title: eCLIP IP-1

data_processing:
Fastq files of technical replicates were concatenated when applicable.
Fastq files were preprocessed with cutadapt (v3.4).
RNA-seq data were analyzed using piPipes rna pipeline (v1.1.0).
Small-RNA data were analyzed using piPipes small pipeline (v1.1.0).
R-loop data were analysed following the BisMapR methods (Wulfridge & Sarma, 2021,  eLife 10:e65146).
eCLIP-seq data were analyzed using htseq-clip and DEWSeq workflow (Schwarzl & Sahadevan et al., 2024 NAR)
Assembly: mm10/Gencode M25
Supplementary files format and content: tab-delimited text files of eXpress estimated number of fragments for each RNA-seq sample
Supplementary files format and content: cluster abundance normalized by uniquexmirna per small RNA-seq sample
Supplementary files format and content: normalized bigwig files for forward and reverse strand per R-loop sample.
Supplementary files format and content: htseq-clip counts based on Gencode M25 annotation.
Library strategy: eCLIP-seq

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2.0 ug of total RNA was used for the construction of sequencing libraries.
RNA and BisMapR libraries were prepared using NEB protocols. Small RNA libraries were prepared using the QIAseq miRNA Library Kit for small RNA-seq. eCLIP-seq libraries were prepared using the Yeo group's protocol (Nostrand et al., 2016 Nat Methods)

value: Testis

value: male germ cell

value: KI

value: UV cross-linking

tag: experiment type

value: D1PAS-bound RNA


title: MITF-Sl-IgG

status: Public on Nov 06 2024

type: SRA

city: Reykjavik

first: Hong Nhung

last: Vu

address: Sturlugata 8

country: Iceland

institute: University of Iceland

library_source: genomic

data_processing:
Bowtie2 version 2.1.0 (Langmead and Salzberg, 2012) was utilized for read mapping against the hg38 genome assembly, employing settings such as --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 700 -p 10.
For peak calling from the BAM file, MACS version 2.1 (Zhang et al., 2008) was applied with the narrowPeak configuration and a p-value cutoff of 1e-5.
Peaks were annotated to genes using the R package ChIPseeker (Yu et al., 2015).
Differential binding analysis between the two groups was carried out using the Diffbind R package (Stark and Brown, 2011).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for the IgG control)

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: The cells were maintained in RPMI 1640 medium (Gibco, #5240025) supplemented with 10% FBS (Gibco #10270–106) at 5% CO2 and 37°C in a humidified incubator

extract_protocol:
5.105 cells were then harvested using scrapers, centrifuged at 600 g for 5 minutes, and washed twice with washing buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, and 1X protease inhibitor cocktail). Afterward, cells were immobilized on pre-activated Concanavalin A-coated magnetic beads (EpiCypher #Cat 21-1401) at 4°C for 10 minutes. Incubation with anti-Flag (Sigma, #F3165) or Rabbit IgG (Cell Signaling, #3900S) in antibody buffer (washing buffer supplemented with 2 mM EDTA and 0.025% digitonin) followed, held overnight at 4°C with rotation. The following day, cells were washed with a washing buffer containing 0.025% digitonin. Subsequently, pAG-MNase enzyme (500 μg/mL) was introduced, and CaCl2 at 2mM final concentration was added to activate the enzyme at 0°C for 30 minutes. The reaction was terminated using 2X Stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% Digitonin, 100 μg/mL RNAse A, 50 μg/mL Glycogen, and 500 pg/mL E. coli spike-in control). The Protein-DNA complex was released by undergoing incubation with the Proteinase K (1 μL/mL, Thermo Fisher Scientific, #EO0491) for 1 hour at 50°C. DNA fragment purification utilized the Genomic DNA Clean & Concentrator kit (ZymoResearch, #D465). CUT&RUN experiments were conducted in triplicate.
Illumina’s NEBNext Ultra II library preparation reagents (E7645L)
Cut and Run

treatment_protocol: A375P cells were induced to express FLAG-tagged MITF mutant fusion proteins (MITF-WT and MITF-sl) for 48 hours

tag: cell line

tag: cell type

value: Human melanoma cell line

tag: chip antibody

value: IgG (Cell Signaling, #3900S)


title: eCLIP IP-2

city: Bethesda

first: Heejin

last: Choi

state: Maryland

address: 50 South drive, Building 50, Room 3131

department: NIDDK

country: USA

institute: NIH

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Testis

treatment_protocol: To enrich the piRNA population for the small RNA-seq, b-oxidization was subjected to a total of 20 ug of RNA.

tag: tissue

tag: genotype

tag: treatment


title: Group C, O2-05, 0-6psi, 1 day, D4, S09

city: Minneapolis

first: Philippa

middle: R

last: Kennedy

state: Minnesota

address: 425 East River Parkway, Rm 660A

department: Medicine

institute: University of Minnesota

data_processing:
The overall quality of sequencing reads was evaluated using FastQC (v.0.11.9).
Sequence alignments to the reference human genome (GRCh38) were performed using HISAT2 (v2.0.4).
Read count was generated using featureCounts, differential expression analysis between normoxia and different O2 groups were performed using DESeq2, genes were considered significantly differentially expressed when the absolute log2 fold change > 1 and padj < 0.05.
Gene Ontology and KEGG pathway enrichment analysis were done using the g:Profiler – a web server for functional enrichment analysis (https://biit.cs.ut.ee/gprofiler/).
Assembly: hg19
Supplementary files format and content: comma separated text file contains raw counts for each Sample

source_name: blood

growth_protocol: Healthy donor blood was processed to obtain peripheral blood mononuclear cells using density gradient Ficoll-Paque (GE Healthcare, Cat. No. GE17-5442-03). PBMCs were processed fresh using EasySep Human NK Cell Enrichment Kit (STEMCELL Technologies, Cat. No:19055). NK cells were cultured in RPMI (Gibco Cat. No. 2240-089) + 10% fetal bovine serum (Gibco Cat. No. 26140079) + 100 U/mL Penicillin and Streptomycin (Gibco Cat. No. 15140122) supplemented with 1 ng/mL IL-15 (R&D Systems). 300,000 NK cells/well were placed in 96-well U-bottom plates and media was replaced on day 4 of culture when harvesting on day 7.

extract_protocol:
Total RNA was extracted by RNeasy Plus mini kit (Qiagen, Valencia, CA, USA), RNA quality was evaluated by analysis of the RNA integrity number determined using a 2100 bioanalyzer (Agilent RNA 6000 Nano Kit, Agilent Technologies, Santa Clara, CA, USA).
0.5μg total RNA was used for library prep with TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. Validation of the library preparations was performed on an Agilent Bioanalyzer using the high sensitivity DNA kit (5067-4626, Agilent Technologies).

treatment_protocol:
NK cells were lysed after 1, 3 or 7 days in culture
NK cells were cultured in a standard humidified incubator (20% O2, 5% CO2, 37℃, atmospheric pressure) or AVATAR System (Xcell Biosciences) incubator imitating blood (12% O2, 5% CO2, 37℃, + 2 pounds per square inch ‘psi’), bone marrow (5% O2, 5% CO2, 37℃, + 0.6 psi), low pressure tumor (1% O2, 5% CO2, 37℃, + 0.3 psi) or high pressure tumor (1% O2, 5% CO2, 37℃, + 2 psi).

value: blood

value: NK cells

tag: oxygen

tag: pressure

tag: time

value: 1 day


title: MITF-WT-IgG


title: MITF-WT-Flag

value: Flag (Sigma, #F3165)


title: Group A, O2-20, 0psi, 1 day, D3, S03


title: eCLIP SMInput-3


title: Group A, O2-20, 0psi, 1 day, D1, S01


title: Group A, O2-20, 0psi, 1 day, D2, S02


title: SME1

city: Shanghai

first: Yuanjie

last: Tang

state: Shanghai

address: 300 Fenglin Road, Xuhui District

department: CAS Center for Excellence in Molecular Plant Sciences

country: China

institute: CHINESE ACADEMY OF SCIENCES

data_processing:
Adapter sequences and low-quality reads were filtered out using Trimmomatic v0.32. The filtered reads were then mapped to the CHA0 genome (ASM39720v1) using STAR 2.7.9a. Differentially expressed genes (DEGs) were analyzed using the R package DESeq2 v.1.38.0.
Assembly: ASM39720v1
Supplementary files format and content: comma-delimited text file includes rawcounts for each samples

organism: Pseudomonas protegens

source_name: CHA0 treated with sgn3 myb36 root exudates for 1h replicate 1

extract_protocol:
Total bacterial RNA was extracted using RNeasy Mini Kit (Qiagen).
The RNA (10 µg) was treated with DNase I (Takara) to remove any residual DNA, followed by purification with the RNeasy MinElute Cleanup Kit (Qiagen). Ribosomal RNA (rRNA) was depleted using the Ribo-off rRNA Depletion Kit (Vazyme), which involved hybridizing the RNA with plant-specific rRNA probes and probe buffer. The RNA was then incubated with RNase H Buffer and RNase H at 37°C for 30 minutes. The ribosome-depleted RNA was purified using VAHTS RNA Clean Beads (Vazyme). The RNA library was prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

tag: strain

value: sgn3 myb36 root exudates for 1h


title: SME2

source_name: CHA0 treated with sgn3 myb36 root exudates for 1h replicate 2


title: SAMPLE3-Xp-tdT-RNA

city: San Francisco

first: Dena

last: Dubal

state: California

address: 675 Nelson Rising Lane, Rm 292

department: Department of Neurology

institute: University of California San Francisco

data_processing:
The quality of the reads was obtainedd using FastQC
Trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts from exons were calculated usig featureCounts from the Subread package v.1.5.2.
Downstream differential expression analysis was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-delimited excel files include normalised mean gene counts for each Sample

source_name: Brain

extract_protocol:
Cells were stored in TRIzol and extracted using a Qiagen Rneasy micro kit
Library was prepared using the SMART-Seq v4 Ultra Low input RNA kit following the manufacturer's protocol

value: Brain

value: Neurons

value: paternal X (Xp) cells


title: Gln3

source_name: CHA0 treated with Gln for 1h replicate 3

value: Gln for 1h


title: MITF-SL-Flag


title: eCLIP SMInput-2


title: RNAseq_Fg_KO_rep3

first: Shuting

last: Sun

address: yueyang road 320

institute: Shanghai Institute of Nutrition and Health,CAS

data_processing:
Reads were mapped to Fusarium graminearum PH-1 reference genome using HISAT2 v2.1.0 , with default parameters.
FPKM values were calculated using StringTie v1.3.5 (Pertea et al., 2015) based on Refgene annotation from NCBI.
Read counts were generated using HTSeq-count v0.6.1.
Differentially expressed genes (DEGs) were calculated using the R package DESeq2 v1.26.0 .
Assembly: Fusarium graminearum PH-1
Supplementary files format and content: txt format with FPKM

organism: Fusarium graminearum PH-1

source_name: mycelia (hyphae)

growth_protocol: The equal conida of Fusarium graminearum PH-1 (NRRL 31084) wild-type and FGSG_11799 knockout mutant were inoculated in TBI liquid medium and incubated for 3 days at 25°C with shaking at 180 rpm.

extract_protocol:
The RNA samples were extracted with RNAiso Plus (TaKaRa, Code No. 9108)
The libraries were prepared using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme, NRM603-01)

value: mycelia (hyphae)

value: FGSG_11799 knock-out


title: Gln2

source_name: CHA0 treated with Gln for 1h replicate 2


title: SAMPLE5-Xm-GFP-RNA

value: materal X (Xm)


title: SAMPLE2-Xp-tdT-RNA


title: eCLIP IP-3

value: Testis

value: male germ cell

value: KI


title: OA2

city: guangzhou

first: dianbo

last: long

state: guangdong

address: Zhongshan second road

institute: First Affiliated Hospital of Sun Yat-sen University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: count counting

source_name: Knee joint

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocolsRetinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Knee joint

value: chondrocyte

value: damage cartilage


title: Gln1

source_name: CHA0 treated with Gln for 1h replicate 1


title: eCLIP SMInput-1

value: UV cross-linked

value: D1PAS-bound RNA


title: WE3

source_name: CHA0 treated with WT(Col-0) root exudates for 1h replicate 3

value: WT(Col-0) root exudates for 1h


title: RNAseq_Fg_WT_rep3

value: wild-type


title: OA3


title: SAMPLE3-Xm-GFP-RNA

value: Brain


title: WE2

source_name: CHA0 treated with WT(Col-0) root exudates for 1h replicate 2


title: NA2

value: undamage cartilage


title: RNAseq_Fg_KO_rep2


title: SAMPLE4-Xm-GFP-RNA

value: Neurons


title: NA3


title: SAMPLE2-Xm-GFP-RNA


title: OA1


title: SAMPLE1-Xm-GFP-RNA


title: RNAseq_Fg_WT_rep2


title: WE1

source_name: CHA0 treated with WT(Col-0) root exudates for 1h replicate 1


title: SAMPLE1-Xp-tdT-RNA

value: paternal X (Xp) cells


title: RNAseq_Fg_WT_rep1

value: mycelia (hyphae)


title: NA1


title: P14, ICD-humanized mouse PD1 (GEX)

status: Public on Nov 05 2024

city: La Jolla

first: Takeya

last: Masubuchi

state: CA

address: 9500 Gilman Dr.

institute: University of California San Diego

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger Pipeline v7.1.0 on 10x cloud with the default settings
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: polyA RNA

source_name: B16.gp33 melanoma

extract_protocol:
Tumors were harvested from mice, minced with razors and digested with 1 mg/mL collagenase type I and 1 mg/mL soybean trypsin inhibitor in 1x HBSS at 37 ºC for 1 h, filtered through 70-μm cell strainer (BD), and resuspended in 1x PBS to prepare single-cell suspensions. The tumor single-cell suspension samples were subjected to percoll gradient centrifugation at 800 g for 10 min, after which CD8+ T cells were isolated using a CD8 beads selection kit (Biolegend).　Intratumoral CD8+ T cells were stained with Zombie Aqua Fixable Viability Dye (Biolegend) in 1x PBS on ice for 15 min, and subsequently with BV785 anti-moCD8, PE anti-Thy1.1 and FITC anti-TCRVα2 (P14 TCR) in 1x PBS containing 2% FBS on ice for 30 min. Live, CD8+, Thy1.1+, and TCRVα2+ cells were sorted on FACSAria into different tubes containing RPMI-1640 with 5% FBS.
The sorted cell samples were distributed into two groups; cell samples isolated from mice that received moPD1-expressing P14 cells, or cell samples isolated from mice that received moPD1huICD-expressing P14 cells. Each cell sample in the same group was hash-tagged with a unique TotalSeq anti-mouse MHC-I antibody (Biolegend) on ice for 30 min, washed with 1x PBS containing 2% FBS. After the hash-tagging, the cell samples in the same group were pooled into one tube and diluted in 1x PBS containing 2% FBS. Both the gene expression (GEX) library and the hash-tag library of each group were prepared using a Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) with Feature Barcode Technology for Cell Surface Protein (10x Genomics) following manufacturer’s instructions. The prepared libraries were quantified and quality checked using TapeStation (Agilent).

value: B16.gp33 melanoma

value: P14 CD8 T cell

tag: library type

value: gene expression


title: P14, mouse PD1 {Feature_Barcode)

description: 10x Genomics

library_source: other

molecule: protein

value: hash-tag


title: P14, ICD-humanized mouse PD1 (Feature_Barcode)

description: 10x Genomics


title: P14, mouse PD1 (GEX)

description: 10x Genomics


title: RNAseq_Fg_KO_rep1

value: FGSG_11799 knock-out


title: HAFTL

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

description:
Illumina HiScanSQ
Noguera-Castells_Average_Beta_Mus_Musculus.csv

hyb_protocol: Illumina HIIScanSQ with Autoloader system

data_processing:
Data was processed using sesame package pipeline in R environment
hg19 and mm10
.csv format containing Average Beta value and detection P.value

label: Cy3 and Cy5

source_name: HAFTL

label_protocol: Ilumina methylation microarrays

extract_protocol: Genomic DNA was extracted and purified from the different cell lines using Qiagen DNeasy Kit according to standard instructions

value: Hematologic cell line


title: TIB-224

scan_protocol: Illumina HIIScanSQ with Autoloader system


title: CRL-1841


title: CRL-2396


title: CRL-2113


title: TIB-181


title: TIB-71


title: RAW 1

source_name: RAW 1


title: CCL-46


title: L_Cyb5b_shCyb5a_Refed

city: wuhan

first: meiyan

last: ma

institute: wuhan university

data_processing:
BGI Dr.Tom
Assembly: mus_musculus

source_name: liver

extract_protocol:
Total RNA was isolated from liver by TRIzol
RNA-Seq uses high-throughput sequencing to study eukaryotic gene expression patterns, providing accurate digital profiles by sequencing and comparing transcripts. Transcriptome research forms the basis of gene function and structure studies, obtaining comprehensive transcripts of specific tissues or organs.

value: liver

value: Refed


title: TIB-47


title: CRL-9518


title: TIB-68


title: FDC-P1


title: WT_shNC_Refed

value: WT


title: TIB-18


title: TIB-23


title: L_Cyb5b_shCyb5a_Fasted

value: Fasted


title: WT_shNC_Fasted


title: CRL-1597


title: CCL-130


title: CRL-1722


title: TIB-39


title: TIB-48


title: TIB-192


title: CCL-167


title: CRL-1669


title: CRL-1646


title: TIB-197


title: CCL-219


title: TIB-203


title: CRL-1704


title: TIB-158


title: CRL-1702


title: BT67 cells,siNC_2,Day3

city: Jinan

first: Tao

last: Xin

state: Shandong

address: 16766 Jingshi Road

department: Department of Neurosurgery

institute: The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
Clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster.
After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
Reads were then mapped to the human reference genome from UCSC Genome Browser. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Assembly: hg38
Supplementary files format and content: Text file includes raw counts for each Sample
Supplementary files format and content: Text files include RPKM values for each Sample

extract_protocol:
Total RNA from cells was extracted by an RNA isolation kit (Vazyme, China,Cat:RC112-01) according to the manufacturer’s protocol.Qualified RNAs were quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).2 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: glioma stem cells


title: BT67 cells,siPTBP1_3,Day3

value: PTBP1 knockdown


title: BT67 cells,siNC_3,Day3


title: BT67 cells,siNC_1,Day3


title: Stage4_Barley_R1_Fg

city: East Lansing

first: Frances

last: Trail

state: Michigan

address: 612 Wilson Road

department: Plant Biology

institute: Michigan State University

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0. The low-quality reads were removed using the read filtering tool, Trimmomatic, Version 0.39. The 3’ ends of NovaSeq6000 single-end 100 bp reads were trimmed to 50 bp reads (keeping the first 50 bp) using Trimmomatic Version 0.39.
The trimmed reads were mapped to the indexed F. graminearum  reference sequences using HISAT 2.2.1.
The HISAT alignments in SAM format were then sorted and converted to BAM format using SAM tools.
Count files were then generated using HTSeq Version 0.11.1.
The DESeq2 package Version 1.30.1 in R was used to normalize the read counts and to perform differential expression analysis.
Assembly: The reference sequence used for the alignment are Fusarium graminearum PH-1 (GCA_900044135.1).
Supplementary files format and content: Tab-demilited text file includes raw counts for each sample

organism: Fusarium graminearum

source_name: Germinated conidia

growth_protocol: For total RNA extraction of each germination stage on standard medium (potato dextrose agar), a 200 µL aliquot of the conidial suspension (1 x 106 conidia/mL) of each species was inoculated onto a sterile cellophane sheet overlaid on PDA in a Petri dish (60 x 15 mm). Petri dishes containing inoculated sheets were then incubated at RT in continuous light till the conidia reached respective germination stages. Barley leaf sheaths were used to study the germination stages of Fusarium graminearum on the host.

extract_protocol:
Total RNA of F. graminearum  from cellophane membranes and infected host tissue was isolated using Trizol reagent. RNA was treated with RNase-Free DNase (Qiagen), purified further using RNA Clean and ConcentratorTM - 5 (ZymoResearch)
Libraries were prepared using the Illumina Stranded mRNA Prep - Ligation kit with IDT for Illumina RNA UD Indexes.

value: Germinated conidia

value: 42 hours on barley leaf sheath


title: Stage4_Barley_R3_Fg


title: Stage3_Barley_R1_Fg

value: 8 hours on barley leaf sheath


title: Stage3_Barley_R3_Fg


title: BT67 cells,siPTBP1_2,Day3


title: Stage2_Barley_R2_Fg

value: 4 hours on barley leaf sheath


title: Stage2_Barley_R1_Fg


title: Stage2_Barley_R3_Fg


title: Stage1_Barley_R3_Fg

source_name: Conidia

value: Conidia

value: 30 minutes on barley leaf sheath


title: Stage3_Barley_R2_Fg


title: Stage1_Barley_R2_Fg


title: Stage4_Barley_R2_Fg


title: CKO

city: Wuhan

first: 鹏

last: 王

email: wangp00678@163.com, wangp94@whu.edu.cn

state: 湖北省

address: 169 Donghu nan road,Wucang District

institute: 武汉大学

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline (v6.1.2) provided by 10×Genomics was applied to align reads and generate the gene-cell unique molecular identifier (UMI) matrix, using the reference genome mm10 (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A).
For each cell, we quantified the numbers of genes and UMIs and kept high-quality cells with the detection threshold of 600-4000 genes and 1000-25000 UMIs.
We used a relatively high threshold to ensure that we have filtered out the most of barcodes associated with empty partitions or doublet cells.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

growth_protocol: Immune cells were sorted from lung tumors of KL and KLG4m/m mice that were intranasally injected with Ad-Cre (2x106 pfu per mouse) and tamoxifen treatment.

extract_protocol:
the CD45pos population was isolated as described above. Single-cell RNA-seq libraries were generated using Chromium Single cell 3’ Library & Gel Bead Kit v3.0 Kits (10×Genomics) according to the manufacturer’s protocol. Briefly, about 105 single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. About 15000-25000 cells were added to each channel to generate single-cell gel-beads in emulsion (GEMs) for a targeted cell recovery estimate of 10000 single cells (10674 and 7821 for KL and KLG4m/m mice, respectively)
After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). The cDNAs were then amplified by PCR with 12 cycles. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor ligated and library amplification via PCR (8 cycles). The purified libraries were sequenced on the Illumina NovaSeq 6000 with 28 cycles of read1, 8 cycles of i7 index, and 91 cycles of read2. And finally, 150 bp paired-end reads were generated.

value: lung

value: Immune cells

value: 10 weeks after intranasal injection of Ad-Cre


title: WT

value: 10 weeks after intranasal injection of Ad-Cre and tamoxifen treatment


title: Stage1_Barley_R1_Fg


title: BT67 cells,siPTBP1_1,Day3


title: Colon Tumour KPN Rep8

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

description: 10X Genomics

data_processing:
Sequence alignment of single-cell data to the mm10 genome was performed using the count tool from the Cell Ranger package version 6.1.2 according to the developer’s instructions, generating barcodes, features and matrix output files for each sample. Subsequent analysis was done using R version 4.1.1 using Seurat version 4.0.4.
Assembly: mm10
Supplementary files format and content: h5 matrix files

source_name: Colon

growth_protocol: Genetic alterations were induced by Tamoxifen, delivered intraperitoneally to produce tumours from ageing mice and intracolonically in mice with 'intracolonic induction tumours'. Organoids from intestinal tumours of the specified genotypes were injected into wild type mice to generate intracolonic transplant tumours. Tumours were collected at clinical end point.

extract_protocol:
Segments of colon from mice with the noted genetic mutations were homogenised and digested using a Mcllwain Tissue Chopper and the GentleMACS Octo Dissociator (Miltenyi Biotec, 130-096-427) in combination with the mouse tumour dissociation kit (Miltenyi Biotec, 130-096-730). Cells were then sorted using a FACSAria sorter (BD Biosciences) and DAPI (Invitrogen, D1306) to remove dead cells.
Libraries were prepared using reagents from the 10x Chromium Single-Cell 3′ v3 Gel Bead Kit and Library (10x Genomics) according to the manufacturer’s protocol, then analysed using the Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).

value: Colon

tag: Sex

value: Male

tag: sample type

value: Intracolonic Transplant Tumour

value: VilCreER KRasG12D/+ P53fl/fl Notch1Tg


title: Colon Tumour KPN Rep9

description: 10X Genomics


title: Colon Tumour KPN Rep5

description: 10X Genomics

value: Female


title: Colon Tumour KPN Rep6

description: 10X Genomics


title: Colon Tumour KPN Rep7

description: 10X Genomics


title: Colon Tumour KPN Rep2

description: 10X Genomics


title: Colon Tumour KPN Rep1

description: 10X Genomics


title: Colon Tumour KPN Rep4

description: 10X Genomics


title: Colon Tumour BA Rep2

description: 10X Genomics

value: Ageing Tumour

value: VilCreER BrafV600E/+ Alk5fl/fl


title: Colon Tumour BA Rep1

description: 10X Genomics


title: Colon Tumour AKPT Rep9

description: 10X Genomics

value: VilCreER Apcfl/fl KRasG12D/+ P53fl/fl Tgfbr1fl/fl


title: Colon Tumour AKPT Rep8

description: 10X Genomics


title: Colon Tumour AKPT Rep7

description: 10X Genomics


title: Colon Tumour AKPT Rep6

description: 10X Genomics


title: Colon Tumour AKPT Rep3

description: 10X Genomics


title: Colon Tumour AKPT Rep2

description: 10X Genomics


title: Colon Tumour AKPT Rep4

description: 10X Genomics


title: Colon Tumour AKPT Rep1

description: 10X Genomics


title: Colon Tumour AK Rep2

description: 10X Genomics

value: Intracolonic Induction Tumour

value: VilCreER Apcfl/fl KRasG12D/+


title: Colon Tumour AK Rep1

description: 10X Genomics


title: Colon Tumour Apc Rep4

description: 10X Genomics

value: VilCreER Apcfl/fl


title: Colon Tumour AKPT Rep5

description: 10X Genomics


title: Colon Tumour AK Rep3

description: 10X Genomics


title: Colon Tumour Apc Rep3

description: 10X Genomics


title: Colon Tumour Apc Rep1

description: 10X Genomics


title: Colon Tumour Apc Rep2

description: 10X Genomics


title: Colon Tumour BA Rep3

description: 10X Genomics


title: Colon Tumour KPN Rep3

description: 10X Genomics


title: tumor, obese Trem2-/-, replicate 4, scRNAseq VDJ

city: Nashville

first: Matthew

middle: A

last: Cottam

state: TN

address: 2301 Vanderbilt Place

department: Surgical Sciences

institute: Vanderbilt University Medical Center

description: Sample 44_VDJ

data_processing:
Raw sequencing data was processed using CellRanger v7.2.0.
Scanpy v1.9.1 was used for count normalization, integration, clustering, and annotation.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (mRNA): barcodes.tsv.gz, features.tsv.gz, matrix.mtx
Supplementary files format and content: Cell Ranger output files (VDJ):  all_contig_annotations.csv
Supplementary files format and content: Seurat object in R .rds format

source_name: tumor

growth_protocol: All mice were ovariectomized at 6 weeks of age and recovered on chow diet for two weeks. Lean, obese and weight loss groups were generated utilizing modulation of low fat (LFD) and high fat diet (HFD). Lean mice were maintained on LFD the entirety of the study. Obese mice were fed LFD for 12 weeks then switched to HFD for 12 weeks. Weight loss mice were fed HFD for 12 weeks then LFD for 12 weeks. After 20 weeks on diet, mice were injected in the fourth left mammary fat pad with 300,000 GFP-expressing, PD-L1 over-expressing E0771 cells. Tumors were allowed to grow for 4 weeks and all mice with the same tumor cell implantation date were taken down on the same day.

extract_protocol:
Live CD45+ cells were isolated from the tumor-adjacent mammary adipose tissue by first isolating the stromal vascular fraction using fractionation followed by staining for DAPI and CD45 BV510. DAPI negative CD45+ cells were isolated using FACS sorting. Live CD45+ cells were isolated from the tumor by first obtaining a single cell suspension of the tumor then staining with magnetic CD45 microbeads (Miltenyi). Stained samples were magnetically sorted over an LS column followed by an MS column (Miltenyi). CD45+ cells from the tumor were stained with DAPI, and DAPI negative cells were isolated using FACS sorting.
Library construction was performed according to the manufacturer's instructions for the Chromium Next GEM Single Cell 5' HT v2 kit from 10X Genomics. In brief, the CD45+ cells were resuspended in the Master Mix and loaded in conjunction with partitioning oil and gel beads into the Chromium Next GEM Chip N to generate the gel bead-in-emulsion (GEM). Once GEMs were generated, the gel beads dissolved and the copartitioned cell was lysed. Reverse transcription then generated 10X barcoded cDNA from the poly-adenylated mRNA. The cDNA was purified using Silane Dynabeads and amplified to generate sufficient material to construct libraries. The amplified full-length cDNA was used to enrich full-length V(D)J segments by PCR amplification with primers specific to the TCR. Enzymatic fragmentation and size selection were used to optimize for both 5' gene expression library construction and V(D)J library construction. Finally, P5, P7, i5 and i7 sample indexes and Illumina R2 sequence were added to the cDNA via End Repair, A-tailing, Adaptor Ligation, and Sample Index PCR.

value: tumor

value: T cells

tag: dietary group

value: obese


title: tumor-adjacent mAT, weight loss Trem2-/-, replicate 3, scRNAseq VDJ

description: Sample 40_VDJ

source_name: tumor-adjacent mammary adipose tissue

value: tumor-adjacent mammary adipose tissue

value: weight loss


title: tumor, obese Trem2+/+, replicate 4, scRNAseq VDJ

description: Sample 43_VDJ


title: tumor, lean Trem2+/+, replicate 4, scRNAseq VDJ

description: Sample 41_VDJ

value: lean


title: tumor, lean Trem2-/-, replicate 4, scRNAseq VDJ

description: Sample 42_VDJ


title: tumor-adjacent mAT, obese Trem2+/+, replicate 4, scRNAseq VDJ

description: Sample 37_VDJ


title: tumor-adjacent mAT, weight loss Trem2+/+, replicate 4, scRNAseq VDJ

description: Sample 39_VDJ


title: tumor, weight loss Trem2-/-, replicate 2, scRNAseq VDJ

description: Sample 34_VDJ


title: tumor, weight loss Trem2-/-, replicate 3, scRNAseq VDJ

description: Sample 46_VDJ


title: tumor, weight loss Trem2+/+, replicate 4, scRNAseq VDJ

description: Sample 45_VDJ


title: tumor-adjacent mAT, obese Trem2-/-, replicate 4, scRNAseq VDJ

description: Sample 38_VDJ


title: tumor, obese Trem2-/-, replicate 3, scRNAseq VDJ

description: Sample 32_VDJ


title: tumor, weight loss Trem2+/+, replicate 3, scRNAseq VDJ

description: Sample 33_VDJ


title: tumor, obese Trem2+/+, replicate 3, scRNAseq VDJ

description: Sample 31_VDJ


title: tumor, lean Trem2-/-, replicate 3, scRNAseq VDJ

description: Sample 30_VDJ


title: tumor-adjacent mAT, weight loss Trem2-/-, replicate 2, scRNAseq VDJ

description: Sample 29_VDJ


title: tumor-adjacent mAT, weight loss Trem2+/+, replicate 3, scRNAseq VDJ

description: Sample 28_VDJ


title: tumor-adjacent mAT, obese Trem2-/-, replicate 3, scRNAseq VDJ

description: Sample 27_VDJ


title: tumor-adjacent mAT, lean Trem2-/-, replicate 3, scRNAseq VDJ

description: Sample 25_VDJ


title: tumor-adjacent mAT, obese Trem2+/+, replicate 3, scRNAseq VDJ

description: Sample 26_VDJ


title: tumor, weight loss Trem2+/+, replicate 2, scRNAseq VDJ

description: Sample 23_VDJ


title: tumor, obese Trem2-/-, replicate 2, scRNAseq VDJ

description: Sample 22_VDJ


title: tumor, obese Trem2+/+, replicate 2, scRNAseq VDJ

description: Sample 21_VDJ


title: tumor, lean Trem2-/-, replicate 2, scRNAseq VDJ

description: Sample 20_VDJ


title: tumor, lean Trem2+/+, replicate 2, scRNAseq VDJ

description: Sample 19_VDJ


title: tumor-adjacent mAT, lean Trem2+/+, replicate 3, scRNAseq VDJ

description: Sample 18_VDJ


title: tumor-adjacent mAT, lean Trem2-/-, replicate 4, scRNAseq VDJ

description: Sample 36_VDJ


title: tumor-adjacent mAT, weight loss Trem2+/+, replicate 2, scRNAseq VDJ

description: Sample 17_VDJ


title: tumor-adjacent mAT, lean Trem2+/+, replicate 4, scRNAseq VDJ

description: Sample 35_VDJ


title: tumor-adjacent mAT, lean Trem2-/-, replicate 2, scRNAseq VDJ

description: Sample 14_VDJ


title: tumor, obese Trem2-/-, replicate 1, scRNAseq VDJ

description: Sample 10_VDJ


title: tumor-adjacent mAT, obese Trem2+/+, replicate 2, scRNAseq VDJ

description: Sample 15_VDJ


title: tumor, obese Trem2+/+, replicate 1, scRNAseq VDJ

description: Sample 9_VDJ


title: tumor-adjacent mAT, lean Trem2+/+, replicate 2, scRNAseq VDJ

description: Sample 13_VDJ


title: tumor, weight loss Trem2-/-, replicate 1, scRNAseq VDJ

description: Sample 12_VDJ


title: tumor-adjacent mAT, weight loss Trem2-/-, replicate 1, scRNAseq VDJ

description: Sample 6_VDJ


title: tumor, lean Trem2+/+, replicate 3, scRNAseq VDJ

description: Sample 24_VDJ


title: tumor-adjacent mAT, obese Trem2+/+, replicate 1, scRNAseq VDJ

description: Sample 3_VDJ


title: tumor-adjacent mAT, weight loss Trem2+/+, replicate 1, scRNAseq VDJ

description: Sample 5_VDJ


title: tumor, lean Trem2+/+, replicate 1, scRNAseq VDJ

description: Sample 7_VDJ


title: tumor, lean Trem2-/-, replicate 1, scRNAseq VDJ

description: Sample 8_VDJ


title: tumor, weight loss Trem2+/+, replicate 1, scRNAseq VDJ

description: Sample 11_VDJ


title: tumor, obese Trem2-/-, replicate 4, scRNAseq  mRNA

description: Sample 44_mRNA

value: CD45+ cells


title: tumor, lean Trem2-/-, replicate 4, scRNAseq  mRNA

description: Sample 42_mRNA


title: tumor-adjacent mAT, lean Trem2+/+, replicate 1, scRNAseq VDJ

description: Sample 1_VDJ


title: tumor, weight loss Trem2-/-, replicate 3, scRNAseq  mRNA

description: Sample 46_mRNA


title: tumor, weight loss Trem2+/+, replicate 4, scRNAseq  mRNA

description: Sample 45_mRNA


title: tumor-adjacent mAT, weight loss Trem2-/-, replicate 3, scRNAseq  mRNA

description: Sample 40_mRNA


title: tumor-adjacent mAT, obese Trem2-/-, replicate 4, scRNAseq  mRNA

description: Sample 38_mRNA


title: tumor-adjacent mAT, obese Trem2+/+, replicate 4, scRNAseq  mRNA

description: Sample 37_mRNA


title: tumor-adjacent mAT, lean Trem2+/+, replicate 4, scRNAseq  mRNA

description: Sample 35_mRNA


title: tumor-adjacent mAT, lean Trem2-/-, replicate 4, scRNAseq  mRNA

description: Sample 36_mRNA


title: tumor-adjacent mAT, obese Trem2-/-, replicate 2, scRNAseq VDJ

description: Sample 16_VDJ


title: tumor-adjacent mAT, obese Trem2-/-, replicate 1, scRNAseq VDJ

description: Sample 4_VDJ


title: tumor-adjacent mAT, lean Trem2-/-, replicate 1, scRNAseq VDJ

description: Sample 2_VDJ


title: tumor, obese Trem2+/+, replicate 3, scRNAseq  mRNA

description: Sample 31_mRNA


title: tumor, weight loss Trem2+/+, replicate 3, scRNAseq  mRNA

description: Sample 33_mRNA


title: tumor, lean Trem2+/+, replicate 4, scRNAseq  mRNA

description: Sample 41_mRNA


title: tumor-adjacent mAT, obese Trem2-/-, replicate 3, scRNAseq  mRNA

description: Sample 27_mRNA


title: tumor-adjacent mAT, weight loss Trem2+/+, replicate 3, scRNAseq  mRNA

description: Sample 28_mRNA


title: tumor-adjacent mAT, weight loss Trem2-/-, replicate 2, scRNAseq  mRNA

description: Sample 29_mRNA


title: tumor-adjacent mAT, weight loss Trem2+/+, replicate 4, scRNAseq  mRNA

description: Sample 39_mRNA


title: tumor, obese Trem2-/-, replicate 3, scRNAseq  mRNA

description: Sample 32_mRNA


title: tumor, obese Trem2-/-, replicate 2, scRNAseq  mRNA

description: Sample 22_mRNA


title: tumor, lean Trem2+/+, replicate 2, scRNAseq  mRNA

description: Sample 19_mRNA


title: tumor, obese Trem2+/+, replicate 4, scRNAseq  mRNA

description: Sample 43_mRNA


title: tumor-adjacent mAT, lean Trem2-/-, replicate 3, scRNAseq  mRNA

description: Sample 25_mRNA


title: tumor, obese Trem2+/+, replicate 2, scRNAseq  mRNA

description: Sample 21_mRNA


title: tumor, lean Trem2-/-, replicate 2, scRNAseq  mRNA

description: Sample 20_mRNA


title: tumor, weight loss Trem2+/+, replicate 2, scRNAseq  mRNA

description: Sample 23_mRNA


title: tumor, lean Trem2-/-, replicate 3, scRNAseq  mRNA

description: Sample 30_mRNA


title: tumor-adjacent mAT, obese Trem2+/+, replicate 3, scRNAseq  mRNA

description: Sample 26_mRNA


title: tumor-adjacent mAT, weight loss Trem2+/+, replicate 2, scRNAseq  mRNA

description: Sample 17_mRNA


title: tumor, weight loss Trem2-/-, replicate 2, scRNAseq  mRNA

description: Sample 34_mRNA


title: tumor-adjacent mAT, obese Trem2-/-, replicate 2, scRNAseq  mRNA

description: Sample 16_mRNA


title: tumor-adjacent mAT, lean Trem2-/-, replicate 2, scRNAseq  mRNA

description: Sample 14_mRNA


title: tumor, lean Trem2+/+, replicate 3, scRNAseq  mRNA

description: Sample 24_mRNA


title: tumor, weight loss Trem2-/-, replicate 1, scRNAseq  mRNA

description: Sample 12_mRNA


title: tumor-adjacent mAT, lean Trem2+/+, replicate 2, scRNAseq  mRNA

description: Sample 13_mRNA


title: tumor, weight loss Trem2+/+, replicate 1, scRNAseq  mRNA

description: Sample 11_mRNA


title: tumor, obese Trem2-/-, replicate 1, scRNAseq  mRNA

description: Sample 10_mRNA


title: tumor, lean Trem2-/-, replicate 1, scRNAseq  mRNA

description: Sample 8_mRNA


title: tumor, obese Trem2+/+, replicate 1, scRNAseq  mRNA

description: Sample 9_mRNA


title: tumor-adjacent mAT, weight loss Trem2-/-, replicate 1, scRNAseq  mRNA

description: Sample 6_mRNA


title: tumor, lean Trem2+/+, replicate 1, scRNAseq  mRNA

description: Sample 7_mRNA


title: tumor-adjacent mAT, obese Trem2+/+, replicate 1, scRNAseq  mRNA

description: Sample 3_mRNA


title: tumor-adjacent mAT, weight loss Trem2+/+, replicate 1, scRNAseq  mRNA

description: Sample 5_mRNA


title: tumor-adjacent mAT, obese Trem2-/-, replicate 1, scRNAseq  mRNA

description: Sample 4_mRNA


title: Old replicate 4, snRNAseq

city: SAN FRANCISCO

first: Margaret

last: Gadek

address: 675 Nelson Rising Lane

department: Neurology

institute: UCSF

description: 10X Genomics

data_processing:
FASTQ files were aligned to the combined reference genome using Cell Ranger Count v8.0.0 with the -include introns flag. Combined feature–barcode matrixes were formed using the aggregate function of Cell Ranger Aggr v8.0.0.
Assembly: A combined M. musculus (GRCm39) and M. castaneous genome (CAST_EiJ_v1.111) genome was created using the mkref function of CellRanger (Cellranger/8.0 10x Genomics).
Supplementary files format and content: tab seperated values files and matrix files

molecule: nuclear RNA

source_name: Hippocampus

extract_protocol:
Nuclei were extracted using the Nuclei EZ Prep kit (Millipore Sigma), following the manufacturer’s protocol. Frozen hippocampi were homogenized in lysis buffer and centrifuged to twice to isolate the nuclei from the cell debris. The nuclei were resuspended in glycerol-containing buffer and stored at -80ºC.
The libraries were prepped with the goal of 5000 nuclei per sample using the Chromium Single Cell 3′ Library and Gel Bead kit v3.1, Chromium Next GEM Chip G, and Dual Index Kit TT Set A (10X Genomics).
single nuclei RNA-seq

value: Hippocampus


title: tumor-adjacent mAT, lean Trem2+/+, replicate 3, scRNAseq  mRNA

description: Sample 18_mRNA


title: tumor-adjacent mAT, lean Trem2+/+, replicate 1, scRNAseq mRNA

description: Sample 1_mRNA


title: tumor-adjacent mAT, obese Trem2+/+, replicate 2, scRNAseq  mRNA

description: Sample 15_mRNA


title: Old replicate 3, snRNAseq

description: 10X Genomics


title: Old replicate 2, snRNAseq

description: 10X Genomics


title: Young replicate 1, snRNAseq

description: 10X Genomics


title: Young replicate 4, snRNAseq

description: 10X Genomics


title: BLM_KOEV_4

city: Dijon

first: Olivier

last: Burgy

state: Côte-d'Or

address: 7 boulevard Jeanne d'Arc

department: U1231 Center For Translational and Molecular Medicine

country: France

institute: Université de Bourgogne

data_processing:
Data analysis was performed by Novogene Co. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: GRCm38/mm10
Supplementary files format and content: Processed data file indicates the raw counts after alignment for all the 8 samples

source_name: Lung

extract_protocol:
Total RNA was extracted using a Trizol standard protocol. Messenger RNAs were purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. It was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Lung

value: bleomycin + Sfrp1-/-pmLF-EVs


title: BLM_KOEV_2


title: Old replicate 1, snRNAseq

description: 10X Genomics


title: BLM_KOEV_1


title: BLM_KOEV_3


title: BLM_WTEV_4

value: bleomycin + Sfrp1+/+pmLF-EVs


title: Young replicate 2, snRNAseq

description: 10X Genomics


title: BLM_WTEV_1


title: BLM_WTEV_3


title: tumor-adjacent mAT, lean Trem2-/-, replicate 1, scRNAseq  mRNA

description: Sample 2_mRNA


title: FMCVS881; female, mutant, CVS

city: University Park

first: Meiyu

last: Shao

state: PA

address: 301 Life Sciences Building

department: Department of Biology

institute: Penn State University

data_processing:
RNA reads were filtered using fastp v.0.23.2 27 to remove sequencing adapters and reads shorter than 50-bp and aligned to the mouse genome GRCm39 using STAR aligner v.2.7.10b 28.
The STAR genome index was constructed using the annotation v.M32 downloaded from GENCODE.
FeatureCounts 29 was utilized to quantify read pairs aligned to exons at the gene level in a strand-specific mode.
Read pairs aligned to multiple genes were excluded from the analysis.
Assembly: GRCm39
Supplementary files format and content: text file includes raw counts for each sample

source_name: medial prefrontal cortex

extract_protocol:
Mice were sacrificed by cervical dislocation 24 hours after the last stressor. The mPFC was dissected from 1 mm coronal sections prepared using a mouse brain matrix (Stoelting Co., Wood Dale, IL), followed by extraction of total RNA using a GenElute™ Mammalian Total RNA Miniprep Kit and on-column DNase I treatment (Qiagen). The RNA integrity number and concentration were assessed using a Fragment Analyzer (Agilent 5400).
Messenger RNA was purified from 400 ng of total RNA, and libraries were constructed using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs), following manufacturer's protocols. The libraries were sequenced on an Illumina NovaSeq 6000 system at a depth of 20 million 150-bp paired-end reads per sample.

value: medial prefrontal cortex

value: female

tag: strain genetic_information

value: mutant (SSTCre:γ2f/f)

value: chronic variable stress (CVS)


title: FMCVS777; female, mutant, CVS


title: FMCVS825; female, mutant, CVS


title: FMCVS753; female, mutant, CVS


title: FMCVS889; female, mutant, CVS


title: FMNS888; female, mutant, NS

value: non-stress (NS)


title: FCCVS931; female, control, CVS

value: control (SSTCre)


title: FCCVS851; female, control, CVS


title: FMNS190; female, mutant, NS


title: FMNS751; female, mutant, NS


title: FCCVS786; female, control, CVS


title: FCCVS37; female, control, CVS


title: Young replicate 3, snRNAseq

description: 10X Genomics


title: FMNS814; female, mutant, NS


title: FCNS917; female, control, NS


title: FCNS808; female, control, NS


title: FCCVS812; female, control, CVS


title: BLM_WTEV_2


title: FCNS192; female, control, NS


title: FCNS32; female, control, NS


title: YMCVS356; male, mutant, CVS

value: male


title: YMCVS279; male, mutant, CVS


title: YMCVS404; male, mutant, CVS


title: YMNS345; male, mutant, NS


title: YMNS397; male, mutant, NS


title: YMNS290; male, mutant, NS


title: YCCVS407; male, control, CVS


title: YCCVS247; male, control, CVS


title: YCCVS353; male, control, CVS


title: YCCVS262; male, control, CVS


title: YCCVS287; male, control, CVS


title: FMNS826; female, mutant, NS


title: YCCVS305; male, control, CVS


title: FCNS880; female, control, NS


title: YCNS322; male, control, NS


title: YCNS354; male, control, NS


title: YCNS263; male, control, NS


title: YCNS405; male, control, NS


title: YCNS304; male, control, NS


title: NIK KO, medium

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 reference using the Hisat2 aligner
Reads counts were calculated for each sample.
Differential expression of genes were computed between groups using DEseq2
Assembly: Mus musculus(mm10)
Supplementary files format and content: tab-delimited text files include raw count for each sample

source_name: NIK KO B16F10

growth_protocol: WTB16F10 cells were maintained in DMEM with 10% fetal bovine serum and antibiotics; and with additional 1 ug/mL puromycin for IKKbKO and NIK KO B16F10 .

extract_protocol:
Total RNA was extracted using Qiagen Rneasy mini plus kit. 1 ug total RNA used for sequencing library construction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: Cells in 12-well TC treated with 20 uM of each peptide for 30 min, washed and stimulated with 2 ug/mL agonist anti-LTbR Ab (3C8) fro 1 hour or 6 hours.

value: NIK KO B16F10

value: Melanoma cells

value: CRISPR-Cas9 NIK KO


title: NIK KO, anti-LTbR Ab 6 hours


title: WT, nciLT+anti-LTbR Ab 6 hours

source_name: WT B16F10

value: WT B16F10

value: WT


title: YMCVS269; male, mutant, CVS


title: IKKb KO, medium

source_name: IKKb KO B16F10

value: IKKb KO B16F10

value: CRISPR-Cas9 IKKbKO


title: WT, anti-LTbR Ab 6 hours


title: IKKb KO, anti-LTbR Ab 1 hour


title: WT, ciLT+anti-LTbR Ab 1 hour


title: THmycNB6_4

city: Memphis

first: Hongjian

last: Jin

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipelineThe raw reads were firs trimmed (Trim-Galore version 0.60) and mapped to mm10 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation M22
Assembly: GRCm38 (mm10)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

source_name: Tumor

growth_protocol: In order to develop tumor, Dbh-iCre mouse was bred with CAG-STOPflox/flox-MYC, or LSL-MYCN mouse to get Dbh-iCre/CAG-STOPflox/flox-MYC or Dbh-iCre/LSL-MYCN. Ultrasound scanning were using to check and monitor tumor development. In order to get THmycNB6 tumor model, THmycN129 mice were backcross with C57/B6 over 7 generation.

extract_protocol:
Total RNAs from normal pancreas and tumor tissues were performed using the RNeasy Mini Kit (Qiagen, Cat#74136) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the Nationwide Children’s Hospital.

value: Tumor

value: Th-MYCN in C57/B6 background mice

value: Th-MYCN

tag: tumor model


title: THmycNB6_3


title: THmycN129_2

value: Th-MYCN in 129 background mice


title: THmycNB6_2


title: THmycNB6_1


title: THmycN129_1


title: LSLmycN_4

value: Dbh-iCre;LSL-MYCN

value: LSLmycN


title: LSLmycN_2


title: WT, anti-LTbR Ab 1 hour


title: LSLmycN_1


title: LSLmycN_3


title: cMyc_1

value: Dbh-iCre;CAG-MYC

value: cMyc


title: KBP86T2

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60).  GEMM mouse samples were mapped to mm10 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation M22
Assembly: GRCm38 (mm10)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

growth_protocol: In order to develop tumor, TH-Cre mouse was bred with CAG-STOPflox/flox-MYC mouse to get TH-Cre/CAG-STOPflox/flox-MYC. Ultrasound scanning were using to check and monitor tumor development.

extract_protocol:
In order to obtain high-quality and intact RNA from the normal pancreas, the pancreas was perfused with the RNase inhibitor solution RNAlater (Qiagen, 76106) before isolation from the littermate control mice. The isolated pancreas with perfusion was cut into small pieces for total RNA extraction. Total RNAs from normal pancreas and tumor tissues were performed using the RNeasy Mini Kit (Qiagen, Cat#74136) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.


title: KBP86_T1 ScRNASeq

first: Xiang

last: Chen

department: Computational Biology

institute: St.Jude Children's Research Hospital

description: 10X Genomics-ScRNAseq

data_processing:
The sequence data was processed using Cell Ranger V4 software and custom reference included premRNA in the GRCm38
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Neuroblastoma tumor

extract_protocol:
Tumor tissue from mouse model harvested and frozen immediately.
The library constructed 10X Genomics- 3'ScRNASeq V3 kit.

value: Neuroblastoma tumor


title: KBP86_T2 ScRNASeq

description: 10X Genomics-ScRNAseq


title: KBP114


title: KBP_ctrl_01

source_name: Normal Pancreas

value: Normal Pancreas

value: Wild Type


title: Mouse colorectal epithelium，cKO-2

city: Beijing City

first: Shiyang Wang

middle: Shiyang

last: Wang

state: Beijing City

address: 2 West Yuanmingyuan Road, Haidian District, Beijing, China

institute: China Agricultural University

data_processing:
Library preparation for Transcriptome sequencing. Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA waspurified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation wascarried out using divalent cations under elevated temperature in First Strand SynthesisReaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer andM-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis wassubsequently performed using DNA Polymerase I and RNase H. Remaining overhangs wereconverted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’endsof DNA fragments, Adaptor with hairpin loop structure were ligated to prepare forhybridization. In order to select cDNA fragments of preferentially 370420 bp in length, thelibrary fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCRprimers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) andlibrary quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster GenerationSystem using TruSeq PE Cluster Kit v3-cBot-HS (Ilumia) according to the manufacturer'sinstructions. After cluster generation, the library preparations were sequenced on an IlluminaNovaseq platform and 150 bp paired-end reads were generated.
Assembly: Hisat2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colorectum

growth_protocol: Eight-week-old BALB/C mice were selected and grown in SPF environment. MST3(also known as STK24) gene was knocked out in intestinal epithelial cells.

extract_protocol:
RNA was harvested and tissue was lysed using Trizol and homogenized using a homogenizer. Approximately 30µg of total RNA was used for sequencing library construction.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).

treatment_protocol: Normal growing mice, without any drug induction

value: colorectum

value: MST3 knockout


title: Mouse colorectal epithelium，cKO-3


title: Mouse colorectal epithelium，cKO-1


title: Mouse colorectal epithelium，Ctrl-3


title: Mouse colorectal epithelium，Ctrl-2


title: Mouse colorectal epithelium，cKO-4


title: Mouse colorectal epithelium，Ctrl-1


title: cMyc_2


title: Standard proton-irradiated M2 macrophage_3 [ST-M2-0512]

city: Philadelphia

first: Yi

last: Fan

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

data_processing:
Kallisto quantification was performed for the RNA-Seq data using Kallisto version 0.46.1 obtained from github. Kallisto index was built with reference transcriptome GRCh38.
In R (version 4.0.5), transcripts were collapsed to genes using package tximport (version 1.22.0), and then normalized and filtered by edgeR (version 3.36.0) to generate a count matrix.
Assembly: GRCh38
Supplementary files format and content: Raw count matrix

source_name: Mouse macrophages

growth_protocol: Bone marrow cells were cultured in RPMI-1640 medium supplemented with 5% FBS.

extract_protocol:
Treated mouse macrophages and were lysed in TRIzol (Thermo Fisher), and RNA was extracted according to the manufacturer’s instructions, followed by RNA purification using a RNeasy Plus Mini Kit (Qiagen).
The RNA from each step and library DNA quality were analyzed with RNA Nano assay chips, RNA Pico assay chips, and DNA Nano assay chips using a 2100 bioanalyzer (Agilent). Library was subjected to next-generation sequencing analysis in a high-throughput sequencing center with a NovaSeq at the Azenta Life Sciences

treatment_protocol: Bone marrow-derived cells were isolated from femur and tibia of C57BL/6 mice. Cells were irradiated by 5-Gy FLASH or standard proton beam, or un-irradiated as controls. Cells were then incubated with 10 ng/ml mouse CSF-1 for 7 days to induce macrophage differentiation, followed by treatment with 100 ng/ml LPS (for M1 polarization), 20 ng/ml IL-4 (for M2 polarization), or control medium (for M0 condition) for 2 days. RNA was isolated and analyzed by RNAseq.

value: Bone marrow-derived macrophages

tag: cell type/treatment

value: IL4-treated macrophages, irradiated by standard proton

value: 5-Gy irradiation


title: Tumor after FLASH proton irradiation

description: FLASH RT

data_processing:
Reads were aligned with CellRanger (10x Genomics, version 6.1.2) against customized mouse reference library (mm10) to produce sparse numerical matrices for each sample, with gene-level counts of unique molecular identifiers (UMI) identified for all single cells passing default quality control metrics.
Assembly: mm10
Supplementary files format and content: CellRanger-generated filtered count matrix

source_name: Mouse tumor-derived cells

extract_protocol:
Mice bearing medulloblastoma tumors were euthanized and perfused with PBS supplemented with EDTA. Tumor tissues were harvested and digested with collagenase-II and DNase. Single cell suspension was prepared after filtering using a mesh strainer with 100-μm pores.
Cell samples were prepared and analyzed following a manufacturer’s V3 library protocol (10x Genomics) and single-cell RNA-seq at the next-generation sequencing core at the Children's Hopital of Philadelphia.

treatment_protocol: Genetically engineered medulloblastoma was induced in mice, by crossing SmoM2fl/fl mice with Math1-Cre mice

value: Mouse tumor-derived cells

value: Irradiated by FLASH proton


title: Tumor after standard proton irradiation

description: Standard RT

value: Irradiated by standard proton


title: Standard proton-irradiated M2 macrophage_1 [ST-M2-0423]


title: Standard proton-irradiated M1 macrophage_3 [ST-M1-0512]

value: LPS-treated macrophages, irradiated by standard proton


title: Standard proton-irradiated M2 macrophage_2 [ST-M2-0507]


title: Standard proton-irradiated M1 macrophage_2 [ST-M1-0507]


title: Standard proton-irradiated M0 macrophage_2 [ST-M0-0507]

value: Control M0 macrophages, irradiated by standard proton


title: Standard proton-irradiated M0 macrophage_3 [ST-M0-0512]


title: Standard proton-irradiated M1 macrophage_1 [ST-M1-0423]


title: Standard proton-irradiated M0 macrophage_1 [ST-M0-0423]


title: cMyc_4

value: Tumor


title: KBP86T1


title: KBP_ctrl_02


title: Non-irradiated M2 macrophage_3 [NT-M2-0512]

value: IL4-treated macrophages, no radiation

value: 0-Gy irradiation


title: Non-irradiated M2 macrophage_1 [NT-M2-0423]


title: Non-irradiated M1 macrophage_3 [NT-M1-0512]

value: LPS-treated macrophages, no radiation


title: Non-irradiated M2 macrophage_2 [NT-M2-0507]


title: Non-irradiated M1 macrophage_2 [NT-M1-0507]


title: Non-irradiated M0 macrophage_2 [NT-M0-0507]

value: Control M0 macrophages, no radiation


title: Non-irradiated M0 macrophage_3 [NT-M0-0512]


title: Non-irradiated M1 macrophage_1 [NT-M1-0423]


title: Non-irradiated M0 macrophage_1 [NT-M0-0423]


title: FLASH proton-irradiated M2 macrophage_1 [FL-M2-0423]

value: IL4-treated macrophages, irradiated by FLASH proton


title: FLASH proton-irradiated M1 macrophage_3 [FL-M1-0512]

value: LPS-treated macrophages, irradiated by FLASH proton


title: FLASH proton-irradiated M1 macrophage_2 [FL-M1-0507]


title: FLASH proton-irradiated M1 macrophage_1 [FL-M1-0423]


title: FLASH proton-irradiated M0 macrophage_2 [FL-M0-0507]

value: Control M0 macrophages, irradiated by FLASH proton


title: muscle_wildtype_rep6 [S044_9]

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
STAR v2.7.2b was used to align sequence reads onto the GRCm38 mouse genome assembly, with the GENCODE version M24 gene model
reads were summarized onto genes by featureCounts v1.6.4 with the same gene model as when mapping, counting only fragments where both ends of the fragment were aligned
Assembly: mm10
Supplementary files format and content: csv file with read counts

source_name: skeletal muscle

extract_protocol:
Total RNA from tissue was isolated using Qiagen RNeasy kit (Qiagen, GmbH Hilden, Germany) following manufacturer’s protocol. The quantity of the RNA was determined on a Nanodrop ND-1000 (Thermo Scientific, Rockford, IL, USA)
Libraries were prepared using the Universal Plus mRNA-seq with NuQuant kit (Tecan) as recommended by the manufacturer. Libraries were quantified with NuQuant, quality checked using a TapeStation instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing.

value: skeletal muscle

value: Male

tag: cage number

tag: body weight

value: wildtype


title: FLASH proton-irradiated M0 macrophage_1 [FL-M0-0423]

value: Bone marrow-derived macrophages

value: 5-Gy irradiation


title: muscle_heterozygous_rep10 [S044_8]

value: heterozygous


title: muscle_wildtype_rep5 [S044_7]


title: muscle_wildtype_rep4 [S044_5]


title: muscle_heterozygous_rep8 [S044_3]


title: muscle_heterozygous_rep9 [S044_4]


title: muscle_heterozygous_rep7 [S044_22]


title: muscle_heterozygous_rep6 [S044_20]


title: muscle_heterozygous_rep5 [S044_2]


title: muscle_heterozygous_rep4 [S044_18]


title: muscle_heterozygous_rep3 [S044_15]


title: muscle_wildtype_rep2 [S044_12]


title: FLASH proton-irradiated M2 macrophage_3 [FL-M2-0512]


title: muscle_heterozygous_rep2 [S044_11]


title: muscle_heterozygous_rep1 [S044_1]


title: FLASH proton-irradiated M2 macrophage_2 [FL-M2-0507]


title: muscle_wildtype_rep1 [S044_10]


title: FLASH proton-irradiated M0 macrophage_3 [FL-M0-0512]


title: Liver_ZT10_DKO_ΔhIDR_anti-H3K27ac_ChIP-seq-rep1

first: KUN

last: ZHU

address: 3400 Civic Center Blvd, SCTR-12-196

description: Liver_ZT10_DKO_REV-ERBalpha-delhIDR_anti-H3K27ac_ChIP-seq_pooled.norm.bw

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq/Hiseq output.
ChIP-seq reads were trimmed by cutadapt v2.3
ChIP-seq reads were aligned to mm10 by bwa 0.7.17
Read duplicates and low MAPQ (<=30) were removed by picard 2.18.12 and samtools 1.9, respectively
MACS2 2.1.2 was used to call peaks. Peak intensity was calculated by multiBigwigSummary module from deepTools 3.3.0
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: Liver

extract_protocol:
Isolated Liver nuclei were fixed with 1% formaldehyde for 10 minutes and followed by 45 min 1.5 mM EGS. After quenching and cell lysis, chromatin was sheared by probe sonicator.
ChIP-seq libraries were prepared by Tn5-mediated tagmentation and adapter ligation. Adapted DNA was amplified by PCR and size selected for final sequencing.

value: Liver

tag: antibody

tag: vendor

value: Active Motif

tag: cat#

value: REV-ERBaf/fREV-ERBbf/f

tag: circadian time

tag: aav virus_combinational_injection


title: Liver_ZT10_DKO_ΔhIDR_anti-H3K27ac_ChIP-seq-rep3

tag: tissue

tag: genotype


title: Liver_ZT10_DKO_ΔhIDR_anti-H3K27ac_ChIP-seq-rep2


title: Liver_ZT10_DKO_WT_anti-H3K27ac_ChIP-seq-rep1

description: Liver_ZT10_DKO_REV-ERBalpha-WT_anti-H3K27ac_ChIP-seq_pooled.norm.bw


title: Liver_ZT10_DKO_WT_anti-H3K27ac_ChIP-seq-rep2


title: Liver_ZT10_DKO_YFP_anti-H3K27ac_ChIP-seq-rep1

description: Liver_ZT10_DKO_YFP_anti-H3K27ac_ChIP-seq_pooled.norm.bw


title: Liver_ZT10_DKO_YFP_anti-H3K27ac_ChIP-seq-rep2


title: muscle_wildtype_rep3 [S044_17]


title: Liver_ZT10_DKO_ΔhIDR_anti-NCOR1_ChIP-seq-rep3

description: Liver_ZT10_DKO_REV-ERBalpha-delhIDR_anti-NCOR1_ChIP-seq_rep3.norm.bw

value: In-house


title: Liver_ZT10_Ctrl_YFP_anti-H3K27ac_ChIP-seq-rep2

description: Liver_ZT10_Ctrl_YFP_anti-H3K27ac_ChIP-seq_pooled.norm.bw


title: Liver_ZT10_DKO_WT_anti-NCOR1_ChIP-seq-rep1

description: Liver_ZT10_DKO_REV-ERBalpha-WT_anti-NCOR1_ChIP-seq_rep1.norm.bw


title: Liver_ZT10_DKO_WT_anti-NCOR1_ChIP-seq-rep2

description: Liver_ZT10_DKO_REV-ERBalpha-WT_anti-NCOR1_ChIP-seq_rep2.norm.bw


title: Liver_ZT10_DKO_YFP_anti-NCOR1_ChIP-seq-rep2

description: Liver_ZT10_DKO_YFP_anti-NCOR1_ChIP-seq_rep2.norm.bw


title: Liver_ZT10_DKO_YFP_anti-NCOR1_ChIP-seq-rep1

description: Liver_ZT10_DKO_YFP_anti-NCOR1_ChIP-seq_rep1.norm.bw


title: Liver_ZT10_Ctrl_YFP_anti-NCOR1_ChIP-seq-rep2

description: Liver_ZT10_Ctrl_YFP_anti-NCOR1_ChIP-seq_rep2.norm.bw


title: Liver_ZT10_Ctrl_YFP_anti-NCOR1_ChIP-seq-rep1

description: Liver_ZT10_Ctrl_YFP_anti-NCOR1_ChIP-seq_rep1.norm.bw


title: Liver_ZT10_DKO_ΔhIDR_anti-NCOR1_ChIP-seq-rep2

description: Liver_ZT10_DKO_REV-ERBalpha-delhIDR_anti-NCOR1_ChIP-seq_rep2.norm.bw


title: Liver_ZT10_anti-NCOR1_ChIP-seq-rep3

description: Liver_ZT10_anti-NCOR1_ChIP-seq_rep3.norm.bw


title: Liver_ZT10_anti-NCOR1_ChIP-seq-rep1

description: Liver_ZT10_anti-NCOR1_ChIP-seq_rep1.norm.bw


title: Liver_ZT22_anti-NCOR1_ChIP-seq-rep2

description: Liver_ZT22_anti-NCOR1_ChIP-seq_rep2.norm.bw


title: Liver_ZT22_anti-NCOR1_ChIP-seq-rep1

description: Liver_ZT22_anti-NCOR1_ChIP-seq_rep1.norm.bw


title: Liver_ZT10_anti-H3K27ac_ChIP-seq-rep3

description: Liver_ZT10_anti-H3K27ac_ChIP-seq_pooled.norm.bw


title: Liver_ZT22_anti-NCOR1_ChIP-seq-rep3

description: Liver_ZT22_anti-NCOR1_ChIP-seq_rep3.norm.bw


title: Liver_ZT10_anti-H3K27ac_ChIP-seq-rep2


title: Liver_ZT22_anti-H3K27ac_ChIP-seq-rep2

description: Liver_ZT22_anti-H3K27ac_ChIP-seq_pooled.norm.bw


title: Liver_ZT22_anti-H3K27ac_ChIP-seq-rep1


title: Liver_ZT10_anti-H3K27ac_ChIP-seq-rep1


title: Liver_ZT10_Ctrl_YFP_anti-H3K27ac_ChIP-seq-rep1


title: Liver_ZT22_anti-H3K4me3_ChIP-seq-rep2

description: Liver_ZT22_anti-H3K4me3_ChIP-seq_pooled.norm.bw

value: Millipore


title: Liver_ZT10_DKO_ΔhIDR_anti-NCOR1_ChIP-seq-rep1

description: Liver_ZT10_DKO_REV-ERBalpha-delhIDR_anti-NCOR1_ChIP-seq_rep1.norm.bw


title: Liver_ZT22_anti-H3K4me3_ChIP-seq-rep3


title: Liver_ZT10_anti-H3K4me3_ChIP-seq-rep1

description: Liver_ZT10_anti-H3K4me3_ChIP-seq_pooled.norm.bw


title: Liver_ZT22_anti-H3K4me3_ChIP-seq-rep1


title: Liver_ZT10_anti-HA_DKO_ΔhIDR_In-situ_ChIA-PET_rep2

data_processing:
In-situ ChIA-PET fastq reads was processed by ChIA-PIPE tool V1.0
Assembly: mm10
Supplementary files format and content: bigWig, BE3

extract_protocol:
Isolated liver nuclei were fixed with 1% formaldehyde for 10 minutes and followed by 45 min 1.5 mM EGS. After quenching and cell lysis, nuclei were permeabilized by 0.1%SDS at 62 degree for 10min, 37 degree for 20 min, 0.55% SDS at RT for 1h. The nuclei were digested by AluI enzyme and re-ligated by T4 DNA ligase sequentially. Ligated chromatin was sheared by probe sonicator.
Sheared DNA was pulldown by a specific antibody; Immunoprecipied DNA was subjected to Tn5 tagmentation, M280 Dynabeads streptavidin pull-down and PCR amplification; PCR products were subjected to size-selection and pair-end sequencing on Illumina Hiseq or Novaseq platform.

value: Pierce™ Anti-HA Magnetic Beads

value: Thermo Fisher


title: Liver_ZT10_anti-HA_DKO_ΔhIDR_In-situ_ChIA-PET_rep1


title: Liver_ZT10_anti-HA_DKO_WT_In-situ_ChIA-PET_rep2


title: ORSAM23288-1

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38

source_name: skeletal-muscle-10% fat + fiber-female-CC042/GeniUncJ x CC060/UncJ)F1 -Metformin-rep1

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. ibraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit. Libraries were sequenced 100 bp paired-end to a targeted read depth of 30 million read pairs.

treatment_protocol: Liver, liver, and skeletal muscle tissue from 6-month and 12-month CC-RIX cohorts underwent transcriptomic profiling. CC-RIX cohorts were exposed to sensitizer (HFHS diet) and a widely used pharmaceutical intervention (metformin). Chow (control) or high fat high sugar (HFHS) diet started at 6 weeks of age.. At six months of age, a subset of mice from each chow group and of each sex were euthanized for tissue collection.  At 7 months of age, half of the remaining mice in each diet treatment group will receive metformin treatment.  In a subset of the 12 month cohort animals, metformin (5 mg/mL) was delivered ad libitum in the drinking water (Chang, Moro et al. 2018). Terminal phenotyping and tissue collection was done at 12 months of age.  These animals also underwent metabolic phenotyping.

value: gastrocnemius muscle

value: female

tag: strain

value: CC042/GeniUncJ x CC060/UncJ)F1

value: Outbred

tag: treatment

value: Metformin

tag: diet

value: 10% fat + fiber

tag: sequencing id


title: ORSAM23290-1

tag: Sex


title: Liver_ZT10_anti-HA_DKO_WT_In-situ_ChIA-PET_rep1


title: Liver_ZT10_anti-NCOR1_ChIP-seq-rep2

description: Liver_ZT10_anti-NCOR1_ChIP-seq_rep2.norm.bw


title: ORSAM23289-1


title: ORSAM23293-1

source_name: skeletal-muscle-10% fat + fiber-male-CC042/GeniUncJ x CC060/UncJ)F1 -Metformin-rep1

value: male


title: ORSAM23286-1

source_name: skeletal-muscle-10% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC019/TauUncJ x CC042/GeniUncJ)F1


title: Liver_ZT10_anti-H3K4me3_ChIP-seq-rep3


title: ORSAM23285-1

source_name: skeletal-muscle-44% fat + fiber-male-CC042/GeniUncJ x CC060/UncJ)F1 -Metformin-rep1

value: 44% fat + fiber


title: ORSAM23266-1

source_name: skeletal-muscle-10% fat + fiber-female-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM23277-1

source_name: skeletal-muscle-44% fat + fiber-male-CC009/UncJ x CC013/GeniUncJ)F1 -Metformin-rep1

value: CC009/UncJ x CC013/GeniUncJ)F1


title: ORSAM23284-1


title: ORSAM23274-1

source_name: skeletal-muscle-44% fat + fiber-female-CC009/UncJ x CC013/GeniUncJ)F1 -None-rep1


title: ORSAM23282-1

source_name: skeletal-muscle-44% fat + fiber-female-CC009/UncJ x CC013/GeniUncJ)F1 -Metformin-rep1


title: Liver_ZT10_anti-H3K4me3_ChIP-seq-rep2

value: Liver


title: ORSAM23260-1

source_name: skeletal-muscle-44% fat + fiber-female-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM23264-1

source_name: skeletal-muscle-10% fat + fiber-male-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM23265-1


title: ORSAM23280-1


title: ORSAM23111-1

source_name: skeletal-muscle-10% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -Metformin-rep1

value: CC019/TauUncJ x CC075/UncJ)F1


title: ORSAM23107-1

source_name: skeletal-muscle-44% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -Metformin-rep1


title: ORSAM23104-1

source_name: skeletal-muscle-44% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -Metformin-rep1


title: ORSAM23096-1

source_name: skeletal-muscle-44% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1


title: ORSAM23093-1

source_name: skeletal-muscle-44% fat + fiber-male-CC030/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: CC030/GeniUncJ x CC002/UncJ)F1


title: ORSAM22733-1

source_name: skeletal-muscle-10% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM22725-1

source_name: skeletal-muscle-10% fat + fiber-male-CC011/UncJ x CC005/TauUncJ)F1 -Metformin-rep1

value: CC011/UncJ x CC005/TauUncJ)F1


title: ORSAM22722-1

source_name: skeletal-muscle-10% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: CC051/TauUncJ x CC060/UncJ)F1


title: ORSAM22728-1

source_name: skeletal-muscle-10% fat + fiber-male-CC030/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1


title: ORSAM22721-1

source_name: skeletal-muscle-10% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM22715-1

source_name: skeletal-muscle-44% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -Metformin-rep1


title: ORSAM22719-1

source_name: skeletal-muscle-10% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -Metformin-rep1


title: ORSAM22716-1


title: ORSAM22712-1

source_name: skeletal-muscle-44% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM22498-1

source_name: skeletal-muscle-10% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -Metformin-rep1


title: ORSAM22492-1

source_name: skeletal-muscle-10% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -Metformin-rep1


title: ORSAM22491-1


title: ORSAM22477-1

source_name: skeletal-muscle-10% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM22490-1

source_name: skeletal-muscle-10% fat + fiber-female-CC043/GeniUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC043/GeniUncJ x CC042/GeniUncJ)F1


title: ORSAM23099-1


title: ORSAM22470-1

source_name: skeletal-muscle-10% fat + fiber-female-CC011/UncJ x CC005/TauUncJ)F1 -Metformin-rep1


title: ORSAM22469-1


title: ORSAM22474-1

source_name: skeletal-muscle-44% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -Metformin-rep1


title: ORSAM22472-1


title: ORSAM22481-1

source_name: skeletal-muscle-10% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -Metformin-rep1


title: ORSAM21517-1

source_name: skeletal-muscle-44% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -Metformin-rep1

value: CC042/GeniUncJ x CC040/TauUncJ)F1


title: ORSAM21644-1

source_name: skeletal-muscle-10% fat + fiber-female-CC051/TauUncJ x CC059/TauUncJ)F1 -Metformin-rep1

value: gastrocnemius muscle

value: CC051/TauUncJ x CC059/TauUncJ)F1


title: ORSAM21667-1

source_name: skeletal-muscle-44% fat + fiber-male-CC004/TauUncJ x CC019/TauUncJ)F1 -Metformin-rep1

value: CC004/TauUncJ x CC019/TauUncJ)F1


title: ORSAM21650-1

source_name: skeletal-muscle-44% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: female

value: Outbred


title: ORSAM21507-1

source_name: skeletal-muscle-44% fat + fiber-female-CC043/GeniUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: Metformin


title: ORSAM21511-1

source_name: skeletal-muscle-44% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1


title: ORSAM22736-1

source_name: skeletal-muscle-10% fat + fiber-female-CC009/UncJ x CC013/GeniUncJ)F1 -Metformin-rep1

value: 10% fat + fiber


title: ORSAM22730-1

source_name: skeletal-muscle-44% fat + fiber-male-CC030/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: male


title: ORSAM21506-1

value: 44% fat + fiber


title: ORSAM21503-1

source_name: skeletal-muscle-44% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC019/TauUncJ x CC042/GeniUncJ)F1


title: ORSAM21501-1

source_name: skeletal-muscle-44% fat + fiber-male-CC009/UncJ x CC013/GeniUncJ)F1 -None-rep1

value: CC009/UncJ x CC013/GeniUncJ)F1


title: ORSAM21502-1


title: ORSAM21499-1

source_name: skeletal-muscle-44% fat + fiber-female-CC009/UncJ x CC013/GeniUncJ)F1 -None-rep1


title: ORSAM21496-1

source_name: skeletal-muscle-10% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1

value: CC019/TauUncJ x CC075/UncJ)F1


title: ORSAM21500-1


title: cMyc_3

source_name: Tumor

value: Tumor

value: Dbh-iCre;CAG-MYC

value: cMyc


title: ORSAM21491-1

source_name: skeletal-muscle-10% fat + fiber-female-CC043/GeniUncJ x CC011/UncJ)F1 -None-rep1

value: CC043/GeniUncJ x CC011/UncJ)F1


title: ORSAM20596-1

source_name: skeletal-muscle-10% fat + fiber-male-CC009/UncJ x CC013/GeniUncJ)F1 -Metformin-rep1


title: ORSAM20597-1


title: ORSAM20585-1

value: CC051/TauUncJ x CC060/UncJ)F1


title: ORSAM20579-1

source_name: skeletal-muscle-44% fat + fiber-female-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1

value: gastrocnemius muscle

value: CC042/GeniUncJ x CC060/UncJ)F1


title: ORSAM20588-1

source_name: skeletal-muscle-10% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -Metformin-rep1


title: ORSAM20208-1

source_name: skeletal-muscle-10% fat + fiber-female-CC043/GeniUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC043/GeniUncJ x CC042/GeniUncJ)F1


title: ORSAM19303-1

source_name: skeletal-muscle-10% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1

value: female


title: ORSAM20205-1

source_name: skeletal-muscle-44% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: Outbred


title: ORSAM19299-1

source_name: skeletal-muscle-10% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM19301-1


title: ORSAM20223-1

source_name: skeletal-muscle-44% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -Metformin-rep1

value: CC042/GeniUncJ x CC040/TauUncJ)F1

value: Metformin


title: ORSAM20222-1

source_name: skeletal-muscle-44% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -Metformin-rep1


title: ORSAM20211-1

source_name: skeletal-muscle-10% fat + fiber-male-CC043/GeniUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: male

value: 10% fat + fiber


title: ORSAM17911-1

source_name: skeletal-muscle-10% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1


title: ORSAM21504-1

source_name: skeletal-muscle-44% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC019/TauUncJ x CC042/GeniUncJ)F1

value: 44% fat + fiber


title: ORSAM17909-1

value: CC019/TauUncJ x CC075/UncJ)F1


title: ORSAM20582-1

source_name: skeletal-muscle-44% fat + fiber-male-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM13790-1

source_name: skeletal-muscle-10% fat + fiber-male-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC075/UncJ x CC042/GeniUncJ)F1


title: ORSAM19297-1

source_name: skeletal-muscle-10% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM23295-1

source_name: skeletal-muscle-10% fat + fiber-male-CC042/GeniUncJ x CC060/UncJ)F1 -Metformin-rep1


title: ORSAM23294-1


title: ORSAM23276-1

source_name: skeletal-muscle-44% fat + fiber-male-CC009/UncJ x CC013/GeniUncJ)F1 -Metformin-rep1

value: CC009/UncJ x CC013/GeniUncJ)F1


title: ORSAM23281-1

source_name: skeletal-muscle-44% fat + fiber-female-CC009/UncJ x CC013/GeniUncJ)F1 -Metformin-rep1


title: ORSAM20581-1

source_name: skeletal-muscle-10% fat + fiber-male-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM23268-1

source_name: skeletal-muscle-10% fat + fiber-female-CC043/GeniUncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM23267-1

source_name: skeletal-muscle-44% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM23263-1

source_name: skeletal-muscle-44% fat + fiber-female-CC042/GeniUncJ x CC060/UncJ)F1 -Metformin-rep1


title: ORSAM23261-1

source_name: skeletal-muscle-44% fat + fiber-female-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM23108-1

source_name: skeletal-muscle-44% fat + fiber-male-CC030/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1

value: CC030/GeniUncJ x CC002/UncJ)F1


title: WT, medium

source_name: WT B16F10

tag: cell line

value: WT B16F10

tag: cell type

value: Melanoma cells

value: WT


title: ORSAM23105-1

source_name: skeletal-muscle-44% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -Metformin-rep1

value: gastrocnemius muscle


title: ORSAM23091-1

source_name: skeletal-muscle-44% fat + fiber-male-CC030/GeniUncJ x CC002/UncJ)F1 -None-rep1


title: ORSAM23297-1

value: CC042/GeniUncJ x CC060/UncJ)F1


title: ORSAM23102-1

source_name: skeletal-muscle-44% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -Metformin-rep1


title: ORSAM23086-1

source_name: skeletal-muscle-44% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -Metformin-rep1

value: female


title: ORSAM23097-1

source_name: skeletal-muscle-44% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1

value: Outbred


title: ORSAM22738-1

source_name: skeletal-muscle-10% fat + fiber-female-CC009/UncJ x CC013/GeniUncJ)F1 -Metformin-rep1


title: ORSAM23296-1


title: ORSAM22487-1

source_name: skeletal-muscle-44% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM22714-1

source_name: skeletal-muscle-44% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -Metformin-rep1

value: CC051/TauUncJ x CC060/UncJ)F1


title: ORSAM22711-1

source_name: skeletal-muscle-44% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM22724-1

source_name: skeletal-muscle-10% fat + fiber-male-CC011/UncJ x CC005/TauUncJ)F1 -Metformin-rep1

value: CC011/UncJ x CC005/TauUncJ)F1

value: Metformin


title: ORSAM22497-1

source_name: skeletal-muscle-10% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -Metformin-rep1

value: male

value: 10% fat + fiber


title: ORSAM22727-1

source_name: skeletal-muscle-10% fat + fiber-male-CC030/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1


title: ORSAM22493-1

source_name: skeletal-muscle-10% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -Metformin-rep1


title: ORSAM23273-1

source_name: skeletal-muscle-10% fat + fiber-female-CC009/UncJ x CC013/GeniUncJ)F1 -None-rep1


title: ORSAM21666-1

value: 44% fat + fiber


title: ORSAM22485-1

source_name: skeletal-muscle-44% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC019/TauUncJ x CC042/GeniUncJ)F1


title: ORSAM21665-1

value: CC019/TauUncJ x CC075/UncJ)F1


title: ORSAM22471-1

source_name: skeletal-muscle-10% fat + fiber-female-CC011/UncJ x CC005/TauUncJ)F1 -Metformin-rep1


title: ORSAM21661-1

source_name: skeletal-muscle-44% fat + fiber-male-CC012/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: CC012/GeniUncJ x CC002/UncJ)F1


title: ORSAM23114-1

source_name: skeletal-muscle-44% fat + fiber-male-CC043/GeniUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC043/GeniUncJ x CC042/GeniUncJ)F1


title: ORSAM21649-1

source_name: skeletal-muscle-44% fat + fiber-male-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1

value: CC051/TauUncJ x CC059/TauUncJ)F1


title: ORSAM21646-1

source_name: skeletal-muscle-10% fat + fiber-female-CC051/TauUncJ x CC059/TauUncJ)F1 -Metformin-rep1


title: ORSAM21490-1

source_name: skeletal-muscle-10% fat + fiber-female-CC043/GeniUncJ x CC011/UncJ)F1 -None-rep1

value: CC043/GeniUncJ x CC011/UncJ)F1


title: ORSAM20598-1

source_name: skeletal-muscle-44% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1


title: ORSAM22731-1

source_name: skeletal-muscle-10% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -Metformin-rep1


title: ORSAM20592-1

source_name: skeletal-muscle-44% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -Metformin-rep1


title: ORSAM20595-1

source_name: skeletal-muscle-44% fat + fiber-female-CC009/UncJ x CC013/GeniUncJ)F1 -None-rep1

value: CC009/UncJ x CC013/GeniUncJ)F1


title: ORSAM22486-1

value: gastrocnemius muscle


title: ORSAM20583-1

source_name: skeletal-muscle-44% fat + fiber-male-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1

value: CC042/GeniUncJ x CC060/UncJ)F1


title: ORSAM20584-1

source_name: skeletal-muscle-44% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: female


title: ORSAM20586-1

source_name: skeletal-muscle-44% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: Outbred


title: ORSAM20225-1

source_name: skeletal-muscle-44% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -Metformin-rep1

value: CC042/GeniUncJ x CC040/TauUncJ)F1


title: ORSAM20578-1

source_name: skeletal-muscle-10% fat + fiber-female-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM20227-1

source_name: skeletal-muscle-10% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1


title: ORSAM20214-1

source_name: skeletal-muscle-10% fat + fiber-male-CC009/UncJ x CC013/GeniUncJ)F1 -None-rep1


title: ORSAM20202-1

source_name: skeletal-muscle-44% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -Metformin-rep1


title: ORSAM20201-1

source_name: skeletal-muscle-10% fat + fiber-male-CC075/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC075/UncJ x CC042/GeniUncJ)F1


title: ORSAM20212-1

source_name: skeletal-muscle-10% fat + fiber-male-CC043/GeniUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: Metformin


title: ORSAM16607-1

source_name: skeletal-muscle-44% fat + fiber-male-CC011/UncJ x CC005/TauUncJ)F1 -Metformin-rep1

value: male

value: CC011/UncJ x CC005/TauUncJ)F1


title: ORSAM18512-1

source_name: skeletal-muscle-10% fat + fiber-female-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: CC004/TauUncJ x CC019/TauUncJ)F1

value: 10% fat + fiber


title: ORSAM19304-1

source_name: skeletal-muscle-44% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC019/TauUncJ x CC042/GeniUncJ)F1

value: 44% fat + fiber


title: ORSAM20221-1

source_name: skeletal-muscle-44% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -Metformin-rep1


title: ORSAM9288-1

source_name: skeletal-muscle-44% fat + fiber-female-CC043/GeniUncJ x CC011/UncJ)F1 -None-rep1


title: ORSAM9276-1

source_name: skeletal-muscle-10% fat + fiber-male-CC043/GeniUncJ x CC011/UncJ)F1 -None-rep1


title: ORSAM9273-1

source_name: skeletal-muscle-10% fat + fiber-female-CC043/GeniUncJ x CC011/UncJ)F1 -None-rep1


title: ORSAM8359-1

source_name: skeletal-muscle-44% fat + fiber-female-CC011/UncJ x CC005/TauUncJ)F1 -None-rep1


title: ORSAM8346-1

source_name: skeletal-muscle-10% fat + fiber-male-CC002/UncJ x CC075/UncJ)F1 -None-rep1

value: CC002/UncJ x CC075/UncJ)F1


title: ORSAM21498-1

source_name: skeletal-muscle-10% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1

value: CC019/TauUncJ x CC075/UncJ)F1


title: ORSAM8331-1

source_name: skeletal-muscle-10% fat + fiber-female-CC011/UncJ x CC005/TauUncJ)F1 -None-rep1


title: ORSAM7385-1

source_name: skeletal-muscle-44% fat + fiber-female-CC002/UncJ x CC075/UncJ)F1 -None-rep1


title: ORSAM7382-1


title: ORSAM7373-1

source_name: skeletal-muscle-44% fat + fiber-male-CC011/UncJ x CC027/GeniUncJ)F1 -None-rep1

value: CC011/UncJ x CC027/GeniUncJ)F1


title: ORSAM6421-1


title: ORSAM20213-1

source_name: skeletal-muscle-10% fat + fiber-male-CC009/UncJ x CC013/GeniUncJ)F1 -None-rep1

value: CC009/UncJ x CC013/GeniUncJ)F1


title: ORSAM5537-1

source_name: skeletal-muscle-44% fat + fiber-female-CC011/UncJ x CC027/GeniUncJ)F1 -None-rep1

value: gastrocnemius muscle


title: ORSAM4065-1

source_name: skeletal-muscle-10% fat + fiber-male-CC011/UncJ x CC027/GeniUncJ)F1 -None-rep1


title: ORSAM23278-1

source_name: skeletal-muscle-44% fat + fiber-male-CC009/UncJ x CC013/GeniUncJ)F1 -Metformin-rep1


title: ORSAM23113-1

source_name: skeletal-muscle-10% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -Metformin-rep1


title: ORSAM22478-1

source_name: skeletal-muscle-10% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM22495-1

source_name: skeletal-muscle-44% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -Metformin-rep1

value: CC051/TauUncJ x CC060/UncJ)F1


title: ORSAM5540-1


title: ORSAM22479-1

source_name: skeletal-muscle-10% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: female


title: ORSAM22723-1

source_name: skeletal-muscle-10% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: Outbred


title: ORSAM22499-1

source_name: skeletal-muscle-10% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -Metformin-rep1


title: ORSAM22737-1

source_name: skeletal-muscle-10% fat + fiber-female-CC009/UncJ x CC013/GeniUncJ)F1 -Metformin-rep1


title: ORSAM22488-1

source_name: skeletal-muscle-44% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM21647-1

source_name: skeletal-muscle-10% fat + fiber-female-CC051/TauUncJ x CC059/TauUncJ)F1 -Metformin-rep1

value: CC051/TauUncJ x CC059/TauUncJ)F1


title: ORSAM23283-1

source_name: skeletal-muscle-10% fat + fiber-male-CC009/UncJ x CC013/GeniUncJ)F1 -Metformin-rep1


title: ORSAM23270-1

source_name: skeletal-muscle-44% fat + fiber-female-CC043/GeniUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC043/GeniUncJ x CC042/GeniUncJ)F1


title: ORSAM21640-1

source_name: skeletal-muscle-44% fat + fiber-male-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1


title: ORSAM21497-1

source_name: skeletal-muscle-10% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1


title: ORSAM21505-1

source_name: skeletal-muscle-44% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: Metformin


title: ORSAM22720-1

source_name: skeletal-muscle-10% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -Metformin-rep1


title: ORSAM21493-1

source_name: skeletal-muscle-44% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1


title: ORSAM22734-1

source_name: skeletal-muscle-10% fat + fiber-female-CC009/UncJ x CC013/GeniUncJ)F1 -None-rep1


title: ORSAM22482-1

source_name: skeletal-muscle-10% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: male


title: ORSAM20204-1


title: ORSAM20207-1

source_name: skeletal-muscle-10% fat + fiber-female-CC043/GeniUncJ x CC042/GeniUncJ)F1 -Metformin-rep1


title: ORSAM20599-1


title: ORSAM19896-1

source_name: skeletal-muscle-44% fat + fiber-female-CC004/TauUncJ x CC019/TauUncJ)F1 -Metformin-rep1


title: ORSAM23112-1

source_name: skeletal-muscle-10% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -Metformin-rep1


title: ORSAM19693-1

source_name: skeletal-muscle-44% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1

value: CC042/GeniUncJ x CC040/TauUncJ)F1


title: ORSAM19703-1

source_name: skeletal-muscle-44% fat + fiber-male-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC075/UncJ x CC042/GeniUncJ)F1


title: ORSAM19691-1


title: ORSAM19680-1

source_name: skeletal-muscle-10% fat + fiber-female-CC001/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC001/UncJ x CC042/GeniUncJ)F1

value: 10% fat + fiber


title: ORSAM22475-1

source_name: skeletal-muscle-10% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC019/TauUncJ x CC042/GeniUncJ)F1


title: ORSAM19298-1

source_name: skeletal-muscle-10% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM19142-1

source_name: skeletal-muscle-10% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1


title: ORSAM19288-1

source_name: skeletal-muscle-10% fat + fiber-female-CC075/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1


title: ORSAM19687-1

source_name: skeletal-muscle-10% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -Metformin-rep1


title: ORSAM19133-1

source_name: skeletal-muscle-44% fat + fiber-female-CC002/UncJ x CC043/GeniUncJ)F1 -Metformin-rep1

value: CC002/UncJ x CC043/GeniUncJ)F1

value: 44% fat + fiber


title: ORSAM19293-1


title: ORSAM19126-1

source_name: skeletal-muscle-10% fat + fiber-female-CC012/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1

value: CC012/GeniUncJ x CC002/UncJ)F1


title: ORSAM18781-1

source_name: skeletal-muscle-44% fat + fiber-male-CC051/TauUncJ x CC059/TauUncJ)F1 -Metformin-rep1


title: ORSAM18778-1

source_name: skeletal-muscle-10% fat + fiber-female-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1


title: ORSAM18506-1


title: ORSAM18504-1

source_name: skeletal-muscle-44% fat + fiber-female-CC012/GeniUncJ x CC002/UncJ)F1 -None-rep1


title: ORSAM18798-1

source_name: skeletal-muscle-44% fat + fiber-female-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: CC004/TauUncJ x CC019/TauUncJ)F1


title: ORSAM18513-1

source_name: skeletal-muscle-10% fat + fiber-female-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: gastrocnemius muscle


title: ORSAM18502-1


title: ORSAM18494-1

source_name: skeletal-muscle-44% fat + fiber-male-CC001/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1


title: ORSAM19122-1

source_name: skeletal-muscle-10% fat + fiber-male-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM17584-1

source_name: skeletal-muscle-44% fat + fiber-male-CC024/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1

value: CC024/GeniUncJ x CC002/UncJ)F1


title: ORSAM19884-1

source_name: skeletal-muscle-44% fat + fiber-female-CC075/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: female


title: ORSAM17583-1

value: Outbred


title: ORSAM18500-1

source_name: skeletal-muscle-10% fat + fiber-male-CC030/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1

value: CC030/GeniUncJ x CC002/UncJ)F1


title: ORSAM17575-1

source_name: skeletal-muscle-44% fat + fiber-female-CC051/TauUncJ x CC019/TauUncJ)F1 -Metformin-rep1

value: CC051/TauUncJ x CC019/TauUncJ)F1


title: ORSAM17894-1

source_name: skeletal-muscle-44% fat + fiber-female-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1

value: CC051/TauUncJ x CC059/TauUncJ)F1


title: ORSAM17205-1


title: ORSAM17206-1

source_name: skeletal-muscle-10% fat + fiber-male-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1

value: male


title: ORSAM17204-1


title: ORSAM17556-1

source_name: skeletal-muscle-44% fat + fiber-male-CC001/UncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM17203-1

source_name: skeletal-muscle-44% fat + fiber-male-CC051/TauUncJ x CC019/TauUncJ)F1 -Metformin-rep1

value: Metformin


title: ORSAM17198-1

source_name: skeletal-muscle-10% fat + fiber-male-CC051/TauUncJ x CC019/TauUncJ)F1 -Metformin-rep1


title: ORSAM17194-1

source_name: skeletal-muscle-10% fat + fiber-female-CC051/TauUncJ x CC019/TauUncJ)F1 -None-rep1


title: ORSAM17171-1

source_name: skeletal-muscle-10% fat + fiber-male-CC051/TauUncJ x CC019/TauUncJ)F1 -None-rep1


title: ORSAM16601-1

source_name: skeletal-muscle-10% fat + fiber-female-CC011/UncJ x CC005/TauUncJ)F1 -None-rep1

value: CC011/UncJ x CC005/TauUncJ)F1


title: ORSAM16608-1

source_name: skeletal-muscle-44% fat + fiber-male-CC011/UncJ x CC005/TauUncJ)F1 -Metformin-rep1


title: ORSAM16392-1

source_name: skeletal-muscle-44% fat + fiber-female-CC043/GeniUncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC043/GeniUncJ x CC042/GeniUncJ)F1


title: ORSAM18489-1

source_name: skeletal-muscle-44% fat + fiber-female-CC001/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC001/UncJ x CC042/GeniUncJ)F1


title: ORSAM17910-1

source_name: skeletal-muscle-10% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1

value: CC019/TauUncJ x CC075/UncJ)F1

value: 10% fat + fiber


title: ORSAM16625-1

source_name: skeletal-muscle-44% fat + fiber-male-CC043/GeniUncJ x CC011/UncJ)F1 -Metformin-rep1

value: CC043/GeniUncJ x CC011/UncJ)F1

value: 44% fat + fiber


title: ORSAM16274-1

source_name: skeletal-muscle-44% fat + fiber-male-CC002/UncJ x CC043/GeniUncJ)F1 -Metformin-rep1

value: CC002/UncJ x CC043/GeniUncJ)F1


title: ORSAM16603-1

source_name: skeletal-muscle-44% fat + fiber-female-CC011/UncJ x CC005/TauUncJ)F1 -Metformin-rep1

value: gastrocnemius muscle


title: ORSAM17177-1

source_name: skeletal-muscle-44% fat + fiber-male-CC051/TauUncJ x CC019/TauUncJ)F1 -None-rep1


title: ORSAM16260-1

source_name: skeletal-muscle-44% fat + fiber-female-CC011/UncJ x CC027/GeniUncJ)F1 -Metformin-rep1

value: CC011/UncJ x CC027/GeniUncJ)F1


title: ORSAM16252-1

source_name: skeletal-muscle-44% fat + fiber-male-CC030/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1


title: ORSAM15802-1

source_name: skeletal-muscle-44% fat + fiber-female-CC043/GeniUncJ x CC011/UncJ)F1 -None-rep1

value: female


title: ORSAM16259-1

source_name: skeletal-muscle-10% fat + fiber-male-CC011/UncJ x CC027/GeniUncJ)F1 -None-rep1

value: Outbred


title: ORSAM15797-1

source_name: skeletal-muscle-10% fat + fiber-female-CC001/UncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM15004-1

source_name: skeletal-muscle-44% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC019/TauUncJ x CC042/GeniUncJ)F1


title: ORSAM14980-1

source_name: skeletal-muscle-44% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: CC051/TauUncJ x CC060/UncJ)F1


title: ORSAM15002-1

source_name: skeletal-muscle-44% fat + fiber-male-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1

value: CC042/GeniUncJ x CC060/UncJ)F1


title: ORSAM15001-1

value: male


title: ORSAM14798-1

source_name: skeletal-muscle-44% fat + fiber-male-CC011/UncJ x CC027/GeniUncJ)F1 -None-rep1


title: ORSAM14795-1

source_name: skeletal-muscle-10% fat + fiber-female-CC011/UncJ x CC027/GeniUncJ)F1 -Metformin-rep1

value: Metformin