ensure the expression distributions of each sample are within a similar range. We normalized using the trimmed mean of M-values (TMM), which scales to library size. Heteroscedasticity was accounted for using the voom function, DEGs were identified using an empirical Bayes moderated linear model, and log coefficients and Benjamini-Hochberg (BH) adjusted p-values were generated for each comparison of interest (Benjamini and Hochberg, 2018).
Assembly: #!genome-build GRCm38 #!genome-build-accession NCBI:GCA_000001635.7
Supplementary files format and content: GeneExpression.csv; GeneLog2FoldChanges.csv

source_name: Liver, Fasted

extract_protocol:
RNA was extracted from liver using TRIzol Reagent according to the manufacturer’s protocol (Thermo Fisher Scientific). The concentration and purity of RNA were determined by absorbance at 260/280nm using Nanodrop (Thermo Fisher Scientific) and samples were diluted to roughly 1000 ng/µl. RNA was submitted to the University of Wisconsin-Madison Biotechnology Center Gene Expression Center (RRID:SCR_017757) & DNA Sequencing Facility (RRID:SCR_017759). Each RNA sample was assayed on an Agilent RNA NanoChip to assess its integrity. RNA samples that met Illumina’s TruSeq Stranded Total RNA Reference Guide (#1000000040499 v00) (Illumina, San Diego, CA) quality criteria were prepared for sequencing following the protocol as recommended using a 250ng total RNA input. Libraries were multiplexed and sequenced on the NovaSeq6000 sequencer. Reads were aligned to the mouse (Mus musculus) with genome-build GRCm38.p5 of accession NCBI:GCA_000001635.7 and expected counts were generated with ensembl gene IDs (Zerbino et al., 2018).
Illumina’sTruSeq Stranded Total RNA Reference Guide (#1000000040499 v00)

treatment_protocol: To compare the effects of isoleucine in different quantities in a Western Diet, animals were put on their experimental diet for 12 weeks starting at 18 weeks of age.

value: Liver, Fasted

value: Male

value: 18 weeks

tag: diet

value: WD High Ile


title: INTS11 ChIP-seq, 0h, rep2, input

description:
Library name: INTS11 ChIP-seq_0h_rep2_input
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)

value: Human epithelial


title: NOD-pancreas-vehicle-mouse4rep1

value: NOD/ShiLT

value: 6-week old

value: Female


title: INTS11 knockdown RNA-seq, scramble, 72h, rep1

description:
Library name: INTS11 KD RNA-seq_72h_Scr_rep1
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: DBAM-8N


title: NOD-pancreas-BMS-mouse3rep10


title: EpiLC, RNA, Rep2


title: DBAM-7R

value: WD Low Ile


title: EpiLC, RNA, Rep1


title: NOD-pancreas-BMS-mouse3rep9


title: NOD-pancreas-vehicle-mouse6rep2

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: E8.5

city: London

first: Sergio

last: Menchero

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: 10X Genomics

data_processing:
Quantification by kallisto (0.46.2) bustools (0.40.0) workflow
Cell selection using DropletUtils (1.12.1)
Analysis using Seurat (4.0.3)
Assembly: ASM229v1 with Y chromosome
Supplementary files format and content: kallisto bustools expression matrix in cell ranger-format in tarball
Supplementary files format and content: 10x loupe for embryonic cells
Supplementary files format and content: Seurat rds object for embryonic cells
Supplementary files format and content: Metadata table for embryonic cells in CSV format

organism: Monodelphis domestica

source_name: embryo

extract_protocol:
Samples were incubated on FACSmax Cell Dissociation Solution (Amsbio, T200100) with 10% Papain (30 U/mg, Sigma-Aldrich, 10108014001) for 11-12 min at 37°C to dissociate the cells. Samples were then resuspended in HBSS with 5% FBS, 10 µM rock inhibitor (Stemcell Technologies, Y-27632), and 1x non-essential aminoacids (Life Technologies, 11140050). Cells were filtered through 35 µm cell strainers (Falcon, 352235) and 20 µm filters (Miltenyi Biotec, 130-101-812).
Libraries were prepared using the Single Index Kit T Set A (PN-1000213) from the 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 (PN-1000121)

value: embryo

tag: developmental stage

value: wildtype


title: EpiLC, RNA, Rep4


title: DBAM-7N


title: INTS11 knockdown RNA-seq, KD, 48h, rep1

description:
Library name: INTS11 KD RNA-seq_48h_KD_rep1
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: NOD-pancreas-BMS-mouse3rep8

value: pancreas


title: ZNFX1_2

city: Harbin

first: Yang

last: Shi

state: Heilongjiang

address: No.157 Baojian Rd, Harbin, HEILONGJIANG

department: Department of Pharmacology

country: China

institute: Harbin medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: Genes differential expression analysis was performed by DESeg2 software between two different groups (and byedgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolutefold change > 2 were considered differentially expressed genes. Differentially expressed genes were then subjectedto enrichment analysis of GO functions and KEGG pathways

source_name: heart

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: heart

value: primary mouse cardiomyocytes


title: INTS11 knockdown RNA-seq, scramble, 48h, rep1

description:
Library name: INTS11 KD RNA-seq_48h_Scr_rep1
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: NOD-pancreas-BMS-mouse3rep7


title: NOD-pancreas-BMS-mouse3rep6


title: INTS11 knockdown RNA-seq, scramble, 48h, rep2

description:
Library name: INTS11 KD RNA-seq_48h_Scr_rep2
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: DBAM-6R

value: WD Control


title: INTS11 knockdown RNA-seq, KD, 24h, rep2

description:
Library name: INTS11 KD RNA-seq_24h_KD_rep2
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: ZNFX1_3


title: NOD-pancreas-BMS-mouse3rep5


title: INTS11 knockdown RNA-seq, KD, 24h, rep1

description:
Library name: INTS11 KD RNA-seq_24h_KD_rep1
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: DBAM-4N


title: UPF1_3


title: DBAM-4R


title: INTS11 knockdown RNA-seq, KD, 48h, rep2

description:
Library name: INTS11 KD RNA-seq_48h_KD_rep2
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: UPF1_2


title: NOD-pancreas-BMS-mouse3rep4


title: ZNFX1_1


title: UPF1_1


title: DBAM-3R


title: NOD-pancreas-BMS-mouse3rep3


title: INTS11 knockdown RNA-seq, scramble, 24h, rep1

description:
Library name: INTS11 KD RNA-seq_24h_Scr_rep1
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)

value: Scramble shRNA


title: INTS11 knockdown RNA-seq, scramble, 24h, rep2

description:
Library name: INTS11 KD RNA-seq_24h_Scr_rep2
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: Hypoxia_3

value: hypoxia


title: DBAM-3N

value: Liver, Fasted

value: Male


title: NOD-pancreas-BMS-mouse3rep2


title: DBAM-6N

value: 18 weeks


title: DBAM-2R


title: Hypoxia_2


title: INTS11 knockdown RNA-seq, KD, 0h, rep1

description:
Library name: INTS11 KD RNA-seq_0h_KD_rep1
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)

value: Human epithelial


title: NOD-lymphnode-BMS-mouse2rep12

value: lymph node

value: NOD/ShiLT


title: DBAM-2N


title: NOD-pancreas-BMS-mouse3rep1

value: 6-week old

value: Female


title: INTS11 knockdown RNA-seq, scramble, 0h, rep2

description:
Library name: INTS11 KD RNA-seq_0h_Scr_rep2
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: Hypoxia_1


title: DBAM-12R

value: WD High Ile


title: mycardial infarction+ZNFX1_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genes differential expression analysis was performed by DESeg2 software between two different groups (and byedgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolutefold change > 2 were considered differentially expressed genes. Differentially expressed genes were then subjectedto enrichment analysis of GO functions and KEGG pathways
Assembly: mm9
Supplementary files format and content: 1_genes_fpkm_expression.txt
Supplementary files format and content: 2_transcripts_fpkm_expression.txt
Supplementary files format and content: gene_count_matrix.txt
Supplementary files format and content: transcript_count_matrix.txt

value: primary cardiomyocytes


title: DBAM-12N


title: INTS11 knockdown RNA-seq, scramble, 0h, rep1

description:
Library name: INTS11 KD RNA-seq_0h_Scr_rep1
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: NOD-lymphnode-BMS-mouse2rep10


title: DBAM-11R

value: WD Low Ile


title: mycardial infarction+ZNFX1_2


title: NOD-lymphnode-BMS-mouse2rep11


title: D681 GEX library 2

first: Donna

middle: L

last: Farber

state: NY

address: 701 West 168th Street

institute: Columbia University Irving Medical Center

description: Library name: D681 GEX library 2

data_processing:
Alignment to the GRCh38 reference (Gencode v24 annotation) was performed using Cell Ranger (v7.1.0; 10X Genomics). Events with under 250 unique genes profiled, 1,000 GEX counts or 50 ADT counts, and events with over 50,000 GEX counts, 10,000 ADT counts, or 20% mitochondrial counts were removed. Hashtags were demultiplexed using HashSolo with priors determined by commercially provided multiplet rates (scanpy). Multiplets and hashtag-negative events were removed. An initial clustering on highly variable genes (as above) for each donor was used to identify and remove clusters enriched for markers of contaminant lineages (e.g., G0S2, CD3E, CD19, JCHAIN, KRT7, DCN; <2% of total events) or low-quality events (abnormally high mitochondrial content or low GEX counts).
Assembly: GRCh38
Supplementary files format and content: Gene expression count matrix. The first two columns specify gene symbol and accession number. The remaining columns each represent a cell. The name of each column corresponds to the cell barcode, donor id, library number, hashtag assignment (as determined by HashSolo), tissue, and treatment, delimited by an underscore.
Supplementary files format and content: Antibody derived tag (ADT) expression count matrix. The first two columns specify the oligonucleotide barcode and the antibody (either listing the target or the hashtag oligo (HTO) number). The remaining columns each represent a cell. The name of each column corresponds to the cell barcode, donor id, library number, hashtag assignment (as determined by HashSolo), tissue, and treatment, delimited by an underscore.
Library strategy: CITE-seq

source_name: blood, lung, jejunum lamina propria, spleen

extract_protocol:
UpCell plates were incubated on ice for 20 min for non-enzymatic cell dissociation. Samples were stained for 30 min with TotalSeq-C Hashtags following manufacturer’s directions (BioLegend). Samples were counted, pooled at equal proportions, treated with human TruStain FcX and stained for 30 min with TotalSeq-C Universal Cocktail following manufacturer’s directions (BioLegend). Samples for each donor were loaded across two lanes of a 10X Genomics Chromium instrument targeting between 8,000-10,000 cells each. cDNA synthesis and amplification was performed using Next GEM Single Cell 5’ Kit v2 (10X Genomics).  In this experiment, the hashtags correspond combinations of tissues and treatment combinations. For D667, HTO1: Unstimulated blood, HTO2: LPS stimulated blood, HTO3: IL4 stimulated blood, HTO4: Unstimulated lung, HTO5: LPS stimulated lung, HTO6: IL4 stimulated lung, HTO7: Unstimulated spleen, HTO8: LPS stimulated spleen, HTO10: IL4 stimulated spleen, HTO12: Unstimulated jejunum, HTO13: LPS stimulated jejunum, HTO14: IL4 stimulated jejunum For D674, HTO2: Unstimulated blood, HTO3: LPS stimulated blood, HTO4: IL4 stimulated blood, HTO5: Unstimulated lung, HTO6: LPS stimulated lung, HTO7: IL4 stimulated lung, HTO8: Unstimulated spleen, HTO9: LPS stimulated spleen, HTO10: IL4 stimulated spleen, HTO12: Unstimulated jejunum, HTO13: LPS stimulated jejunum, HTO14: IL4 stimulated jejunum For D681, HTO2: Unstimulated blood, HTO4: LPS stimulated blood, HTO5: IL4 stimulated blood, HTO6: Unstimulated lung, HTO7: LPS stimulated lung, HTO8: IL4 stimulated lung, HTO9: Unstimulated spleen, HTO10: LPS stimulated spleen, HTO12: IL4 stimulated spleen, HTO13: Unstimulated jejunum, HTO14: LPS stimulated jejunum, HTO15: IL4 stimulated jejunum
Sequencing libraries were prepared using Next GEM Single Cell 5’ Kit v2 (10X Genomics) and sequenced on a NovaSeq X (Illumina) with 100 cycles for read 1 and 90 cycles for read 2.

treatment_protocol: Mononuclear cells (MNCs) were isolated from organ donor tissues from two subjects as described in Dominguez-Conde et al, Science, 2022. A detailed protocol for each tissue site appears in the supplementary materials. Mononuclear cells from each tissue-site were isolated by mechanical and enzymatic digestion followed by density centrifugation. For BLD, LNG, and SPL samples, further erythrocyte depletion was accomplished by a brief (2min) incubation in ACK lysis buffer (Gibco) at 37°C. To deplete epithelial cells from the JLP, samples were incubated for 5 min in TruStain FcX blocking buffer (BioLegend), stained for 10 min with biotinylated α-CD326, and subjected to negative selection by streptavidin and annexin V microbubbles following manufacturer’s instructions (Akadeum). Samples were washed with buffer (DPBS, 5% FBS, 2mM EDTA) by centrifugation (400 x g, 5 min, 4°C), resuspended in Zombie NIR Viability dye (BioLegend) for 20 min, washed twice, incubated for 10 min in TruStain FcX and Monocyte Blocker (BioLegend) and stained with surface antibodies for 20 min. Samples were sorted using a FACS Aria II (BD Biosciences) to isolate monocytes and MΦs (CD45+ CD33+ CD3- CD19- CD66b- CD117- CD326- cells). Each donor was processed and sequenced separately. Sorted cells were seeded at 100,000 cells per well and cultured for 12 hours at 37°C in 0.5 mL media (RPMI, 10% FBS, 1X PSQ) on 24-well Nunc UpCell plates (ThermoFisher) either untreated, or treated with 0.02μg/mL LPS (Sigma) and 40ng/mL recombinant human IFNγ (R&D Systems), or 20ng/mL recombinant human IL-4 (R&D Systems).

value: Monocytes and macrophages

value: unstimulated, LPS and IFNg, IL4


title: D681 GEX library 1

description: Library name: D681 GEX library 1

value: blood, lung, jejunum lamina propria, spleen


title: mycardial infarction+ZNFX1_1

value: heart


title: myocardial infarction_3

value: MI


title: DBAM-11N


title: D681 ADT library 2

description: Library name: D681 ADT library 2

library_source: other

molecule: protein


title: NOD-lymphnode-BMS-mouse2rep8


title: INTS11 knockdown RNA-seq, KD, 0h, rep2

description:
Library name: INTS11 KD RNA-seq_0h_KD_rep2
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: DBAM-10R

value: WD Control


title: NOD-lymphnode-BMS-mouse2rep9


title: D681 ADT library 1

description: Library name: D681 ADT library 1


title: NOD-lymphnode-BMS-mouse2rep7


title: DBAM-10N

value: Liver, Fasted


title: myocardial infarction_1


title: NOD-lymphnode-BMS-mouse2rep6


title: NOD-lymphnode-BMS-mouse2rep5


title: liver, Female iGHRKO group sample 5

first: Shoshana

last: Yakar

address: 345E 24th Street

institute: New York University

data_processing:
The quality of raw data was checked by FastQC (v. 0.11.9)
Read counts were quantified using Salmon (v. 1.7.0)
Differential expression analysis was performed by DESeq2 R/Bioconductor package
Assembly: GRCm38.p6
Supplementary files format and content: Salmon Output File Formats
Supplementary files format and content: quant.sf for each sample

source_name: liver

extract_protocol:
RNA was extracted from livers using Qiagen RNeasy plus mini kit (Qiagen, cat# 74204)
RNA libraries were prepared according to the QIAseq Stranded RNA Library Kits protocol.

treatment_protocol: To induce Ghr gene ablation, 12 or 6 months-old mice received 100-uL intraperitoneal injections of 0.32 mg of Tamoxifen/g of body weight dissolved in peanut oil once per day over five consecutive days, for a total of 1.5 mg of tamoxifen. Controls received identical injections of peanut oil.

value: liver

value: iGHR knock out


title: D674 GEX library 1

description: Library name: D674 GEX library 1


title: DBAF-36N

value: 18 weeks


title: liver, Female iGHRKO group sample 4


title: D674 GEX library 2

description: Library name: D674 GEX library 2


title: NOD-lymphnode-BMS-mouse2rep4

value: lymph node


title: NOD-lymphnode-vehicle-mouse5rep5

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)

value: NOD/ShiLT


title: D674 ADT library 2

description: Library name: D674 ADT library 2

value: Female


title: liver, Female iGHRKO group sample 3


title: NOD-lymphnode-BMS-mouse2rep3

value: 6-week old


title: DBAF-35N


title: DBAF-35R


title: D674 ADT library 1

description: Library name: D674 ADT library 1


title: liver, Female iGHRKO group sample 2


title: D667 GEX library 2

description: Library name: D667 GEX library 2

value: Male


title: NOD-lymphnode-BMS-mouse2rep2


title: myocardial infarction_2

value: primary cardiomyocytes


title: DBAF-34R


title: NOD-lymphnode-BMS-mouse2rep1


title: liver, Female iGHRKO group sample 1


title: D667 GEX library 1

description: Library name: D667 GEX library 1

value: Monocytes and macrophages


title: liver, Female Control group sample 5

value: WT


title: DBAF-36R

value: WD High Ile


title: DBAF-34N


title: NOD-pancreas-BMS-mouse2rep8

value: pancreas


title: D667 ADT library 2

description: Library name: D667 ADT library 2

value: blood, lung, jejunum lamina propria, spleen

value: unstimulated, LPS and IFNg, IL4


title: DBAF-32R

value: Liver, Fasted


title: liver, Female Control group sample 4

value: liver


title: NOD-pancreas-BMS-mouse2rep7


title: D667 ADT library 1

description: Library name: D667 ADT library 1


title: liver, Female Control group sample 3


title: EL.LS5.ed.010.Stroma

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

description: Library name: DSP-1001660011049-D-H03

data_processing:
Sequencing files were processed into DCC format using the GeoMx NGS Pipeline software v1.0. GeoMx counts were log2 transformed in preparation for statistic data analysis.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files include raw read counts along with RTS_IDs for each ROI
Supplementary files format and content: PKC file includes probe metadata describing the targets and is needed to interpret RTS_IDs in the DCC files

source_name: Stroma

extract_protocol:
FFPE tissue sections (5 μm) sliced consecutively to Deep Viusal Proteomics samples were processed following the Nanostring GeoMx user manual (MAN-10132-04). In brief, tissue slides were deparaffinized and rehydrated, followed by protein target retrieval using antigen retrieval buffer (Tris-EDTA) for 20 min in a pressure cooker. RNA target retrieval was accomplished by a digest with proteinase K for 15 min at 37°C. Tissue was post-fixed in 10% NBF, followed by an overnight hybridization at 37°C with the RNA probes (Human Whole Transcriptome Atlas, 18,000 protein-coding genes coupled to UV-cleavable oligonucleotide barcodes). Excess probes were removed the next day by washing the samples twice in stringent washes at 37°C, followed by an incubation period in blocking buffer W (Nanostring LOT#:2-23020032). Thereafter, tissue was stained using conjugated primary antibodies targeting pan-cytokeratin (mouse monoclonal antibody, Novus NBP2-33200AF488, 1:100) and vimentin (mouse monoclonal IgG1κ, Santa Cruz sc-373717, 1:100) as well as the SYTO13 nuclear stain (ThermoFisher Scientific, S7575) for one hour at room temperature. For transcriptomics data acquisition, slides were placed on the GeoMx Digital Spatial Profiler (DSP) and scanned in 20x magnification. Based on immunofluorescence images, regions of interest (ROI) were collected under supervision of an experienced pathologist (AB) and matched to the regions selected in DVP. Upon ROI selection, oligonucleotide barcodes were collected into a 96-well plate by UV-ablation while precisely separating compartments in each region.
Sequencing libraries were prepared using the Illumina TruSeq technology for the ligation of sequencing adaptors and amplification. Amplified libraries were purified using two rounds of Ampure XP magnetic bead cleanup (ratio 1.2:1 (beads: library)) (HighPrep PCR from MAGBIO (Cat#: AC-60500). Purified libraries were sequenced in an Illumina NovaSeq flowcell PE50 at a depth of 100x /μm2.

value: Ovarian Cancer, Omental Metastasis

value: Stroma

tag: cohort

value: LGSC-Met


title: DBAF-32N

value: 18 weeks


title: DBAF-31R

value: WD Low Ile


title: NOD-pancreas-BMS-mouse2rep6

value: NOD/ShiLT

value: Female


title: EL.LS5.ed.010.Epithelium

description: Library name: DSP-1001660011049-D-H02

source_name: Epithelium

value: Epithelium


title: liver, Female Control group sample 2


title: DBAF-31N


title: NOD-pancreas-BMS-mouse2rep5

value: 6-week old


title: NOD-pancreas-BMS-mouse2rep4


title: EL.LS5.ed.009.Stroma

description: Library name: DSP-1001660011049-D-H01


title: NOD-pancreas-BMS-mouse2rep3


title: DBAF-30N

value: WD Control


title: liver, Male iGHRKO group sample 3

value: Male

value: iGHR knock out


title: EL.LS5.ed.008.Epithelium

description: Library name: DSP-1001660011049-D-G10


title: DBAF-28R

value: WD High Ile


title: liver, Male iGHRKO group sample 2


title: DBAF-28N


title: NOD-pancreas-BMS-mouse2rep1

value: pancreas


title: liver, Male iGHRKO group sample 1


title: EL.LS5.ed.007.Epithelium

description: Library name: DSP-1001660011049-D-G08


title: DBAF-27R


title: EL.LS5.ed.006.Stroma

description: Library name: DSP-1001660011049-D-G07


title: DBAF-27N


title: liver, Male Control group sample 5

value: WT


title: liver, Female Control group sample 1


title: EL.LS5.ed.006.Epithelium

description: Library name: DSP-1001660011049-D-G06


title: EL.LS5.ed.009.Epithelium

description: Library name: DSP-1001660011049-D-G12


title: DBAF-30R

value: Liver, Fasted


title: liver, Male iGHRKO group sample 4

value: liver


title: NOD-lymphnode-BMS-mouse1rep5

value: lymph node


title: NOD-pancreas-BMS-mouse2rep2


title: liver, Male Control group sample 4


title: EL.LS5.ed.005.Stroma

description: Library name: DSP-1001660011049-D-G05

value: Ovarian Cancer, Omental Metastasis

value: Stroma


title: DBAF-26N

value: 18 weeks


title: EL.LS5.ed.005.Epithelium

description: Library name: DSP-1001660011049-D-G04

value: LGSC-Met


title: liver, Male Control group sample 3


title: EL.LS5.ed.007.Stroma

description: Library name: DSP-1001660011049-D-G09


title: liver, Male Control group sample 2


title: B6M-8R


title: NOD-lymphnode-BMS-mouse1rep8

value: NOD/ShiLT


title: B6M-8N


title: EL.LS5.ed.004.Epithelium

description: Library name: DSP-1001660011049-D-G02


title: liver, Male Control group sample 6


title: NOD-lymphnode-BMS-mouse1rep7

value: Female


title: NOD-lymphnode-BMS-mouse1rep6


title: EL.LS5.ed.004.Stroma

description: Library name: DSP-1001660011049-D-G03


title: NRG1-treated MyC-CaP 24hr Biological Replicate 3

city: Nashville

first: Hong Yuen

last: Wong

state: Tennessee

address: 2220 Pierce Ave # PRB648, Preston Research Building

department: Medicine

institute: VUMC

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v4.567 and aligned to corresponding genomes (Gencode GRCh38.p13 for human and Gencode GRCm38.p6 for mouse) using STAR v2.7.11a68.
GTF gene annotation (Gencode v38 for human and Gencode vM24 for mouse) was provided to STAR to improve the accuracy of mapping.
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC v0.11.9 (www.bioinformatics.babraham.ac.uk/projects/fastqc). featureCounts v2.0.269 was used to count the number of mapped reads to each gene.
Heatmap3 v1.1.970 was used for cluster analysis and visualization.
Significantly differential expressed genes with absolute fold change ≥ 1.5 and FDR adjusted p value ≤ 0.05 were detected by DESeq2 v1.30.171.
Assembly: GRCm38.p6
Supplementary files format and content: Comma-separated value file contains gene counts of all samples.

source_name: MyC-CaP

growth_protocol: Cells were plated in triplicate in 6 well plates (500,000-750,000 cells/well) and allowed to adhere for 24-48 hrs.

extract_protocol:
Total RNA was extracted from treated cells with the RNeasy Protect Cell Mini Kit (Qiagen) as per manufacturer’s protocol.
Illumina TruSeq mRNA sequencing libraries were prepared by sequencing core (VANTAGE, Vanderbilt Technologies for Advanced Genomics).
RNA-seq performed at multiplex paired-end 150 bp on the Illumina NovaSeq 6000 (Illumina).

treatment_protocol: Cells were starved in serum-free and calcium-free media (Vanderbilt Cell Culture Core) for 6-12 hours prior to treatment with buffer, 100 ng/mL rASPN (MyBioSource, Origene) or 15 ng/mL rNRG1 (R&D Systems).

value: MyC-CaP

value: Prostate Cancer Epithelial-like Cells

tag: time


title: DBAF-26R

value: WD Control


title: liver, Male Control group sample 1

value: Male


title: EL.LS5.ed.003.Stroma

description: Library name: DSP-1001660011049-D-G01


title: B6M-7N


title: NRG1-treated MyC-CaP 24hr Biological Replicate 2


title: EL.LS5.ed.002.Stroma

description: Library name: DSP-1001660011049-D-F11


title: NRG1-treated MyC-CaP 24hr Biological Replicate 1


title: EL.LS5.ed.002.Epithelium

description: Library name: DSP-1001660011049-D-F10

value: Epithelium


title: B6M-4R

value: WD High Ile


title: NRG1-treated MyC-CaP 12hr Biological Replicate 3


title: NOD-lymphnode-BMS-mouse1rep4

value: 6-week old


title: NOD-lymphnode-BMS-mouse1rep3


title: NOD-lymphnode-BMS-mouse1rep2


title: NRG1-treated MyC-CaP 12hr Biological Replicate 2


title: NOD-pancreas-BMS-mouse1rep8

value: pancreas


title: EL.LS5.ed.003.Epithelium

description: Library name: DSP-1001660011049-D-F12


title: B6M-6R

value: Liver, Fasted

value: WD Low Ile


title: NOD-pancreas-BMS-mouse1rep6


title: EL.LS5.ed.001.Stroma

description: Library name: DSP-1001660011049-D-F09


title: NOD-pancreas-BMS-mouse1rep5


title: NRG1-treated MyC-CaP 12hr Biological Replicate 1


title: NOD-pancreas-BMS-mouse1rep4


title: EL.LS5.ed.001.Epithelium

description: Library name: DSP-1001660011049-D-F08


title: NOD-lymphnode-BMS-mouse1rep1

value: lymph node


title: NOD-pancreas-BMS-mouse1rep3


title: NRG1-treated MyC-CaP 0hr Biological Replicate 3


title: B6M-3R


title: EL.LS5.m.007.Stroma

description: Library name: DSP-1001660011049-D-F05

value: Ovarian Cancer, Tumor

value: LGSC-PT


title: B6M-3N

value: 18 weeks


title: NOD-pancreas-BMS-mouse1rep7


title: NOD-pancreas-BMS-mouse1rep2


title: NRG1-treated MyC-CaP 0hr Biological Replicate 2


title: B6M-6N


title: EL.LS5.m.007.Epithelium

description: Library name: DSP-1001660011049-D-F04


title: B6M-2R


title: NRG1-treated MyC-CaP 0hr Biological Replicate 1


title: EL.LS5.m.006.Epithelium

description: Library name: DSP-1001660011049-D-F02


title: NOD-pancreas-BMS-mouse1rep1


title: B6M-4N


title: B6M-2N


title: B6M-14R


title: ASPN-treated MyC-CaP 24hr Biological Replicate 2

value: ASPN-treated


title: LCMV-spleen-Vehicle-3Day-mouse8rep9

source_name: spleen

value: spleen

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)

tag: sample collection_day_post_inoculation

value: RIP-LCMV-GP

value: 8-week old


title: ASPN-treated MyC-CaP 24hr Biological Replicate 3

value: MyC-CaP

value: Prostate Cancer Epithelial-like Cells


title: ASPN-treated MyC-CaP 24hr Biological Replicate 1


title: LCMV-spleen-Vehicle-3Day-mouse8rep8

value: Male


title: EL.LS5.m.005.Epithelium

description: Library name: DSP-1001660011049-D-E12

value: Epithelium


title: B6M-14N

value: WD High Ile


title: B6M-7R

value: WD Control


title: ASPN-treated MyC-CaP 12hr Biological Replicate 3


title: B6M-11R

value: Liver, Fasted


title: EL.LS5.m.004.Stroma

description: Library name: DSP-1001660011049-D-E11

value: Stroma


title: LCMV-lymphnode-Vehicle-3Day-mouse9rep6

value: lymph node


title: B6M-11N


title: EL.LS5.m.004.Epithelium

description: Library name: DSP-1001660011049-D-E10

value: Ovarian Cancer, Tumor


title: ASPN-treated MyC-CaP 12hr Biological Replicate 2


title: LCMV-lymphnode-Vehicle-3Day-mouse9rep5


title: B6M-10R

value: WD Low Ile


title: EL.LS5.m.003.Stroma

description: Library name: DSP-1001660011049-D-E09

value: LGSC-PT


title: ASPN-treated MyC-CaP 12hr Biological Replicate 1

value: ASPN-treated


title: EL.LS5.m.006.Stroma

description: Library name: DSP-1001660011049-D-F03


title: B6M-10N

value: 18 weeks


title: LCMV-lymphnode-Vehicle-3Day-mouse9rep4

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: LCMV-spleen-Vehicle-3Day-mouse8rep10

value: spleen

value: RIP-LCMV-GP


title: ASPN-treated MyC-CaP 0hr Biological Replicate 2

value: MyC-CaP


title: EL.LS5.m.002.Stroma

description: Library name: DSP-1001660011049-D-E07


title: EL.LS5.m.003.Epithelium

description: Library name: DSP-1001660011049-D-E08


title: EL.LS5.m.005.Stroma

description: Library name: DSP-1001660011049-D-F01


title: ASPN-treated MyC-CaP 0hr Biological Replicate 3

value: Prostate Cancer Epithelial-like Cells


title: LCMV-lymphnode-Vehicle-3Day-mouse9rep2

value: 8-week old

value: Male


title: B6F-8N

value: Female

value: WD High Ile


title: ASPN-treated MyC-CaP 0hr Biological Replicate 1


title: B6F-8R

value: Liver, Fasted


title: EL.LS5.m.002.Epithelium

description: Library name: DSP-1001660011049-D-E06

value: Epithelium


title: LCMV-lymphnode-Vehicle-3Day-mouse9rep1

value: lymph node


title: LCMV-pancreas-Vehicle-3Day-mouse9rep10

value: pancreas


title: EL.LS5.m.001.Stroma

description: Library name: DSP-1001660011049-D-E05

value: Ovarian Cancer, Tumor

value: Stroma


title: colon, CebpbΔ IEC AOM/DSS 5

city: Nanjing

first: li

last: mingyue

address: 163 Xianlin Avenue

institute: Nanjing university

data_processing:
The expression readcount is computed using Stringtie software
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text file includes raw count for each Sample

source_name: colon

extract_protocol:
Total RNA was extracted from the mid-distal colon tissues of AOM/DSS model mice using TRIzol reagent according to the manufacturer’s protocol. To avoid the contamination of genomic DNA, RNA samples were treated with RNase-free DNase.
RNA-seq was performed by CapitalBio Corporation according to Illumina’s protocols.

value: colon

tag: disease state

value: AOM/DSS mouse model

value: Cebpb-knockout


title: B6F-7R

value: 18 weeks

value: WD Low Ile


title: B6F-7N


title: B6F-6R

value: WD Control


title: EL.LS5.m.001.Epithelium

description: Library name: DSP-1001660011049-D-E04

value: LGSC-PT


title: colon, CebpbΔ IEC AOM/DSS 4


title: LCMV-pancreas-Vehicle-3Day-mouse9rep9

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)

value: RIP-LCMV-GP

value: 8-week old


title: colon, CebpbΔ IEC AOM/DSS 3


title: LCMV-pancreas-Vehicle-3Day-mouse9rep8

value: Male


title: EL.LS4.ed.008.Stroma

description: Library name: DSP-1001660011049-D-E03

value: Ovarian Cancer, Omental Metastasis

value: LGSC-Met


title: B6F-6N

value: Liver, Fasted

value: Female


title: colon, CebpbΔ IEC AOM/DSS 2


title: EL.LS4.ed.008.Epithelium

description: Library name: DSP-1001660011049-D-E02

value: Epithelium


title: LCMV-lymphnode-Vehicle-3Day-mouse9rep3

source_name: lymph node

value: lymph node


title: LCMV-pancreas-Vehicle-3Day-mouse9rep7

value: pancreas


title: colon, CebpbΔ IEC AOM/DSS 1

value: colon

value: AOM/DSS mouse model


title: B6F-4R

value: 18 weeks

value: WD High Ile


title: B6F-4N


title: EL.LS4.ed.007.Stroma

description: Library name: DSP-1001660011049-D-E01

value: Stroma


title: LCMV-pancreas-Vehicle-3Day-mouse9rep6


title: EL.LS4.ed.007.Epithelium

description: Library name: DSP-1001660011049-D-D12


title: colon, WT AOM/DSS IEC 4

value: WT


title: LCMV-pancreas-Vehicle-3Day-mouse9rep5

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: EL.LS4.ed.006.Stroma

description: Library name: DSP-1001660011049-D-D11


title: colon, WT AOM/DSS IEC 5


title: B6F-3R

value: WD Low Ile


title: LCMV-pancreas-Vehicle-3Day-mouse9rep4

value: RIP-LCMV-GP

value: 8-week old


title: B6F-3N


title: EL.LS4.ed.006.Epithelium

description: Library name: DSP-1001660011049-D-D10

value: Ovarian Cancer, Omental Metastasis


title: colon, WT AOM/DSS IEC 3


title: colon, WT AOM/DSS IEC 2


title: EL.LS4.ed.005.Stroma

description: Library name: DSP-1001660011049-D-D09

value: LGSC-Met


title: LCMV-pancreas-Vehicle-3Day-mouse9rep3

value: Male


title: B6F-2R

value: Liver, Fasted

value: Female

value: WD Control


title: B6F-2N


title: LCMV-pancreas-Vehicle-3Day-mouse9rep2

value: pancreas


title: LCMV-pancreas-Vehicle-3Day-mouse9rep1


title: B6F-12R


title: colon, WT AOM/DSS IEC 1

value: colon


title: EL.LS4.ed.005.Epithelium

description: Library name: DSP-1001660011049-D-D08

value: Epithelium


title: colon, WT Control IEC 5

value: control


title: LCMV-spleen-Vehicle-3Day-mouse8rep7

value: spleen


title: EL.LS4.ed.004.Epithelium

description: Library name: DSP-1001660011049-D-D06


title: EL.LS4.ed.004.Stroma

description: Library name: DSP-1001660011049-D-D07

value: Stroma


title: colon, WT Control IEC 4

value: WT


title: LCMV-spleen-Vehicle-3Day-mouse8rep6

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: B6F-12N

value: 18 weeks

value: WD High Ile


title: EL.LS4.ed.003.Epithelium

description: Library name: DSP-1001660011049-D-D04


title: EL.LS4.ed.003.Stroma

description: Library name: DSP-1001660011049-D-D05


title: B6F-10R


title: colon, WT Control IEC 2


title: colon, WT Control IEC 3


title: B6F-11R

value: WD Low Ile


title: LCMV-spleen-Vehicle-3Day-mouse8rep4

value: RIP-LCMV-GP

value: 8-week old


title: LCMV-spleen-Vehicle-3Day-mouse8rep5

value: Male


title: EL.LS4.ed.002.Stroma

description: Library name: DSP-1001660011049-D-D03

value: Ovarian Cancer, Omental Metastasis

value: LGSC-Met


title: B6F-10N

value: Liver, Fasted

value: Female

value: WD Control


title: LCMV-spleen-Vehicle-3Day-mouse8rep3


title: EL.LS4.ed.002.Epithelium

description: Library name: DSP-1001660011049-D-D02

value: Epithelium


title: Proser1 KO Hoxb8-FL EM-seq biol rep 2

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

institute: School of Life Sciences, University of Dundee

data_processing:
Raw sequencing reads were trimmed using TrimGalore and mapped against the mouse genome (mm10) using Bismark (https://github.com/FelixKrueger/Bismark) with standard setting allowing for 1000bp insert size (--X 1000)
Bismark deduplicate was used to remove PCR duplicates
Bismark methylation extractor was used with the following parameter setting (--paired-end --no-overlap  --ignore_r2 3 --ignore_3prime_r2 1) to remove methylation call bias due to adaptor ligation and avoid scoring methylation calls twice in case of overlapping paired-end reads.
Methylation calls in a CpG context were merged (combining CpG methylation calls from both strands of a single CG dinucleotide) to produce a comprehensive “Methreport_CpGcomb_mm10” file containing summarised methylation calls for all CG sites in the mouse genome.
Supplementary files format and content: Tab-delimited file containing methylation calls for all CG sites in the mouse genome from Bismark methylation extractor. Files contain the following columns <chr><start><end><total reads><methylated reads>
Library strategy: EM-seq

source_name: Hoxb8-FL cells

growth_protocol: RPMI-1640, 10% ES-qualified foetal bovine serum, 2mM L-Glutamine, 0.1mM β-mercaptoethanol, 100IU/mL pen/strep, 1µM β-estradiol, 5% filtered cell culture supernatant from a Flt3L-producing B16 melanoma cell line

extract_protocol:
gDNA was extracted using the Monarch Genomic DNA Purification Kit (NEB) and sheared to ~400bp using a Bioruptor Pico sonicator (Diagenode).  Libraries were prepared using the NEBNext® Enzymatic Methyl-seq Kit (NEB)
Libraries were prepared using the NEBNext® Enzymatic Methyl-seq Kit (NEB)

tag: cell line

value: Hoxb8-FL cells

value: immortalised haematopoietic progenitors

value: Proser1 knockout

value: EM-seq


title: LCMV-spleen-Vehicle-3Day-mouse8rep2

value: spleen

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: EL.LS4.ed.001.Stroma

description: Library name: DSP-1001660011049-D-D01

tag: cell type

value: Stroma


title: D3_IL25_ADM2

first: Jazib

last: Uddin

address: 413 E 69th Street, BB-709

institute: Weill Cornell Medicine

data_processing:
Total RNAs were  processed to generate a mRNA-seq library640(poly-A enrichment) and libraries were paired-end (NGS) sequenced on Illumina NovaSeq 4000 at Novogene. Sequence reads were mapped onto mouse genome build mm10 usingHISAT2. Gene expression values were calculated with featureCounts.Differential gene expression analysis was performed on the count matrices output from featureCounts with limma with default parameters.
Assembly: mm10
Supplementary files format and content: excel file include counts values for each sample

source_name: large intestine

growth_protocol: ILC2s from large intestine were sorted and incubated in RPMI supplemented with 10% FCS, 10mM Hepes, 1mM sodium pyruvate, 10% FBS, 80μm 2-mercaptoethanol, 2mM glutamine, 100U/ml penicillin, 100μg/ml streptomycin, 100 ng/ml IL-2 and 100 ng/ml IL-7 in 96-well round bottom plates at 37°C and 5% CO2. As indicated, the culture was supplemented with 100 ng/ml IL-25 and/or 0.4 μg/ml ADM2 for 3 hours.

extract_protocol:
RNA were extracted from cells usingPicoPure RNA Isolation Kit (Thermo)
RNA-seq libraries were prepared from the single cell suspensions by Novogene. Libraries were sequenced on an Illumina HiSeq 4000, generating 150 bp paired-end reads.

tag: tissue

value: large intestine

value: WT C57BL/6

value: IL125 and ADM2


title: D2_IL25_ADM2


title: LCMV-spleen-Vehicle-3Day-mouse8rep1

tag: mouse number

value: RIP-LCMV-GP

value: 8-week old

value: Male


title: Tet2 KO Hoxb8-FL EM-seq biol rep 2

value: Tet2 knockout

tag: treatment


title: EL.LS4.ed.001.Epithelium

description: Library name: DSP-1001660011049-D-C12

value: Ovarian Cancer, Omental Metastasis

value: LGSC-Met


title: LCMV-lymphnode-Vehicle-3Day-mouse8rep7

value: lymph node

tag: roi


title: EL.LS4.m.006.Stroma

description: Library name: DSP-1001660011049-D-B01

value: Ovarian Cancer, Tumor

value: LGSC-PT


title: LCMV-lymphnode-Vehicle-3Day-mouse8rep6

tag: strain


title: Tet2 KO Hoxb8-FL EM-seq biol rep 1

value: Hoxb8-FL cells

value: immortalised haematopoietic progenitors


title: B6F-11N

value: Liver, Fasted

value: Female

tag: age

value: 18 weeks

value: WD Low Ile


title: C2_IL25

value: large intestine

value: WT C57BL/6


title: colon, WT Control IEC 1

value: colon

value: control

value: WT


title: EL.LS4.m.006.Epithelium

description: Library name: DSP-1001660011049-D-A12

value: Epithelium


title: wildtype Hoxb8-FL EM-seq biol rep 2

value: wildtype

value: EM-seq


title: EL.LS4.m.005.Stroma

description: Library name: DSP-1001660011049-D-A11

value: Stroma


title: C1_IL25


title: LCMV-lymphnode-Vehicle-3Day-mouse8rep5

value: lymph node

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)

value: RIP-LCMV-GP

value: 8-week old

tag: Sex

value: Male


title: wildtype Hoxb8-FL EM-seq biol rep 1

value: Hoxb8-FL cells

value: immortalised haematopoietic progenitors

tag: genotype


title: B3_ADM2


title: LCMV-lymphnode-Vehicle-3Day-mouse8rep4


title: wildtype Hoxb8-FL ChIP input

data_processing:
Adapter sequences and low-quality nucleotides were trimmed using Trimmomatic
Genome mapping to mm10 was performed using Bowtie2 with (--very-sensitive) preset settings
Mapped reads were de-duplicated using MarkDuplicates
Mapped reads were filtered to remove those from non-chromosomal DNA, mtDNA and the Y chromosome
Peaks were called using MACS2 with paired-end settings (--format BAMPE --mfold 5 50 --bw 300 using 0.05 q-value threshold for Tet2 and Proser1 peaks and a 0.001 threshold for H3K4me1 and H3K27ac. In addition, H3K4me1 peaks were called as broad, with a broad region cutoff of 0.1
Replicate sets of peaks were merged to produce a consensus peak set using Diffbind
Bigwig files were generated from consensus peak sets or Bam files after filtering using BamCoverage from deepTools with removal of mm10 blacklisted genomic regions (--binsize 10 --normalizeUsing RPKM --extendReads --ignoreDuplicates --blackListFileName "mm10-blacklist.v2.bed.gz")
Assembly: mm10
Supplementary files format and content: Chromosome coordinates (mm10) of Proser1 binding sites in mESCs

extract_protocol:
RPMI-1640, 10% ES-qualified foetal bovine serum, 2mM L-Glutamine, 0.1mM β-mercaptoethanol, 100IU/mL pen/strep, 1µM β-estradiol, 5% filtered cell culture supernatant from a Flt3L-producing B16 melanoma cell line
cells were fixed with 1% formaldehyde for 10min. After quenching and cell lysis, the chromatin was sheared using a Bioruptor Pico sonicator (Diagenode)

value: input


title: Proser1 KO Hoxb8-FL EM-seq biol rep 1

value: Proser1 knockout


title: EL.LS4.m.005.Epithelium

description: Library name: DSP-1001660011049-D-A10

value: Ovarian Cancer, Tumor

value: LGSC-PT


title: B2_ADM2

value: large intestine

value: WT C57BL/6


title: EL.LS4.m.004.Stroma

description: Library name: DSP-1001660011049-D-A09


title: LCMV-lymphnode-Vehicle-3Day-mouse8rep3

data_processing:
Fastq files were processed to dcc files using GeoMx NGS pipeline software. Using the dcc files, spatial transcriptomics analysis was conducted in R studio v4.2.1 using the GeomxTools 3.4.0 package
The GeoMx whole mouse transcriptome atlas was used as the probe assay metadata
Sequencing quality was assessed using the default quality control (QC) parameter cut-offs, namely: minimum number of reads (1000); minimum percentage of reads trimmed (80%), stitched (80%), and aligned (80%); sequencing saturation (50%); negative control counts (10); maximum counts observed in no treatment control (NTC) well (1000); minimum number of nuclei estimated (100); and minimum segment area (5000). Any ROI that did not satisfy the above criteria was removed as part of QC filtering.
Following segment QC, probe QC was also performed to remove any outlier either globally or locally before generating gene-level count data.
The limit of quantification was determined per segment using the value recommended in the workflow, and segments with less than 1-5% of genes detected were removed. Furthermore, only genes that were detected in at least 1% of segments were retained.
The data was normalized using the quartile 3 method and log transformed.
For each organ, a linear mixed model without random slope was used to identify differentially expressed genes between vehicle and treatment groups for both the 3- and 7-day timepoints. Genes with linear scale fold change ³ 1.5 and p-value < 0.05 were considered as differentially expressed.
Assembly: GeoMx mouse whole transcriptome assay v1
Supplementary files format and content: .dcc files = Digital count conversion file (dcc file)
Supplementary files format and content: Rawcounts_LCMV.txt = raw counts for LCMV mouse dataset
Supplementary files format and content: q3 normalized counts_LCMV.txt = q3 normalized and log transformed values for LCMV mouse dataset
Supplementary files format and content: Rawcounts_NOD.txt = raw counts for NOD mouse dataset
Supplementary files format and content: q3 normalized counts_NOD.txt = q3 normalized and log transformed values for NOD mouse dataset
Library strategy: Spatial transcriptomics

extract_protocol:
Mouse pancreas sections (5 µm) were fixed, sectioned, and mounted on positively charged slides. The slideswere deparaffinized, heated in antigen retrieval solution (Thermo Fisher Scientific) at 100 °C for 20 min, and treated with 1 µg/mL proteinase K at 37 °C for 15 min. Mouse transcriptomics was visualized using the GeoMx mouse whole transcriptome atlas (NanoString Technologies, GMX-RNA-NGS-MsWTA). An overnightin situhybridization was performed with a mouse WTA probe, and the next day, the slides were washed twice at 37 °C for 25 min with 50% formamide/2X SSC buffer to remove unbound probes. The slides were then washed twice with 2X SSC buffer for 2 minutes at RT and blocked with blocking buffer containing Buffer W (Nanostring) with 1% Fc-Receptor blocker (Milteny) and 5% Normal Donkey Serum (Jackson Laboratories) as described previously (98). The slides were incubated with guinea pig anti-insulin (Dako), 1:200 rabbit anti-CD3 (Abcam), mouse anti-CD68 (Santa Cruz).The slides were washed twice with 2xSSC and incubated with secondary antibodies (1:400 goat-anti-guinea pig Alexa-488; 1:200 goat-anti rabbit Alexa-594 and 1:200 goat-anti mouse Alexa-647) for 30 minutes. Then, the slides were washed four times with 2xSSC for 3 minutes and counter-stainedwith 1:20,000 Syto83 (Invitrogen) for 1 h at room temperature. Stained slides were loaded onto the GeoMx instrument and scanned. After visual inspection using the GeoMx Digital Spatial Profiler (DSP; NanoString Technologies), geometrical ROIs (100 μm diameter) with different histologies were selected for oligonucleotide collection. Photocleaved oligonucleotides from each spatially resolved ROI were sequenced with the Illumina NextSeq500 sequencer (Illumina).
The GeoMx libraries were prepared according to the GeoMx DSP NGS Readout User Manual. Briefly, for each plate, 4 μl of a GeoMx DSP sample was used for amplification. Each GeoMx DSP sample in a well was uniquely indexed with dual indexes. 4 μL of each resulting PCR product, including the NTC negative control, were pooled and purified with AMPure XP beads (Beckman Coulter). The final libraries were qualified and quantified using TapeStation and Qubit, respectively. The libraries were sequenced on an Illumina NextSeq 500 to generate 27 bp paired-end sequence reads.


title: LCMV-lymphnode-Vehicle-3Day-mouse8rep2


title: Proser1 knockout Hoxb8-FL H3K27me3 biol rep 2

value: H3K27me3 antibody (AB_2616029)


title: A3_Veh

value: Vehicle


title: Proser1 knockout Hoxb8-FL H3K27me3 biol rep 1


title: EL.LS4.m.004.Epithelium

description: Library name: DSP-1001660011049-D-A08

value: Epithelium


title: LCMV-lymphnode-Vehicle-3Day-mouse8rep1


title: LCMV-pancreas-Vehicle-3Day-mouse8rep11

source_name: pancreas

value: pancreas


title: C3_IL25


title: EL.LS4.m.003.Stroma

description: Library name: DSP-1001660011049-D-A07

value: Stroma


title: A2_Veh


title: EL.LS4.m.003.Epithelium

description: Library name: DSP-1001660011049-D-A06


title: LCMV-pancreas-Vehicle-3Day-mouse8rep10

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: A1_Veh


title: Proser1 knockout Hoxb8-FL H3K4me1 biol rep 3

value: H3K4me1 antibody (AB_10695148)


title: wildtype Hoxb8-FL H3K27me3 biol rep 1

value: wildtype


title: EL.LS4.m.002.Stroma

description: Library name: DSP-1001660011049-D-A05


title: EL.LS4.m.002.Epithelium

description: Library name: DSP-1001660011049-D-A04


title: LCMV-pancreas-Vehicle-3Day-mouse8rep9

value: RIP-LCMV-GP

value: 8-week old

value: Male


title: Proser1 knockout Hoxb8-FL H3K4me1 biol rep 1

value: Hoxb8-FL cells

value: immortalised haematopoietic progenitors


title: LCMV-pancreas-Vehicle-3Day-mouse8rep8


title: Proser1 knockout Hoxb8-FL H3K4me1 biol rep 2

value: Proser1 knockout


title: MICT1 KO-3, BAT cells

city: Berkeley

first: Danielle

last: Yi

state: CA

address: 220 Morgan Hall

institute: UC Berkeley

data_processing:
Illumina NovaSeq platforms
For analysis, we used Partek Flow software. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Trimmed sequence reads were mapped to GrCM38/m10 using STAR
Read count extraction and normalization were performed using DEseq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene counts for each Sample ...

source_name: brown adipocytes

growth_protocol: Preadipocytes were differentiated to brown adipocytes

extract_protocol:
RNA was harvested using QIAGEN Rneasy Prep Kit
Library construction and sequencing were performed by Novogene

treatment_protocol: standard brown adipocyte differentiation protocol. On Day 6 of differentiation, cell were treated with 10uM of forskolin for 6 hr.

value: brown adipocytes

value: MICT1-CRISPR KO

value: Adipogenic differentiation + 6 hr forskolin treatment


title: MICT1 KO-2, BAT cells


title: EL.LS4.m.001.Stroma

description: Library name: DSP-1001660011049-D-A03

value: Ovarian Cancer, Tumor

value: LGSC-PT


title: EL.LS4.m.001.Epithelium

description: Library name: DSP-1001660011049-D-A02

value: Epithelium


title: B1_ADM2

value: large intestine

value: WT C57BL/6


title: MICT1 KO-1, BAT cells


title: LCMV-pancreas-Vehicle-3Day-mouse8rep7

value: pancreas

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: wildtype Hoxb8-FL H3K27me3 biol rep 2

value: wildtype

value: H3K27me3 antibody (AB_2616029)


title: LCMV-pancreas-Vehicle-3Day-mouse8rep6

value: RIP-LCMV-GP

value: 8-week old


title: MICT1 Control-3, BAT cells

value: WT


title: wildtype Hoxb8-FL H3K4me1 ChIP biol rep 2

value: Hoxb8-FL cells

value: immortalised haematopoietic progenitors

value: H3K4me1 antibody (AB_10695148)


title: wildtype Hoxb8-FL H3K4me1 ChIP biol rep 1


title: EL.LS1.ed.007.Stroma

description: Library name: DSP-1001660005767-C-H05

value: Ovarian Cancer, Omental Metastasis

value: Stroma

value: LGSC-Met


title: LCMV-pancreas-Vehicle-3Day-mouse8rep5

value: Male


title: MICT1 Control-2, BAT cells

value: brown adipocytes

value: Adipogenic differentiation + 6 hr forskolin treatment


title: LCMV-pancreas-Vehicle-3Day-mouse8rep4


title: EL.LS1.ed.007.Epithelium

description: Library name: DSP-1001660005767-C-H04

value: Epithelium


title: MICT1 Control-1, BAT cells


title: EL.LS1.ed.006.Stroma

description: Library name: DSP-1001660005767-C-H03


title: Proser1 knockout Hoxb8-FL H3K27ac ChIP biol rep 2

value: Proser1 knockout

value: H3K27ac antibody (AB_2608307)


title: LCMV-pancreas-Vehicle-3Day-mouse8rep3

value: pancreas

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: Proser1 knockout Hoxb8-FL H3K27ac ChIP biol rep 1


title: EL.LS1.ed.006.Epithelium

description: Library name: DSP-1001660005767-C-H02


title: nonGUT_IDL3

city: Berlin

first: Suphansa

last: Sawamiphak

address: Robert-Rössle-Straße, 10

institute: Max Delbruck Center

description: Library name: sample12

data_processing:
Data were trimmed with Trimmomatic v.0.36
Raw reads were mapped to the genome using Kallisto, version 0.51.1
Assembly: GRCz11 (Danio rerio)
Supplementary files format and content: tab-delimited file (.tsv) containing abundances for each sample

organism: Danio rerio

source_name: non-gut

extract_protocol:
Trizol
SMART-Seq mRNA LP

value: non-gut

value: macrophages

value: IDL

tag: batch


title: nonGUT_IDL2

description: Library name: sample11


title: LCMV-pancreas-Vehicle-3Day-mouse8rep1

value: RIP-LCMV-GP

value: 8-week old


title: wildtype Hoxb8-FL H3K27ac ChIP biol rep 2

value: Hoxb8-FL cells

value: immortalised haematopoietic progenitors

value: wildtype


title: wildtype Hoxb8-FL H3K4me1 ChIP biol rep 3

value: H3K4me1 antibody (AB_10695148)


title: wildtype Hoxb8-FL H3K27ac ChIP biol rep 1


title: EL.LS1.ed.005.Stroma

description: Library name: DSP-1001660005767-C-H01

value: Ovarian Cancer, Omental Metastasis

value: Stroma

value: LGSC-Met


title: LCMV-lymphnode-Vehicle-3Day-mouse7rep5

value: lymph node

value: Male


title: EL.LS1.ed.005.Epithelium

description: Library name: DSP-1001660005767-C-G12

value: Epithelium


title: LCMV-lymphnode-Vehicle-3Day-mouse7rep4


title: nonGUT_CTRL3

description: Library name: sample9

value: CTRL


title: Crskip rep 2

city: Beijing

first: Yan

last: Li

address: Haidian

institute: Capital Normal University

description: Library name: Crskip_2

data_processing:
Reads were mapped to the Chlamydomonas reinhardtii genome using bowtie2. Only the uniquely mapped reads were saved.
Chip peaks were identified using macs3 with -q 0.05, --call-summits, -f BAMPE
Assembly: Chlamydomonas reinhardtii CC-4532 v6.1
Supplementary files format and content: peaks.txt files were the output result from macs3 callpeak progress, containing the location and fold enrichment information of peaks.

organism: Chlamydomonas reinhardtii

source_name: single algal cells

extract_protocol:
Through systematic biochemical analyses, we identified a novel protein-protein interaction between PAF1 and SKIP in Chlamydomonas reinhardtii.  To investigate the functional significance of this interaction, we generated targeted mutants using CRISPR-Cas9 genome editing technology.  Phenotypic characterization revealed that both PAF1 and SKIP mutants exhibit coordinated regulation of the cell cycle progression.  To elucidate the molecular mechanism underlying PAF1-SKIP mediated cell cycle regulation, we employed an integrated multi-omics approach.  RNA sequencing (RNA-seq) analysis was performed to identify differentially expressed genes, while chromatin immunoprecipitation sequencing (ChIP-seq) was utilized to map the genomic loci directly bound by the PAF1-SKIP protein complex.  This comprehensive strategy enabled us to delineate the transcriptional network governed by the PAF1-SKIP regulatory module.
The ChIP product was treated with End Prep Enzyme Mix for end repairing, 5' Phosphorylation and dA-tailing in one reaction, followed by ligation to adaptors with a "T" base overhang. Adaptor ligated DNA was then recovered using Beads. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer.

value: single algal cells

value: skip


title: EL.LS1.ed.004.Stroma

description: Library name: DSP-1001660005767-C-G11


title: LCMV-lymphnode-Vehicle-3Day-mouse7rep2

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: GUT_IDL3

description: Library name: sample6

source_name: gut

value: gut

value: macrophages

value: IDL


title: EL.LS1.ed.003.Stroma

description: Library name: DSP-1001660005767-C-G09


title: EL.LS1.ed.004.Epithelium

description: Library name: DSP-1001660005767-C-G10


title: Crpaf1 rep 2

description: Library name: Crpaf1_2


title: Crskip rep 1

description: Library name: Crskip_1


title: nonGUT_CTRL1

description: Library name: sample7

value: non-gut


title: nonGUT_CTRL2

description: Library name: sample8


title: LCMV-lymphnode-Vehicle-3Day-mouse7rep3

value: RIP-LCMV-GP

value: 8-week old


title: Crpaf1 rep 1

description: Library name: Crpaf1_1


title: EL.LS1.ed.003.Epithelium

description: Library name: DSP-1001660005767-C-G08


title: LCMV-lymphnode-Vehicle-3Day-mouse7rep1


title: GUT_IDL2

description: Library name: sample5


title: EL.LS1.ed.002.Stroma

description: Library name: DSP-1001660005767-C-G07


title: GUT_IDL1

description: Library name: sample4


title: EL.LS1.ed.002.Epithelium

description: Library name: DSP-1001660005767-C-G06


title: LCMV-pancreas-BMS-7Day-mouse12rep12

value: pancreas


title: MP38 cells, 24 hour Romidepsin treatment, sample 2

city: Miami

first: Stefan

last: Kurtenbach

address: 1501 NW 10th Ave

department: Ophthalmology

institute: University of Miami

description:
Library name: MP38 Romidepsin 2
Column Name in MP38_RawReadCounts.txt: Romi2
Column Name in MP38_LogCPM.txt: Romi2
Column Name in MP38_QuantileNormalization.txt: Romi2

data_processing:
uploaded concatonated files to BioJupies for paired-end analysis
Assembly: hg38
Supplementary files format and content: MP38_RawReadCounts.txt: Raw read counts of each concatonated MP38 cell line sample
Supplementary files format and content: MP38_LogCPM.txt: Log counts per million for each MP38 cell line sample
Supplementary files format and content: MP38_QuantileNormalization.txt: Normalized gene expression for each MP38 cell line sample

source_name: uveal

growth_protocol: Cells maintained in D-MEM/F-12 media supplemented with 10% heat-inactivated FBS, 2 mmol/L Glutamax, 1mmol/L Non-Essential Amino Acid (NEAA) cell culture supplement, 0.5x Insulin-Transferin-Selenium (ITS), and 1x Pen-Strep. Growth conditions were 37 C° and 5.0% CO2.

extract_protocol:
Media was aspirated out and RNA was extracted from cells according to the Quick-RNA MiniPrep (Zymo Research, R1054) protocol.
Eukaryotic Strand-specific mRNA library with sequencing read length PE150 and clean fastq phred quality score encoding Phred+33

treatment_protocol: Drugs were obtained from TargetMol (Romidepsin T6006, Quisinostat T6055, Mivebresib T3712) and dissolved in sterile DMSO to yeild 10 mM stock concentration. Stocks were dissolved in cell media to yield above conctentrations. Cells were grown in drug media for 24 hours.

value: uveal

value: uveal melanoma

value: 40 nM Romidepsin


title: LCMV-pancreas-BMS-7Day-mouse12rep13

first: Carmella

last: Evans-Molina

institute: Indiana University School of Medicine


title: GUT_CTRL3

description: Library name: sample3


title: MP38 cells, 24 hour Romidepsin treatment, sample 1

description:
Library name: MP38 Romidepsin 1
Column Name in MP38_RawReadCounts.txt: Romi1
Column Name in MP38_LogCPM.txt: Romi1
Column Name in MP38_QuantileNormalization.txt: Romi1


title: GUT_CTRL2

description: Library name: sample2


title: EL.LS1.ed.001.Stroma

description: Library name: DSP-1001660005767-C-G05

value: Ovarian Cancer, Omental Metastasis

value: Stroma

value: LGSC-Met


title: MP38 cells, 24 hour Mivebresib treatment, sample 2

description:
Library name: MP38 Mivebresib 2
Column Name in MP38_RawReadCounts.txt: Miveb2
Column Name in MP38_LogCPM.txt: Miveb2
Column Name in MP38_QuantileNormalization.txt: Miveb2

value: 1200 nM Mivebresib


title: LCMV-lymphnode-BMS-7Day-mouse12rep4

value: lymph node

value: Male


title: LCMV-pancreas-Vehicle-3Day-mouse8rep2

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: nonGUT_IDL1

description: Library name: sample10


title: LCMV-lymphnode-BMS-7Day-mouse12rep5


title: MP38 cells, 24 hour Mivebresib treatment, sample 1

description:
Library name: MP38 Mivebresib 1
Column Name in MP38_RawReadCounts.txt: Miveb1
Column Name in MP38_LogCPM.txt: Miveb1
Column Name in MP38_QuantileNormalization.txt: Miveb1


title: EL.LS1.ed.001.Epithelium

description: Library name: DSP-1001660005767-C-G04

value: Epithelium


title: MP38 cells, 24 hour Quisinostat treatment, sample 2

description:
Library name: MP38 Quisinostat 2
Column Name in MP38_RawReadCounts.txt: Quis2
Column Name in MP38_LogCPM.txt: Quis2
Column Name in MP38_QuantileNormalization.txt: Quis2

value: 40 nM Quisinostat


title: SH_WT_4

city: Belgrade

first: Mirjana

last: Novkovic

address: Vojvode Stepe 444a

country: Serbia

institute: Institute of Molecular Genetic and Genetic Engineering

description: Library name: sample 16

data_processing:
fastp v0.23.4, STAR v2.7.0, RSEM v1.3.3
Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 (qualified_quality_phred=20, nqualified_percent_limit=30, average_qual=25, low_complexity_filter=True, complexity_threshold=30)
passing filter reads were mapped to the genome reference (Danio rerio GRCz11v110, Ensembl v110 ) using STAR v2.7.10 with standard parameters, except for the sjdbOverhang option set on read length
Genome and transcripts annotation provided as input were downloaded from Ensembl v112 repository. Alignments were then elaborated by RSEM v1.3.3, to estimate transcript and gene abundances. Subsequently, the sample-specific gene-level abundances were merged into a single raw expression matrix applying a dedicated RSEM command (rsem-generate-data-matrix).
Assembly: Danio rerio GRCz11v112, Ensembl v112
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

source_name: heart

growth_protocol: Wild-type (wt) fish AB (Oregon) and ankrd1abns502 (mut) were maintained under standard conditions, in a circulating water system, under 14 h light/10 h dark cycle, at 27.5-28 ◦C.

extract_protocol:
Heart ventricles dissected out from cryoinjured and sham-operated wt and ankrd1a mutant fish were homogenized in TRIzol Reagent (Invitorgen, Thermo Fisher Scientific, USA). Three ventricles were pooled as one sample. Total RNA was extracted using RNA Clean and concentrator kit (ZYMO Research, USA), according to the manufacturer instructions and eluted in 23 µl of RNase-free water and its quantity and purity were measured promptly after isolation, using BioSpec-nano (Shimadzu, Japan) and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM (Thermo Scientific Fisher, USA).
cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit (Illumina, California, USA)

treatment_protocol: Before the procedure, adult zebrafish were anesthetized in system water containing 0.02% tricaine (ethyl 3-aminobenzoate methanesulfonate salt, MS-222, Sigma-Aldrich, SAD). A small incision was made in the chest area to expose the heart, followed by the application of a cryoprobe precooled in liquid nitrogen to the ventricular apex, maintaining contact for 25 sec. Subsequently, cryoinjured fish were transferred into fresh system water and allowed to recover for 7 days. The procedure was repeated for sham-operated fish, using a cryoprobe at room temperature.

value: heart

value: wt

value: sham operated


title: LCMV-spleen-BMS-7Day-mouse13rep8

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

value: spleen

value: RIP-LCMV-GP

value: 8-week old


title: SH_WT_3

description: Library name: sample 15


title: MP38 cells, 24 hour 0.1% DMSO treatment, sample 2

description:
Library name: MP38 Control 2
Column Name in MP38_RawReadCounts.txt: Control2
Column Name in MP38_LogCPM.txt: Control2
Column Name in MP38_QuantileNormalization.txt: Control2

value: uveal

value: uveal melanoma

value: 0.1% DMSO


title: LCMV-spleen-BMS-7Day-mouse12rep6


title: GUT_CTRL1

description: Library name: sample1

value: gut

value: macrophages

value: CTRL


title: EL.LS1.m.011.Stroma

description: Library name: DSP-1001660005767-C-G01

value: Ovarian Cancer, Tumor

value: Stroma

value: LGSC-PT


title: MP38 cells, 24 hour Quisinostat treatment, sample 1

description:
Library name: MP38 Quisinostat 1
Column Name in MP38_RawReadCounts.txt: Quis1
Column Name in MP38_LogCPM.txt: Quis1
Column Name in MP38_QuantileNormalization.txt: Quis1


title: SH_WT_2

description: Library name: sample 14


title: LCMV-spleen-BMS-7Day-mouse13rep7

value: Male


title: EL.LS1.m.011.Epithelium

description: Library name: DSP-1001660005767-C-F12

value: Epithelium


title: EL.LS1.m.012.Stroma

description: Library name: DSP-1001660005767-C-G03


title: MP38 cells, 24 hour 0.1% DMSO treatment, sample 1

description:
Library name: MP38 Control 1
Column Name in MP38_RawReadCounts.txt: Control1
Column Name in MP38_LogCPM.txt: Control1
Column Name in MP38_QuantileNormalization.txt: Control1


title: LCMV-spleen-BMS-7Day-mouse13rep6


title: EL.LS1.m.010.Stroma

description: Library name: DSP-1001660005767-C-F11


title: EL.LS1.m.010.Epithelium

description: Library name: DSP-1001660005767-C-F10


title: LCMV-spleen-BMS-7Day-mouse13rep4


title: DBLab_ChIP_seq_WT_anti_SegB_4

city: York

first: Daniela

last: Barilla`

address: Wentworth Way

department: Biology

institute: University of York

data_processing:
Sequence reads were mapped to the S. solfataricus P2 genome (NCBI Reference Sequence: NC_002754) with Bowtie 1.0.0-5 (Langmead et al 2009 PMID: 19261174) using the following command:   bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NC_002754_bowtie --sam *.fastq > output.sam  Samtools 0.1.19-1 and Bedtools 2.17.0-1 (Li et al 2009 PMID:  19505943, Quinland et al 2010 PMID: 20110278) were used to compute and extract the sequencing coverage using the following command:  samtools faidx NC_002754.fna  samtools import NC_002754.fna.fai *.sam output.bam  samtools sort output.bam output.sorted  samtools index output.sorted.bam  bedtools genomecov -d -ibam output.sorted.bam -g NC_002754.fna > coverage_output.txt
Peak calling - Homer v4.9.1
Genome_build: NC_002754
Supplementary_files_format_and_content: Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Saccharolobus solfataricus P2

source_name: Sulfolobus solfataricus P2

growth_protocol: S. solfataricus P2, PBL2025 and ∆Sso_segB strains were grown at 75 °C in 200 ml Brock media, pH 3.0 and supplemented with 0.1% of tryptone. When the cells reached mid-exponential growth phase (OD600nm 0.4 – 0.6), the cultures were taken from 75 °C and cooled down at room temperature before cross-linking with 1% formaldehyde, shaking at 37 °C for 30 minutes. The cross-linked reactions were stopped by adding 125 mM glycine and incubated at 37 °C, shaking for further 15 minutes.

extract_protocol:
DNA was purified from samples using PCR purification kit (Qiagen) and eluted in 40 µl 0.1 x EB buffer (Qiagen).
To construct ChIP-Seq libraries, NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs). Standard library construction for Illumina Miseq (paired end 75bp reads) or Hiseq3000 (paired end 150 bp reads) sequencing platform

treatment_protocol:
Exponentially-growing cells were crosslinked with 1% formadehyde, washed 3 times with 1x PBS then resuspended in 1 ml of Buffer 1 (20 mM HEPES pH 7.9, 50 mM KCl, 10 % glycerol plus EDTA-free protease inhibitors). Cells were then sonicated to shear the DNA. Sample was incubated  with polyclonal anti-SegB rabbit antibodies. Crosslinked products were reversed and DNA was purified.
Exponentially-growing cells were crosslinked with 1% formadehyde, washed 3 times with 1x PBS then resuspended in 1 ml of Buffer 1 (20 mM HEPES pH 7.9, 50 mM KCl, 10 % glycerol plus EDTA-free protease inhibitors). Cells were then sonicated to shear the DNA. Sample was incubated with polyclonal anti-SegB rabbit antibodies. Crosslinked products were reversed and DNA was purified (Detailed protocols are listed in the Supplementary Materials)

value: No synchronization, mixed population of cells, exponential phase

value: wild-type P2

tag: antibody

value: SegB


title: SH_MUT_3

description: Library name: sample 11

value: heart

value: ankrd1a mutant

value: sham operated


title: SH_MUT_2

description: Library name: sample 10


title: LCMV-spleen-BMS-7Day-mouse13rep3

city: Indianapolis

value: spleen

value: RIP-LCMV-GP

value: 8-week old


title: SH_MUT_4

description: Library name: sample 12


title: DBLab_ChIP_seq_WT_anti_SegB_3

tag: developmental stage


title: EL.LS1.m.009.Epithelium

description: Library name: DSP-1001660005767-C-F08

tag: cohort


title: LCMV-spleen-BMS-7Day-mouse13rep5


title: DBLab_ChIP_seq_WT_anti_SegB_1


title: EL.LS1.m.012.Epithelium

description: Library name: DSP-1001660005767-C-G02


title: EL.LS1.m.008.Stroma

description: Library name: DSP-1001660005767-C-F07


title: SH_MUT_1

description: Library name: sample 9


title: EL.LS1.m.007.Epithelium

description: Library name: DSP-1001660005767-C-F05


title: Ethanol extracts of JGT (20 ug/mL dose)_rep3

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

description: Library name: JGE03_L_rep3

data_processing:
Read count and transcripts per million (TPM) were calculated as gene expression abundance using the RSEM software (v1.3.3) and gene annotation mm10 Gene Transfer Format (GTF) file from UCSC browser
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Muscle

growth_protocol: C2C12 murine myoblasts (ATCC CRL-1772) were purchased from the ATCC (Manassas, VA, USA). Myoblasts were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, CARLSBAD, CA, USA) containing 10% fetal bovine serum (FBS; Gibco Grand Island, NY, USA) and 1% penicillin/streptomycin (Invitrogen) at 37°C in an atmosphere of 5% CO2. For differentiation to C2C12 myotubes, myoblasts were cultured in DMEM containing 2% horse serum (HS; Gibco) for 5 days. We used differentiated C2C12 myotubes.

extract_protocol:
One mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI Tech, China) according to manufacturer’s instruction.
Library was quantified by QauntiFluor ssDNA System (Promega, WI, USA).

treatment_protocol: Freeze-dried JG-E powder was obtained from KOC Biotech Co. (Daejeon, Republic of Korea). JGT-E powder was dissolved in 2% DMSO and then sterilized through a 0.22 µm membrane. C2C12 myotubes were treated vehicle or indicated concentrations of JGT-E for 24 h in triplicate.

value: Muscle

value: Myotube

value: JGT-E, 20 ug/ml, 24 h


title: LCMV-spleen-BMS-7Day-mouse13rep2


title: LCMV-pancreas-BMS-7Day-mouse13rep3

value: pancreas


title: Ethanol extracts of JGT (100 ug/mL dose)_rep3

description: Library name: JGE03_M_rep3

value: JGT-E, 100 ug/ml, 24 h


title: SH_WT_1

description: Library name: sample 13

value: wt


title: DBLab_ChIP_seq_WT_anti_SegB_2


title: IN_WT_3

description: Library name: sample 7

value: cryioinjured


title: Ethanol extracts of JGT (500 ug/mL dose)_rep3

description: Library name: JGE03_H_rep3

value: JGT-E, 500 ug/ml, 24 h


title: IN_WT_2

description: Library name: sample 6


title: EL.LS1.m.006.Stroma

description: Library name: DSP-1001660005767-C-F04

source_name: Stroma

value: Ovarian Cancer, Tumor

value: Stroma

value: LGSC-PT


title: IN_WT_1

description: Library name: sample 5

value: heart


title: LCMV-pancreas-BMS-7Day-mouse13rep1

value: Male


title: LCMV-lymphnode-BMS-7Day-mouse12rep3

value: lymph node


title: EL.LS1.m.004.Stroma

description: Library name: DSP-1001660005767-C-E12


title: Ethanol extracts of JGT (500 ug/mL dose)_rep2

description: Library name: JGE03_H_rep2


title: LCMV-lymphnode-BMS-7Day-mouse12rep2


title: IN_MUT_3

description: Library name: sample 3

value: ankrd1a mutant


title: Ethanol extracts of JGT (20 ug/mL dose)_rep1

description: Library name: JGE03_L_rep1


title: IN_WT_4

description: Library name: sample 8


title: EL.LS1.m.003.Stroma

description: Library name: DSP-1001660005767-C-E10


title: LCMV-spleen-BMS-7Day-mouse13rep1

value: spleen

value: RIP-LCMV-GP


title: IN_MUT_2

description: Library name: sample 2


title: LCMV-spleen-BMS-7Day-mouse12rep5

value: 8-week old


title: EL.LS1.m.003.Epithelium

description: Library name: DSP-1001660005767-C-E09

source_name: Epithelium

value: Epithelium


title: IN_MUT_1

description: Library name: sample 1


title: EL.LS1.m.006.Epithelium

description: Library name: DSP-1001660005767-C-F03


title: Ethanol extracts of JGT (500 ug/mL dose)_rep1

description: Library name: JGE03_H_rep1

value: Muscle

value: Myotube


title: LCMV-spleen-BMS-7Day-mouse12rep4


title: Vehicle_rep3

description: Library name: Veh_rep3