title: Lgr5-tdT rep2

data_processing:
ATAC data processing
ATAC sequencing data was analyzed as described previously (PMID: 28648363). In brief, reads were mapped to the mm10/GRCm38 genome using Bowtie2 aligner version 2.3.5.ßMACS2 was used to call peaks using the parameters µ-t $bamfile -f BAMPE -n qc/macs/$base.macs2 -q 0.01 -g mm?.ßBigwig files were generated using deepTools bamCoverage with the options µbamCoverage --binSize 10 --smoothLength 30 -p 4 --normalizeUsing RPGC --effectiveGenomeSize 2730871774 --extendReads $fragLength -b $file -of bigwig? (PMID: 24799436).ßßAll bigwig and bed files were filtered using the ENCODE Blacklist. Only peaks with P-value < 0.00001 were considered for further analyses. Proximal peaks (-2kb to 2kb relative to TSS) called by macs2 were linked/annotated to genes by ChIPseeker version 1.34.1. Then, computeMatrix and plotHeatmap functions from deepTools were used to visualize peaks.ß
Assembly: mm10/GRCm38
Supplementary files format and content: bigwig

growth_protocol: Colonic glands were isolated, treated with EDTA, and then resuspended in 30-50 ul of Matrigel (BD Bioscience) and plated in 24-well plates. WNT/R-spondin/Noggin (WRN) containing DMEM/F12 with HEPES (Sigma-Aldrich) containing 20% FBS, 1% penicillin/streptomycin and 50ng/ml recombinant mouse EGF (Life Technologies) was used for culturing ApcKO colon organoids. For the first 2-3 days after seeding, the media was also supplemented with 10 mM ROCK inhibitor Y-27632 (Sigma Aldrich) and 10 mM SB431542 (Sigma Aldrich), an inhibitor for the transforming growth factor (TGF)-? type I receptor to avoid anoikis. For passage, colon organoids were dispersed by trypsin-EDTA and transferred to fresh Matrigel. Passage was performed every 3-4 days with a 1:3?1:5 split ratio.

extract_protocol: Flow-sorted tdT+ cells (25,000 cells in duplicates) were lysed to prepare nuclear pellets which then underwent transposition with TDE1 Enzyme (Illumina, 20034197). Tagmented DNA was purified using Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) and the purified DNA was PCR amplified with NEBNext 2x MasterMix and Illumina adapters (table S4). The libraries were purified post-PCR using AMPure XP beads (Beckman Coulter). 150-bp paired-end reads were sequenced on a Novaseq instrument (Illumina).

value: flow sorted intestinal epithelial cells


title: IP_11_GDX-HFD

status: Public on Apr 03 2023

type: SRA

city: Oxford

first: Thomas

last: Monfeuga

address: Innovation Building, Old Road Campus, Roosevelt Drive

country: United Kingdom

institute: Novo Nordisk Research Centre Oxford

library_source: transcriptomic

data_processing:
Adaptor trimming with Trim Galore! (v. 0.6.4_dev)
Alignement with Salmon (v. 1.9.0) (with --noLengthCorrection argument)
Abundance data imported with Tximeta (v. 1.10) (with countsFromAbundance = "no" argument)
Assembly: GRCm38, release M23

molecule: polyA RNA

organism: Mus musculus

source_name: Microdissected hypothalami from Aldh1l1 eGFP-L10a mice

extract_protocol:
Dynabeads mRNA DIRECT Kit
QuantSeq 3’mRNA-Seq Library Prep Kit-FWD

treatment_protocol: Aldh1l1eGFP-L10a mice were fed for 4 weeks with either a chow diet or a high-fat diet (HFD), and a subset of mice were subjected to an orchiectomy ORX. TRAP-seq was performed on micro-dissected hypothalami from mice under three experimental conditions: sham-chow, sham-HFD, and ORX-HFD

tag: fraction

value: Immunoprecipitate

tag: diet

value: HFD

tag: treatment

value: GDX

tag: group


title: Lgr5-tdT rep1

city: BOSTON

first: Nilay

last: Sethi

state: Massachusetts

address: 450 Brookline Ave

country: USA

institute: DANA-FARBER CANCER INSTITUTE

library_source: genomic

molecule: genomic DNA

tag: cell line

tag: cell type


title: IP_13_Sham-HFD

value: Sham


title: K27-ccc1(4DEA)-2

city: San Francisco

first: Sujin

last: Lee

state: CA

institute: University of California San Francisco

description:
Affinity purified DNA
WCE raw file used for normalization:
WCE-SL365_S36_L004_R1_001.fastq.gz

data_processing:
ChIP-seq
Illumina adaptor removed from read 3' ends using Cutadapt
Reads were aligned to the genome with bowtie.
Analysis performed using custom scripts
Genome_build: C. neoformans CNA3
Supplementary_files_format_and_content: .bedgraph: Signal of H3K27me3 ChIP-seq of the sample normalized to the corresponding whole cell extract (WCE).

organism: Cryptococcus neoformans

source_name: Yeast

growth_protocol: Samples were inoculated from saturated starter cultures in YPAD at 30C until reaching OD 1.0 then harvested by centrifugation at 2000xg for 5 minutes.

extract_protocol:
ChIP DNA was extracted by bead beater with 0.5mm zirconia beads.  ChIP DNA was isolated by an antibody against H3K27me3 (described in PubMed ID 25533783). DNA was then isolated by incubation with SDS/proteinase K followed by column purification (Macherey-Nagel Nucleospin Gel Cleanup Columns).
NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (E7103, NEB) was used according to the product manual.

tag: strain

tag: genotype

tag: antibody


title: Adipose subcutaneous_4ca0419d-a567-4f62-b0c1-b66654b5a13b at day D3

city: Cambridge

first: Melina

last: Claussnitzer

state: MA

address: 75 Ames Street

institute: Broad Institute of MIT and Harvard

data_processing:
Generating count tables using featureCounts function (Liao, Smyth, and Shi 2013) in the Rsubread package
Normalization using DESeq2
Analysis of variance (ANOVA) in R
Genome_build: hg19
Supplementary_files_format_and_content: normalized count

molecule: total RNA

organism: Homo sapiens

source_name: Adipose subcutaneous

growth_protocol: For RNAseq, cells were seeded at 40K cells/well in 12-well dishes (Corning). Before Induction cells were cultured in proliferation medium (Basic medium consisting of DMEM-F12 1% Penicillin - Streptomycin, 33µM Biotin and 17µM Pantothenate supplemented with 0.13µM Insulin, 0.01ug/ml EGF, 0.001ug/ml FGF, 2.5%FCS). Adipogenic differentiation was induced by changing culture medium to induction medium. (Basic medium supplemented with 0.861μM Insulin, 1nM T3, 0.1μM Cortisol, 0.01mg/ml Transferrin, 1μM Rosiglitazone, 25nM Dexamethasone, 2.5nM IBMX). On day 3 of adipogenic differentiation culture medium was changed to differentiation medium (Basic medium supplemented with 0.861μM Insulin, 1nM T3, 0.1μM Cortisol, 0.01mg/ml Transferrin). Medium was changed every 3 days. Visceral-derived AMSCs were differentiated by further adding 2% FBS as well as 0.1mM oleic and linoleic acid to the induction and differentiation media.

extract_protocol: Library preparation, sequencing and reference genome alignment was carried out by the Genomics Platform at the Broad Institute. After final quality control samples were sequenced generating 50 million paired end reads per sample

treatment_protocol: We used the same differentiation media to investigate different days of differentiation under the same conditions.

tag: tissue

value: adipose

tag: depot

value: subcutaneous

tag: differentation day


title: K27-ccc1(10KRA)-2

description:
Affinity purified DNA
WCE raw file used for normalization:
WCE-SL364_S35_L004_R1_001.fastq.gz


title: SN_11_GDX-HFD

value: Supernatant


title: Adipose subcutaneous_4ca0419d-a567-4f62-b0c1-b66654b5a13b at day D8


title: SN_12_Sham-Chow

value: Chow


title: IP_10_GDX-HFD


title: Lgr5-Apcf/f-Sox9f/+-tdT rep2


title: Lgr5-Apcf/f-Sox9f/+-tdT rep1


title: SN_1_Sham-HFD


title: K27-ccc1(6KRA)-2

description:
Affinity purified DNA
WCE raw file used for normalization:
WCE-SL363_S34_L004_R1_001.fastq.gz


title: Adipose subcutaneous_4ca0419d-a567-4f62-b0c1-b66654b5a13b at day D0


title: Lgr5-Apcf/f-tdT rep2


title: Adipose subcutaneous_c5f7d40d-8f81-4d55-9969-25039c2b1bde at day D3


title: Lgr5-Apcf/f-tdT rep1


title: K27-ccc1(5DEA)-2

description:
Affinity purified DNA
WCE raw file used for normalization:
WCE-SL366_S37_L004_R1_001.fastq.gz


title: K27-ezh2∆-2

description:
Affinity purified DNA
WCE raw file used for normalization:
WCE-CK6644_S27_L004_R1_001.fastq.gz


title: IP_1_Sham-HFD


title: K27-ccc1(4KRA)-2

description:
Affinity purified DNA
WCE raw file used for normalization:
WCE-SL362_S33_L004_R1_001.fastq.gz


title: No_CM_Rux_3

city: Minneapolis

first: Kaylee

last: Schwertfeger

state: MN

address: 420 Delaware St. SE MMC 609

department: Lab Medicine and Pathology

institute: University of Minnesota

data_processing:
CHRUP pipeline (https://dl.acm.org/doi/10.1145/3332186.3333156) used to process raw sequence data
trimmomatic version 0.33 was used to clean reads for adapter contamination and low-quality sequence
HISAT2 version 2.1.0 was used to align samples
featureCounts v1.6.2 was used to count mapped reads to genes
Assembly: Mus musculus GRCm38.100
Supplementary files format and content: count table with raw count data for all genes and samples

source_name: bone marrow

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) from mouse BMDMs treated with either 4T1 CM, CM with 0.5μM ruxolitinib or CM with 0.5μM ruxolitinib and 0.8μM IKK-16
Stranded RNAseq libraries were prepared using the TruSeq RNA library kit

value: Balb/c

value: macrophages

tag: age

value: 8 weeks

value: WT


title: WT-Veh-4 [RNA-seq]

city: Chicago

first: Benjamin

middle: J

last: Weidemann

state: IL

address: 303 E. Superior St.

department: Medicine

institute: NORTHWESTERN UNIVERSITY

data_processing:
Alignment using bowtie2 (ChIP), ENCODE Pipeline (ATAC), Cellranger mkfastq and count (snATAC), STAR (RNA)
Quantification and annotation using HOMER (ChIP, ATAC), Cellranger count (snATAC), RSEM (RNA)
Differential analysis, QC, and visualization using R v4.1.0 (DESeq2, ChIPpeakAnno, Seurat, Signac, ggplot2, rtracklayer)
Rhythmic analysis of synchronized human ATAC-seq data (eJTK_Cycle)
Assembly: mm10
Supplementary files format and content: Comma-delimited raw counts file: RNA_raw_counts.csv

growth_protocol: DMEM + 15% FBS (cells), RPMI + 10% FBS or human AB serum (islets)

extract_protocol:
Omni-ATAC protocol for bulk ATAC-seq, 10X Protocol for snATAC-seq, DirectZol MicroPrep (Zymo) for RNA, AQuA HiChIP for HiChIP
10X Protocol for snATAC-seq. NEBNext Ultra II for RNA, ChIP, and HiChIP-seq. Nextera (Tn5) for ATAC-Seq

treatment_protocol: Cells synchronized using 1 hour 10 micromolar forskolin pulse

value: beta cell

value: WT-Veh


title: K27-ccc1∆-2

description:
Affinity purified DNA
WCE raw file used for normalization:
WCE-CK2308_S28_L004_R1_001.fastq.gz


title: SN_10_GDX-HFD


title: Adipose subcutaneous_4ca0419d-a567-4f62-b0c1-b66654b5a13b at day D14


title: WT-Veh-3 [RNA-seq]


title: No_CM_Rux_2


title: K27-wild type-2

description:
Affinity purified DNA
WCE raw file used for normalization:
WCE-SL372_S29_L004_R1_001.fastq.gz


title: No_CM_Rux_1


title: Adipose visceral_619f345c-9423-4a6a-9d0e-24c634afcc13 at day D3

source_name: Adipose visceral

value: visceral


title: WT-Veh-2 [RNA-seq]


title: Adipose visceral_619f345c-9423-4a6a-9d0e-24c634afcc13 at day D8


title: No_CM_2


title: K27-ccc1(9DEA)-1

description:
Affinity purified DNA
WCE raw file used for normalization:
WCE-SL367_S38_L004_R1_001.fastq.gz


title: WT-Veh-1 [RNA-seq]


title: WT-IL1B-4 [RNA-seq]


title: K27-ccc1(5DEA)-1


title: K27-ccc1-CC∆-1

description:
Affinity purified DNA
WCE raw file used for normalization:
WCE-SL369_S32_L004_R1_001.fastq.gz


title: Adipose visceral_619f345c-9423-4a6a-9d0e-24c634afcc13 at day D14


title: Adipose visceral_619f345c-9423-4a6a-9d0e-24c634afcc13 at day D0


title: CM_Rux_IKK_2


title: WT-IL1B-3 [RNA-seq]


title: Adipose subcutaneous_c5f7d40d-8f81-4d55-9969-25039c2b1bde at day D0


title: CM_Rux_IKK_3


title: WT-IL1B-1 [RNA-seq]


title: Adipose subcutaneous_619f345c-9423-4a6a-9d0e-24c634afcc13 at day D8


title: K27-ccc1(4DEA)-1


title: K27-ccc1(10KRA)-1


title: CM_Rux_IKK_1


title: Adipose subcutaneous_619f345c-9423-4a6a-9d0e-24c634afcc13 at day D3


title: Adipose subcutaneous_619f345c-9423-4a6a-9d0e-24c634afcc13 at day D14


title: K27-ccc1(6KRA)-1


title: PdxA4mut-3-36 [bulk ATAC-seq]

data_processing:
Alignment using bowtie2 (ChIP), ENCODE Pipeline (ATAC), Cellranger mkfastq and count (snATAC), STAR (RNA)
Quantification and annotation using HOMER (ChIP, ATAC), Cellranger count (snATAC), RSEM (RNA)
Differential analysis, QC, and visualization using R v4.1.0 (DESeq2, ChIPpeakAnno, Seurat, Signac, ggplot2, rtracklayer)
Rhythmic analysis of synchronized human ATAC-seq data (eJTK_Cycle)
Assembly: mm10, hg38
Supplementary files format and content: Comma-delimited normalized mouse Bulk ATAC-Seq counts file and P-values: Mm_norm_counts_ATAC.csv
Supplementary files format and content: Tab-delimited eJTK_cycle output from synchronized human Bulk ATAC-Seq: Hs_eJTK_cycle_ATAC.txt

source_name: pancreatic islet

value: pancreatic islet

value: Pdx1A4 mutant

value: 36 hours post-synchronization


title: PdxA4mut-3-48 [bulk ATAC-seq]

value: 48 hours post-synchronization


title: Rep1 input, rsc2 delta, replicate 2

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Basecalls were performed using BCL2FASTQ version 2.20
ChIP-seq reads were aligned to the sacCer3 reference genome using Bowtie version 1.2.3 using default parameters. CUT&Tag reads were aligned using Bowtie version 1.2.3 with parameters '--end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700'
Aligned reads were processed using MACS version 2.1.4 to generate signal density tracks (bigWig files) after combining biological replicates. For ChIP-seq, tracks were generated by comparing ChIP to input samples. For CUT&Tag (lacking inputs), each sample was processed on its own.
Assembly: sacCer3
Supplementary files format and content: bigWig (except for input samples)

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in yeast extract + peptone + raffinose (YPR) medium

extract_protocol:
For ChIP-seq, cells were fixed with 1% formaldehyde for 30 minutes, then quenched with glycine (125 mM) for 5 minutes. After cell lysis, chromatin was sonicated using an immersion tip sonicator. For CUT&Tag, cells were spheroplasted using Zymolase. Nuclei were processed using the CUT&Tag-IT Assay Kit from Active Motif using the manufacturer's instructions.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA kit (NEB, product number E7645). The CUT&Tag protocol results in ready to sequence libraries after the final PCR amplication step and cleanup.

treatment_protocol: Cells were induced with 2% galactose for 2 hours at 30°C

value: MATa ade2-1 his3-11::GAL10-REP1-10Myc-GAL1-3HA-REP2::HIS3  leu2-3,112  trp1  ura3-1 rsc2d::URA3  [Cir0]

tag: chip antibody

value: EZview Red Anti-c-Myc Affinity Gel (Sigma-Aldrich Cat# E6654)


title: K27-ccc1(4KRA)-1


title: CM_Rux_4h_3


title: CM_Rux_4h_2


title: PdxA4mut-2-36 [bulk ATAC-seq]


title: PdxA4mut-2-48 [bulk ATAC-seq]


title: K27-ezh2∆-1


title: No_CM_1


title: CM_Rux_4h_1


title: Adipose visceral_83b36bec-aac0-410a-9c1a-93d7cc720efe at day D8

value: adipose


title: Adipose visceral_83b36bec-aac0-410a-9c1a-93d7cc720efe at day D3


title: K27-ccc1∆-1


title: PdxA4mut-1-48 [bulk ATAC-seq]


title: CM_Rux_2h_3


title: K27-wild type-1


title: Adipose visceral_83b36bec-aac0-410a-9c1a-93d7cc720efe at day D14


title: CM_Rux_2h_2


title: Adipose visceral_83b36bec-aac0-410a-9c1a-93d7cc720efe at day D0


title: CM_3


title: No Template Control (DSP-1012500008771-F-A01)

city: Paris

first: Emilia

last: Puig Lombardi

address: 24 Boulevard du Montparnasse

department: INSERM UMR1163 - Bioinformatics Core

country: France

institute: Institut Imagine

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

data_processing:
FASTQ files were processed using the NanoString GeoMx NGS Pipeline v2.0 or v2.2
Reads were trimmed to remove low quality bases and adapter sequences
Paired end reads were aligned and stitched, and the barcode and UMI sequences were extracted. Barcodes were matched to known probe barcodes with maximum 1 mismatch allowed. Reads matching the same barcode were deduplicated by UMI. All analyses used UMI deduplicated counts to correct for any PCR amplification bias.
Segment and Probe QC with the NanoStringNCTools, GeomxTools and GeoMxWorkflows R/Bioconductor packages
Create gene-level count data and filter genes based on detection rate with the NanoStringNCTools, GeomxTools and GeoMxWorkflows R/Bioconductor packages
Differential expression analysis with the DESeq2 and RUVSeq R/Bioconductor packages
Assembly: Sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Mm_R_NGS_WTA_v1.0.pkc)
Supplementary files format and content: Excel spreadsheet with segment information, raw and normalized counts for each probe
Supplementary files format and content: Digital Count Conversion (DCC) scan attributes, one for each ROI
Supplementary files format and content: Probe Kit Configuration (PKC) file containing probe assay metadata describing the gene targets present in the data (GeoMx Mouse Whole Transcriptome)
Library strategy: Nanostring GeoMx

organism: synthetic construct

growth_protocol: All the experiments were conducted in Fgfr3N534K/+ mice (Fgfr3Asn534Lys/+), a mouse model that mimics clinical features of human hypochondroplasia (ref Loisay et al), and wild type littermates, used as controls. The mutant mice expressed the Asn534Lys mutation in exon 12 of Fgfr3 (corresponding to Asn540Lys in human) and the loxP flanked neo/STOP cassette. All mice were on a C57BL/6 background. Experiments were done using calluses of mutants and control littermates at 14-day post fracture, using the same non-stabilized mandibular fracture protocol. All samples were collected in 4% paraformaldehyde for 4 hours, fully decalcified in EDTA pH 7.4 during 72 hours and paraffin embedded. Six µm serial sections were performed, dried overnight at room temperature, and stored hermetically with dessicant at 4°C before further processing.

extract_protocol:
FFPE mouse bone samples were baked overnight at 37°C followed by 3 hours of baking at 65°C, then loaded onto a Leica Bond RX Fully Automated Research Stainer for subsequent processing steps. The processing protocol included three major steps: 1) slide baking, 2) antigen retrieval for 20min at 100°C, and 3) treatment with Proteinase K (1.0 µg/mL in 1xPBS) for 15min. Following these steps, slides were removed from the Leica Bond RX, and a cocktail of GeoMx Mouse Whole Transcriptome Atlas probes (targeting over 19,000 targets) were applied to each slide and allowed to hybridize at 37°C overnight in a humidity chamber. The following day, slides were washed, blocked, and allowed to incubate with a combination of Alexa Fluor 594 Anti-alpha smooth muscle Actin antibody (Abcam antibody ab202368; clone: 1A4) and Syto83 nucleic acid stain. Slides were stained for 1h at room temperature in a humidity chamber.
Slides were then washed and loaded onto the GeoMx instrument. On the GeoMx machine, slides were fluorescently scanned, and ROIs were manually placed in the following areas: trabecular bone and cartilage. The GeoMx device exposed ROIs to 385 nm light (UV), releasing the indexing oligos. Indexing oligos were collected with a microcapillary and deposited into a 96-well plate. Samples were dried down overnight, then resuspended in 10 µL of DEPC-treated water. PCR was performed using four µL of each sample and the oligos from each ROI were indexed using unique i5 and i7 dual-indexing systems (Illumina). PCR reactions were purified twice using AMPure XP beads (Beckman Coulter, Inc) according to the manufacturer’s protocol. Purified libraries were sequenced on an Illumina NovaSeq 6000 according to the manufacturer’s instructions, with 27x27 pair end reads.

tag: status

tag: roi

tag: roi type

tag: animal


title: CM_2


title: Adipose subcutaneous_c5f7d40d-8f81-4d55-9969-25039c2b1bde at day D8

value: subcutaneous


title: PdxA4het-3-36 [bulk ATAC-seq]

value: Pdx1 heterozygote


title: Adipose subcutaneous_83b36bec-aac0-410a-9c1a-93d7cc720efe at day D8


title: Adipose subcutaneous_83b36bec-aac0-410a-9c1a-93d7cc720efe at day D3


title: PdxA4het-2-48 [bulk ATAC-seq]


title: PdxA4het-2-36 [bulk ATAC-seq]


title: 4222GastCtrl

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

country: Germany

institute: German Diabetes Center

data_processing:
Raw Illumina paired-end reads were converted into FastQ format by executing bcl2fastq2 Conversion Software version 2.20 (Illumina, San Diego, USA). FastQ files of methylation analyses were analyzed using the Illumina Dragen® (Dynamic Read Analysis for Genomics) Bio-IT platform v 3.9.5 (Edico Genome, Illumina San Diego) on the Illumina cloud providing predesigned analyses pipelines. Paired read FastQ files were than mapped using a Hash table generated by DRAGEN Reference builder (v.3.10.4) based on the mouse genome (GRCm38.p6.genome.fa, including methylation information).
Runs were prepared and quality checked using Fast Q toolkit pipeline (v1.0.0.) with a minimum length of 32 bp adapter trimming using the TRUESEQ HT/LT adapters sequence (Illumina San Diego, USA). Settings were: trimming strength: 4 and a quality score < 10 to trim bases at 5’ and 3’ sites prior to mapping.
Paired read FastQ files were than mapped using a Hash table generated by DRAGEN Reference builder (v.3.10.4) based on the mouse genome (GRCm38.p6.genome.fa, including methylation information). Mapping was performed using the DRAGEN Methylation pipeline (version v3.9.5) for read conversion (C-to-T and G-to-A), deduplication, sorting, and alignment of bisulfite converted reference genome, genome wide methyl calling and the calculation of alignment and methylation metrics.
The outputs of sequence alignment/map files were further analyzed using the R package MethylKit (BaseSpaceLabs, provided on the Illumina cloud). CpG sites with a minimum read quality of at least 20 and a minimum read coverage of at least 5, as well as a maximum coverage of 99.9%, were considered for differential methylation analysis with >2% difference in conditions. In the single base CpG resolution analysis, methylation calls were optimized by combining methylated sites from both the forward and reverse reads. Settings were as: 5x CpG Coverage, 2% methylation difference and q value of 0.05)
Assembly: GRCm38.p6.genome.fa
Supplementary files format and content: Dragen (TM) methylation pipeline results file (txt.gz)

source_name: m. gastrocnemius

growth_protocol: C57/Bl6 male mice were bred and maintained in a regular 12h light/dark cycle (22°C ± 1°C, 50% ± 5% humidity). All mice were group housed (max. 5 mice per cage) with ad libitum access to standard chow (58% carbohydrates, 9% fat, 33% protein, R/M-H Extrudat, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water. Animal protocols were approved by the Landesamt für Natur, Umwelt und Verbraucherschutz (LANUV), NRW, Germany (81-02.04.2017.A421) and performed according to the ‘Principle of laboratory animal care’ (NIH publication No. 85-23, revised 1996) and the German law on the protection of animals.

extract_protocol:
Qiagen, Dneasy Blood & tissue Kit
500 ng of DNA were shared by ultrasound to an average length of 200 nt (Bioruptor® Pico; Diagenode SA, Seraing, Belgium). DNA was then processed in two steps and subsequently analyzed by Next-Generation Sequencing. First, sample complexity was reduced by enrichment of DNA fragments with methylated cytosines using the EpiXplore™ Methylated DNA Enrichment Kit (Takara Bio Inc., Japan). Next, to facilitate the direct identification of methylated Cs, enriched methylated DNA fragment were subjected to TET mediated enzymatic conversion of unmethylated cytosines and subsequent library preparation using NEBNext® Enzymatic Methyl-seq Kit (NewEngland BioLabs® Inc.) according to manufacturer's instructions. Libraries were paired-end sequenced on the NextSeq550™ instrument with automated FastQ raw data analyses (Illumina, San Diego, USA).

treatment_protocol: The mice were stressed with our Cvs protocol as previously described (doi:https://doi.org/10.1016/j.molmet.2018.06.012). In brief,  the  Cvs protocoll consists of five different stressors (warm swim, cold exposure, shaking, restraint and overnight isolation) applied in a random manner 2 per day for 15 days.

value: m. gastrocnemius

tag: Sex

value: male

value: Ctrl


title: Adipose subcutaneous_83b36bec-aac0-410a-9c1a-93d7cc720efe at day D0


title: Adipose subcutaneous_83b36bec-aac0-410a-9c1a-93d7cc720efe at day D14


title: 4219GastCtrl

tag: treatment


title: Adipose subcutaneous_619f345c-9423-4a6a-9d0e-24c634afcc13 at day D0


title: CK6

city: Hangzhou

first: Ling

last: Chen

address: 12 Lingyin Road

country: China

institute: Zhejiang Hospital

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 14

data_processing:
First, Oligo(dT) magnetic beads were used to separate the mature mRNA from total RNA. Then, the fragmented mRNA was set as template for the synthesis of the first and second strands of cDNA. After being purified, the cDNA was subjected to PCR amplification, and the cDNA library was obtained accordingly. Finally, Illumina Novaseq 6000 was used for RNA sequencing after quality inspection of the obtained library. The statistical power of this experimental design, calculated inRNASeqPower is 0.88, based on an average sequencing depth of 117X, CV of 0.4.
FASTP was used for quality control on the original FASTQ data. HISAT2 was applied to compare the data after quality control to reference genome (GRCm39). VM28 GTF file was obtained from GENCODE, and raw Read Counts were obtained by tSEQ-count.
Assembly: GRCm39
Supplementary files format and content: count

source_name: Mouse liver tissue, Acute liver failure, Control group

growth_protocol: Normal healthy C57BL/6 male mice weighing 21.5-25 g at 5-6 weeks of age were acclimatised for one week prior to the experiment and all were allowed free access to food and water throughout the period of domestication and experimentation. Mice were housed in cages at 22±2°C with a 12 h light/dark cycle.

extract_protocol:
After the mice were killed, their liver tissues were removed and the RNA in the tissues was extracted for sequencing by the experimental Trizol method.
First, Oligo(dT) magnetic beads were used to separate the mature mRNA from total RNA. Then, the fragmented mRNA was set as template for the synthesis of the first and second strands of cDNA. After being purified, the cDNA was subjected to PCR amplification, and the cDNA library was obtained accordingly. Finally, Illumina Novaseq 6000 was used for RNA sequencing after quality inspection of the obtained library. The statistical power of this experimental design, calculated inRNASeqPower is 0.88, based on an average sequencing depth of 117X, CV of 0.4.

treatment_protocol: The mice in the model group were injected intraperitoneally with LPS (10 μg/kg) and D-GalN (300 mg/kg), while mice in the control group were injected with normal saline.

value: liver

tag: disease state

value: healthy control

value: The mice were injected with normal saline

tag: time

value: The mice were executed 24 hours after such injection by neck-stripping method, and their liver tissues were collected for subsequent testing.


title: 4221GastCtrl


title: 4220GastCtrl


title: CM_1

value: Balb/c

value: macrophages

value: 8 weeks

value: WT


title: PdxA4mut-1-36 [bulk ATAC-seq]

value: pancreatic islet

value: Pdx1A4 mutant

value: 36 hours post-synchronization


title: CK5

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 13


title: 4218GastCtrl


title: PdxA4het-3-48 [bulk ATAC-seq]

value: 48 hours post-synchronization


title: Adipose visceral_050fd597-279f-4d7d-a250-68a6df216da6 at day D3

value: adipose

value: visceral


title: 4210GastCvs

value: m. gastrocnemius

value: CVS


title: PdxA4het-1-48 [bulk ATAC-seq]

value: Pdx1 heterozygote


title: CK4

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 12

value: liver

value: male


title: Adipose visceral_050fd597-279f-4d7d-a250-68a6df216da6 at day D14


title: scATAC_Mut2

description:
Mm_scATAC.rds
Mm_peak_matrix.h5
Mm_fragments.tsv.gz

data_processing:
Alignment using bowtie2 (ChIP), ENCODE Pipeline (ATAC), Cellranger mkfastq and count (snATAC), STAR (RNA)
Quantification and annotation using HOMER (ChIP, ATAC), Cellranger count (snATAC), RSEM (RNA)
Differential analysis, QC, and visualization using R v4.1.0 (DESeq2, ChIPpeakAnno, Seurat, Signac, ggplot2, rtracklayer)
Rhythmic analysis of synchronized human ATAC-seq data (eJTK_Cycle)
Assembly: mm10, hg38
Supplementary files format and content: scATAC 10X Cellranger h5 compressed peak matrix: Hs_peak_matrix.h5, Mm_peak_matrix.h5
Supplementary files format and content: scATAC 10X Cellranger single-cell metadata (*metadata*.csv)
Supplementary files format and content: scATAC 10X Cellranger tab-delimited fragments file (*fragments*.tsv)
Supplementary files format and content: Seurat R data structure files: Hs_scATAC.rds, Mm_scATAC.rds


title: CK3

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 11

value: healthy control

value: The mice were injected with normal saline


title: 4209GastCvs


title: CK2

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 10

value: The mice were executed 24 hours after such injection by neck-stripping method, and their liver tissues were collected for subsequent testing.


title: scATAC_Mut1


title: WT-PDX1-HiChIP-2

data_processing:
library strategy: HiChIP-Seq
Alignment using bowtie2 (ChIP), ENCODE Pipeline (ATAC), Cellranger mkfastq and count (snATAC), STAR (RNA)
Quantification and annotation using HOMER (ChIP, ATAC), Cellranger count (snATAC), RSEM (RNA)
Differential analysis, QC, and visualization using R v4.1.0 (DESeq2, ChIPpeakAnno, Seurat, Signac, ggplot2, rtracklayer)
Rhythmic analysis of synchronized human ATAC-seq data (eJTK_Cycle)
Assembly: mm10
Supplementary files format and content: bigWig files (*.bw.gz)
Supplementary files format and content: HiCPro validPair files (*.validPairs)
Supplementary files format and content: Homer peak files (*peaks.txt)

tag: cell line

tag: cell type

value: beta cell


title: siPDX1-p65-2 ChIP-seq

data_processing:
Alignment using bowtie2 (ChIP), ENCODE Pipeline (ATAC), Cellranger mkfastq and count (snATAC), STAR (RNA)
Quantification and annotation using HOMER (ChIP, ATAC), Cellranger count (snATAC), RSEM (RNA)
Differential analysis, QC, and visualization using R v4.1.0 (DESeq2, ChIPpeakAnno, Seurat, Signac, ggplot2, rtracklayer)
Rhythmic analysis of synchronized human ATAC-seq data (eJTK_Cycle)
Assembly: mm10
Supplementary files format and content: bigWig files (*.bw.gz)
Supplementary files format and content: HiCPro validPair files (*.validPairs)
Supplementary files format and content: Homer peak files (*peaks.txt)

tag: genotype

value: Pdx1 siRNA


title: 4206GastCvs


title: M6

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 6

source_name: Mouse liver tissue, Acute liver failure, Model group

value: acute liver failure

tag: strain

value: The mice were injected intraperitoneally with LPS (10 ug/kg) and D-GalN (300 mg/kg)


title: Adipose visceral_050fd597-279f-4d7d-a250-68a6df216da6 at day D0

tag: tissue


title: WAT_atac_rep1

city: Berlin

first: Julia

last: Polansky

address: Augustenburger Platz 1

institute: Charité - Universitätsmedizin Berlin

data_processing:
Reads were trimmed with BBMap 35.58
Reads were aligned with BWA-MEM 0.7.15 with default parameters
Duplicated reads were filtered with Picard 2.20.4
bigwig files were generated with Deeptools 3.3.0 by normalizing counts per million in 10 bp bins. ENCODE DAC blacklisted regions were removed.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: WAT MSC

extract_protocol:
5 x 10E5 cells were lysed using the lysis buffer described in Buenrostro et al 2015.
Libraries were generated following Buenstro et al 2015 using Illumina/Nextera adapters and size selected (100-1000bp) with AMPure Beads (Beckman Coulter).

value: WAT-derived mesenchymal stromal cell


title: siPDX1-p65-1 ChIP-seq

value: WT

tag: antibody


title: Adipose subcutaneous_050fd597-279f-4d7d-a250-68a6df216da6 at day D14

tag: depot

value: subcutaneous

tag: differentation day


title: Adipose subcutaneous_050fd597-279f-4d7d-a250-68a6df216da6 at day D3

value: adipose


title: M4

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 4


title: 4207GastCvs


title: scATAC_Con1

value: pancreatic islet


title: PdxA4het-1-36 [bulk ATAC-seq]

value: 36 hours post-synchronization


title: M5

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 5


title: M8

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 8


title: CK1

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 9


title: WAT_atac_rep3


title: M7

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 7


title: WAT_atac_rep2


title: 4208GastCvs

value: m. gastrocnemius

value: CVS


title: scATAC_Con2

value: Pdx1 heterozygote


title: UC_atac_rep2

source_name: UC MSC

value: umbilical cord-derived mesenchymal stromal cell


title: Adipose subcutaneous_050fd597-279f-4d7d-a250-68a6df216da6 at day D0


title: siPDX1-input


title: WT-PDX1-HiChIP-1


title: M3

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 3

value: liver

value: male


title: CCl4-induced liver fibrosis for 8 weeks, biological rep3

type: RNA

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description: Gene expression of mouse fibrose liver 8 weeks after CCl4 induction

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 8, from SAS. Gene expression profiling was performed using arrays of Mogene-2_0 type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: Fibrosed liver,  8 weeks of CCl4 injections, biological replicate no 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: CCl4-induced fibrosis is described in https://doi.org/10.21203/rs.3.rs-2009380/v1

extract_protocol: Total liver RNA isolation was performed using InviTrap®Spin Universal RNA Mini Kit from Stratec (1060100300, Birkenfeld, Germany) according to the manufacturer's instructions.

treatment_protocol: Mice were subjected to 1.6 g/kg CCl4 i.p. twice/week. Then two days after last CCl4 injection mice were sacrificed and liver was harvested

value: Liver

tag: gentoype

tag: age


title: CCl4-induced liver fibrosis for 10 weeks, biological rep3

description: Gene expression of mouse fibrose liver 10 weeks after CCl4 induction

source_name: Fibrosed liver,  10 weeks of CCl4 injections, biological replicate no 3


title: CCl4-induced liver fibrosis for 10 weeks, biological rep2

source_name: Fibrosed liver,  10 weeks of CCl4 injections, biological replicate no 2


title: UC_atac_rep1


title: M2

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 2

value: The mice were executed 24 hours after such injection by neck-stripping method, and their liver tissues were collected for subsequent testing.


title: siCon-p65-2 ChIP-seq

value: beta cell

value: control siRNA


title: M1

description:
The average sequencing depth was 117X, CV was 0.4, and RNA-seqpower was 0.88
Sample 1

value: acute liver failure

value: The mice were injected intraperitoneally with LPS (10 ug/kg) and D-GalN (300 mg/kg)


title: siCon-p65-1 ChIP-seq

value: WT


title: ATACseq.RevScapTKO.KC.ZT22.req3

city: Houston

first: Dongyin

last: Guan

address: 1 Baylor Plaza, ABBR

institute: Baylor College of Medicine

data_processing:
The ATAC-seq analysis pipeline developed by Anshul Kundaje (Stanford University, Stanford, CA, USA) (https://github.com/kundajelab/atac_dnase_pipelines) was applied. For each sample, adapters were trimmed and aligned to the mouse genome mm9 with Bowtie. The The ATAC-seq analysis pipeline developed by Anshul Kundaje (Stanford University, Stanford, CA, USA) (https://github.com/kundajelab/atac_dnase_pipelines) was applied. For each sample, adapters were trimmed and aligned to the mouse genome mm9 with Bowtie. The aligned bam files of biological replicates were then merged and subjected to peak calling of open chromatin regions. The tag directories were established, and normalized read counts were measured using Homer.aligned bam files of biological replicates were then merged and subjected to peak calling of open chromatin regions. The tag directories were established, and normalized read counts were measured using Homer.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include all peaks of nucleosome free region (NFR)

source_name: liver

extract_protocol:
50,000 isolated KCs were resuspended in 50 μl of transposase mixture (25 μl of 2× TD buffer, 2.5ul of TDE1, 0.5 ul of 1% digitonin, and 22 ul of nuclease-free water) (15027865, Illumina). Transposition reactions were incubated at 37 °C for 30 min in an Eppendorf Thermo Mixer with agitation at 300 rpm. Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit (28204), and purified DNA was eluted in 10 ul of elution buffer (10 mM Tris-HCl, pH 8).
Transposed fragments were amplified and purified as described previously (PMID: 25559105).

value: Liver macrophage

value: Reverb/ScaphTKO

tag: diet

value: 4-week high fat and sucrose diet, D12492i


title: siCon-input


title: ATACseq.RevScapTKO.KC.ZT22.req2


title: cartilage_WT (DSP-1012500008771-F-C09)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

source_name: cartilage

value: cartilage

tag: status

tag: roi

tag: roi type

value: Full


title: BM_atac_rep2

source_name: BM MSC

value: bone marrow-derived mesenchymal stromal cell


title: FB_atac_rep1

source_name: FB

value: skin fibroblasts


title: ATACseq.RevScapTKO.KC.ZT22.req1

tag: Sex


title: cartilage_WT (DSP-1012500008771-F-C06)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

tag: animal


title: FB_atac_rep2


title: CCl4-induced liver fibrosis for 10 weeks, biological rep1

source_name: Fibrosed liver,  10 weeks of CCl4 injections, biological replicate no 1


title: FB_atac_rep3


title: BM_atac_rep3


title: CCl4-induced liver fibrosis for 6 weeks, biological rep2

description: Gene expression of mouse fibrose liver 6 weeks after CCl4 induction

source_name: Fibrosed liver,  6 weeks of CCl4 injections, biological replicate no 2


title: BM_atac_rep1


title: CCl4-induced liver fibrosis for 4 weeks, biological rep3

description: Gene expression of mouse fibrose liver 4 weeks after CCl4 induction

source_name: Fibrosed liver,  4 weeks of CCl4 injections, biological replicate no 3


title: CCl4-induced liver fibrosis for 6 weeks, biological rep3

source_name: Fibrosed liver,  6 weeks of CCl4 injections, biological replicate no 3


title: ATACseq.RevScapTKO.KC.ZT10.req3


title: CCl4-induced liver fibrosis for 8 weeks, biological rep1

source_name: Fibrosed liver,  8 weeks of CCl4 injections, biological replicate no 1


title: CCl4-induced liver fibrosis for 6 weeks, biological rep1

source_name: Fibrosed liver,  6 weeks of CCl4 injections, biological replicate no 1


title: bone_WT (DSP-1012500008771-F-C05)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

source_name: bone

value: bone


title: bone_WT (DSP-1012500008771-F-C08)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: cartilage_WT (DSP-1012500008771-F-C04)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: ATACseq.RevScapTKO.KC.ZT10.req2

value: liver


title: WAT_H3K27ac_rep3

data_processing:
Reads were trimmed with BBMap 35.58
Reads were aligned with BWA-MEM 0.7.15 with default parameters
Duplicated reads were filtered with Picard 2.20.4
Peaks were called with MACS2 2.2.7 on default settings with the removal of ENCODE hg19 black listed regions. Narrow peaks were called for H3K27ac and H3K4me3, while broad peaks were called for H3K4me1.
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 peak files

source_name: WAT

extract_protocol:
5-10x10^6 cells were digested with Trypsin–EDTA 0.05% (Gibco) for 10 min at 37 °C. The cells were mixed with 10% FCS–PBS, and a single-cell suspension was obtained using a 40-µm cell strainer. Following centrifugation, cells were resuspended in 10% FCS-PBS solution and fixed in 1% paraformaldehyde (PFA) for 10 min at room temperature and the reaction quenched on ice with 2.5M glycine (Merck) and centrifuged at 400g for 8min. Pelleted cells were then resuspended in lysis buffer (50 mM Tris, pH 7.5; 150 mM NaCl; 5 mM EDTA; 0.5% NP-40; 1.15% Triton X-100; protease inhibitors (Roche), 5mM Na-butarate), and nuclei were pelleted again by centrifugation at 750g for 5min. For sonication, nuclei were resuspended in sonication buffer (10 mM Tris–HCl, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0,1% Na-deoxycholate; 0.5% N-lauroylsarcosine; protease inhibitors (Roche complete), 5mM Na-butarate). Chromatin was sheared using a Diagenode Bioruptor (35-40 cycles with a 30sec on/off pulse and HI power mode) until reaching a fragment size of 200–500 base pairs (bp). Lysates were clarified from sonicated nuclei, and protein–DNA complexes were immunoprecipitated overnight at 4 °C with the respective antibody. A total of 10–15 μg chromatin was used for each replicate of histone ChIP. The immunoprecipitation was performed in 1200µl precipitation buffer (10 mM Tris–HCl, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0,1% Na-deoxycholate; 0.5% N-lauroylsarcosine; protease inhibitors (Roche complete), 5mM Na-butarate, 1% Triton X-100). One of the following antibodies was used for the immunoprecipitation: Anti-H3K27ac (Diagenode c15410174; lot A7071-001P; dilution 1:500), anti-H3K4me1 (Abcam ab8895; lot GR141677-1; dilution 1:1200), anti-H3K4me3 (Millipore 07-473; lot 3191394; dilution 1:800).
Sequencing libraries were prepared using standard Nextera adapters (Illumina) according to the supplier’s recommendations.

value: white adipose derived mesenchymal stromal cells

tag: chip antibody

value: Anti-H3K27ac (Diagenode c15410174)

tag: donor id


title: bone_WT (DSP-1012500008771-F-C07)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: CCl4-induced liver fibrosis for 8 weeks, biological rep2

source_name: Fibrosed liver,  8 weeks of CCl4 injections, biological replicate no 2

value: Liver


title: CCl4-induced liver fibrosis for 4 weeks, biological rep2

source_name: Fibrosed liver,  4 weeks of CCl4 injections, biological replicate no 2


title: WAT_H3K27ac_rep2

tag: cell type


title: ATACseq.RevScapTKO.KC.ZT10.req1

value: male

tag: genotype


title: bone_WT (DSP-1012500008771-F-C03)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: cartilage_WT (DSP-1012500008771-F-C02)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: ATACseq.RevDKO.KC.ZT22.req3

tag: strain

value: ReverbhDKO


title: ATACseq.RevDKO.KC.ZT22.req2

tag: tissue


title: CCl4-induced liver fibrosis for 4 weeks, biological rep1

source_name: Fibrosed liver,  4 weeks of CCl4 injections, biological replicate no 1


title: WAT_H3K4me3_rep2

value: anti-H3K4me3 (Millipore 07-473)


title: ATACseq.RevDKO.KC.ZT22.req1


title: cartilage_WT (DSP-1012500008771-F-C01)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: WAT_H3K27ac_rep1


title: WAT_H3K4me3_rep3


title: cartilage_WT (DSP-1012500008771-F-B12)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: CCl4-induced liver fibrosis for 2 weeks, biological rep3

description: Gene expression of mouse fibrose liver 2 weeks after CCl4 induction

source_name: Fibrosed liver,  2 weeks of CCl4 injections, biological replicate no 3


title: WAT_H3K4me1_rep2

value: anti-H3K4me1 (Abcam ab8895)


title: WAT_H3K4me3_rep1


title: ATACseq.RevDKO.KC.ZT10.req2


title: WAT_H3K4me1_rep1


title: Input, 5

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

data_processing:
Fastq files were downloaded from Illumina's BaseSpace for analysis.
Quality control (QC) of the raw sequence data was performed using FastQC for each sequencing sample
The majority of the trailing G's were removed at the ends of the sequences as well as the transposon sequence CATAACTTCTTTTACGTTTCCGCC.
Trimmed reads were then aligned to the P. gingivalis genome ATCC 33277 (accession NC_009785.1) using STAR aligner.
For the analysis using DESeq2, raw insertion counts for every genomic position were obtained from parsing the STAR aligned bam format files
Assembly: NC_009785.1
Supplementary files format and content: tab-delimited text files with raw insertion counts at each genomic position for each sample
Supplementary files format and content: Matrix table with raw insertion counts for every genomic position and every sample collated into one file

organism: Streptococcus gordonii

source_name: Culture

growth_protocol: A saturating transposon library using a EZ-Tn5-based transposon was created by transposon mutagenesis in Streptococcus gordonii DL1 strain.

extract_protocol:
DNA isolation was performed with the Wizard genomic DNA isolation kit (Promega). A total of 5 μg of DNA suspended in 130 μl of TE were sheared by sonication (Covaris) to an average size of 300 bp and then purified and concentrated using a PCR cleanup kit (NEB Monarch) according to the manufacturer’s instructions. Poly-C tails were added to sheared DNA using 1 μg DNA, 15 units TdT enzyme, dCTP (475 μM final concentration), and ddCTP (25 μM final concentration) in a total volume of 40 μl for 1 h at 37°C followed by 75°C for 20 min. DNA was purified using the Monarch PCR cleanup kit according to the manufacturer’s instructions. DNA adjacent to each transposon insertion site was amplified by PCR using one primer targeting the poly-C tail (poly G primer, Table S3), and one targeting the end of the transposon (Tn end primer, Table S3). For PCR, 2.5 units of AccuPrime Pfx DNA polymerase (ThermoFisher), 1.5 μl of each primer (20 µM), and 250 ng template were used in a 50 µl reaction. Cycling conditions were 95°C for 2 min followed by 24 cycles of 95°C for 15 sec, 55°C for 30 sec, and 68°C for 2 min. A final 2 min extension at 68°C was also performed. PCR reactions were run on a 1.5% agarose gel and a range from 250-1000 bp was excised and purified using a gel extraction kit (NEB). Barcodes and primer sites for next-generation sequencing (Illumina) were added according to the manufacturer’s protocol.
Single-end sequencing was performed on an Illumina Nextseq 500/550 75-cycle High Output Kit v2 (Illumina) at the University of Louisville Center for Genetics and Molecular Biology.

treatment_protocol: This library was inoculated either alone (Sg) or in conjunction with Porphyromonas gingivalis (PgSg) subcutaneously into BALB/cJ mice. Bacteria recovered from developed abscesses were inoculated and cultured in vitro anaerobically until turbid and genomic DNA was isolated. Isolated genomic DNA from the S. gordonii transposon library (Input) grown in vitro was not used to infect mice and instead used as a control.

value: Culture

tag: group

value: S. gordonii transposon library (Input)

tag: coinfection

value: No


title: Control at 10 weeks, biological rep3

description: Gene expression of liver from control healthy mouse

source_name: Control liver, healthy,10 weeks, biological replicate no 3


title: ATACseq.RevDKO.KC.ZT10.req1

source_name: liver

value: Liver macrophage

value: 4-week high fat and sucrose diet, D12492i


title: bone_WT (DSP-1012500008771-F-B10)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

value: WT

value: Full


title: WAT_input_rep3


title: cartilage_WT (DSP-1012500008771-F-B09)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

source_name: cartilage

value: cartilage


title: Input, 4


title: CCl4-induced liver fibrosis for 2 weeks, biological rep1

source_name: Fibrosed liver,  2 weeks of CCl4 injections, biological replicate no 1


title: ATACseq.Control.KC.ZT22.req3

value: Control


title: WAT_input_rep2


title: bone_WT (DSP-1012500008771-F-B08)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

value: bone


title: Input, 2


title: WAT_input_rep1

value: white adipose derived mesenchymal stromal cells


title: ATACseq.Control.KC.ZT22.req2

value: liver


title: CCl4-induced liver fibrosis for 2 weeks, biological rep2

source_name: Fibrosed liver,  2 weeks of CCl4 injections, biological replicate no 2

value: Liver


title: ATACseq.Control.KC.ZT22.req1

value: male


title: cartilage_WT (DSP-1012500008771-F-B06)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: ATACseq.RevDKO.KC.ZT10.req3

value: ReverbhDKO


title: UC_H3K27ac_rep3

source_name: UC

value: umbilical cord derived mesenchymal stromal cells

value: Anti-H3K27ac (Diagenode c15410174)


title: Control at 10 weeks, biological rep2

source_name: Control liver, healthy,10 weeks, biological replicate no 2


title: Control at 10 weeks, biological rep1

source_name: Control liver, healthy,10 weeks, biological replicate no 1


title: bone_mutant (DSP-1012500008771-F-B05)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

value: Mutant


title: PgSg, 5

source_name: Mouse abscess

value: Mouse abscess

value: Pg + Sg

value: Yes


title: Input, 1

value: Culture

value: S. gordonii transposon library (Input)

value: No


title: ATACseq.Control.KC.ZT10.req2

value: Liver macrophage

value: 4-week high fat and sucrose diet, D12492i


title: UC_H3K27ac_rep2


title: ATACseq.Control.KC.ZT10.req3

value: Control


title: cartilage_mutant (DSP-1012500008771-F-B04)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

value: cartilage

value: Full


title: PgSg, 4


title: UC_H3K27ac_rep1


title: bone_mutant (DSP-1012500008771-F-B03)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

value: bone


title: ATACseq.Control.KC.ZT10.req1

value: liver

value: male


title: bone_mutant (DSP-1012500008771-F-B02)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: RNAseq.RevScapTKO.KC.ZT22.req3

data_processing:
RNA-seq reads were aligned to the University of California, Santa Cruz (UCSC) mm9 genome browser using STAR. The tag directories were established and normalized read counts were measured with RefSeq genes using Homer.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include tag counts for each Sample

extract_protocol:
Total RNA was extracted from liver tissue or isolated endothelial cells and kupffer cells using Trizol reagent followed by RNeasy Mini Kit (#74104).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Reverb/ScaphTKO


title: PgSg, 3


title: PgSg, 2


title: UC_H3K4me3_rep2

value: umbilical cord derived mesenchymal stromal cells

value: anti-H3K4me3 (Millipore 07-473)


title: UC_H3K4me3_rep3


title: bone_WT (DSP-1012500008771-F-B07)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

value: WT


title: RNAseq.RevScapTKO.KC.ZT22.req2


title: cartilage_mutant (DSP-1012500008771-F-B01)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

value: Mutant


title: UC_H3K4me3_rep1


title: PgSg, 1

value: Mouse abscess

value: Pg + Sg

value: Yes


title: bone_mutant (DSP-1012500008771-F-A12)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: RNAseq.RevScapTKO.KC.ZT22.req1


title: Sg, 5

value: Sg only

value: No


title: RNAseq.RevScapTKO.KC.ZT16.req2

value: Liver macrophage

value: 4-week high fat and sucrose diet, D12492i


title: UC_H3K4me1_rep2

value: anti-H3K4me1 (Abcam ab8895)


title: Sg, 3


title: UC_input_rep3


title: UC_H3K4me1_rep1


title: cartilage_mutant (DSP-1012500008771-F-A11)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

value: cartilage

value: Full


title: RNAseq.RevScapTKO.KC.ZT16.req1

value: liver


title: bone_mutant (DSP-1012500008771-F-A10)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

value: bone


title: cartilage_mutant (DSP-1012500008771-F-A09)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: Sg, 2


title: Sg, 1


title: cartilage_mutant (DSP-1012500008771-F-A08)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: UC_input_rep1


title: bone_mutant (DSP-1012500008771-F-A07)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc


title: Batch1_AP_combination_rep3

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description: sample 1-3-6

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

growth_protocol: Human non-small cell lung cancer cells (NSCLC) line, A549 (CCL-185) was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). The cells were maintained in RPMI 1640 medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 5% CO2 incubator. A549 cells were subcultured every 3 or 4 days, depending on the cell density.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: Roswell Park Memorial Institute (RPMI) 1640 medium, phosphate-buffered saline (PBS), TrypLE Express, penicillin-streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO) and QIAzol lysis reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA) and Qiagen (Germantown, MD, USA), respectively. The Ez-Cytox cell viability assay kit was purchased from Dogen Bio (Seoul, Korea). Oleanolic acid (CFN98800), hederagenin (CFN98695), and gallic acid (CFN99624) were purchased from ChemFace (Wuhan, Hubei, China) and all compounds had purities ≥ 98%. The compounds were dissolved at 20 mM in DMSO and stored at –20 °C until use. Before drug treatment, 20 mM drug solutions were diluted to 100 and 200 μM with PBS, filtered through a 0.22-μm membrane syringe filter (Sartorius, Goettingen, Germany). PBS with 2% DMSO was used as the vehicle. One day before drug treatment, A549 cells were plated at 3 × 105 cells/well in a 6-well plate containing 3 mL growth medium. The cells were exposed to 5 or 10 μM by treatment with 150 uL of 100 or 200 μM diluted drug per well. There was no cytotoxicity when treated with a high dose (10 μM) in all drugs, and it was confirmed using the Ez-cytox cell viability assay kit. After 24 h of drug treatment, the cells were washed three times with ice-cold PBS. The total cell lysate was prepared with add QIAzol lysis reagent and stored in a -70 °C deep freezer until RNA extraction.

tag: cell line

tag: treatment

value: combination of albiflorin 5 uM and paeoniflorin 5 uM

tag: time


title: FB_H3K27ac_rep3

source_name: FB

value: skin fibroblasts

value: Anti-H3K27ac (Diagenode c15410174)


title: RNAseq.RevScapTKO.KC.ZT16.req3

value: male

value: Reverb/ScaphTKO

tag: diet


title: cartilage_mutant (DSP-1012500008771-F-A06)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

tag: status

value: Mutant


title: FB_H3K27ac_rep2


title: RNAseq.RevScapTKO.KC.ZT4.req3


title: RNAseq.RevScapTKO.KC.ZT4.req2


title: bone_mutant (DSP-1012500008771-F-A05)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

source_name: bone

tag: roi


title: Batch1_Paeoniflorin_rep3

description: sample 1-3-5

value: Paeoniflorin 10 uM


title: FB_H3K27ac_rep1


title: FB_H3K4me3_rep3

value: anti-H3K4me3 (Millipore 07-473)


title: Batch1_Albiflorin_rep3

description: sample 1-3-4

value: Albiflorin 10 uM


title: cartilage_mutant (DSP-1012500008771-F-A04)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

tag: roi type


title: RNAseq.RevScapTKO.KC.ZT4.req1

tag: Sex


title: Sg, 4

value: Mouse abscess

value: Sg only

value: No


title: UC_input_rep2

value: umbilical cord derived mesenchymal stromal cells


title: RNAseq.RevScapTKO.KC.ZT10.req2

value: Liver macrophage

value: 4-week high fat and sucrose diet, D12492i


title: RNAseq.RevDKO.KC.ZT22.req3

value: liver

value: ReverbhDKO


title: FB_H3K4me3_rep2


title: FB_H3K4me3_rep1


title: cartilage_mutant (DSP-1012500008771-F-A02)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

value: cartilage

value: Full

tag: animal


title: Batch1_Vehicle(DMSO)_rep3

description: sample 1-3-1

value: 0.1% DMSO


title: RNAseq.RevScapTKO.KC.ZT10.req3

value: male


title: RNAseq.RevDKO.KC.ZT22.req2


title: 8Mo naïve (M), C57BL/6 control CC, rep 3

city: College Station

first: Jianrong

last: Li

address: VBEC Receiving, VICI Bldg Rm127, 4458 TAMUS

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

description:
CC-12
Supple_Chronic_Expression Data-CC-12

data_processing:
Acute (Illumina HiSeq 2500 used for base calling) Chronic (Illumina NovaSeq 6000 for base calling)
Reads were mapped to the mouse genome (GRCm38/mm10) using TopHat version 2.0.13 with default settings.
DEseq2 normalized fold-changes of all samples were done using DESeq2 and were then used to estimate differential gene expression between samples.
Assembly: mm10
Supplementary files format and content: Excel files include log-transformed values

source_name: brain corpus callosum

extract_protocol:
Mice were anesthetized followed by transcardial perfusion with 20mL of sterile PBS (Kim et al., 2012, Steelman et al., 2012). The brain was removed, and the corpus callosum, cortex, and hippocampus were microdissected. Each piece of tissue was flash frozen in liquid nitrogen and stored at -80°C until use. RNA was extracted with Tri Reagent.
Messenger RNA sequencing libraries were prepared using the TruSeq Stranded mRNA library preparation kit (Illumina). Libraries were pooled and sequenced on a one hundred fifty  base pair, paired-end sequencing run on an Illumina NovaSeq 6000.

value: brain corpus callosum

value: M

value: wild type

value: untreated-Chronic

tag: treatment period


title: RNAseq.RevScapTKO.KC.ZT10.req1

value: Reverb/ScaphTKO


title: Batch1_Albiflorin_rep2

description: sample 1-2-4

value: Albiflorin 10 uM


title: RNAseq.RevDKO.KC.ZT22.req1


title: FB_H3K4me1_rep3

value: skin fibroblasts

tag: chip antibody

value: anti-H3K4me1 (Abcam ab8895)

tag: donor id


title: FB_H3K4me1_rep2

tag: cell type


title: bone_mutant (DSP-1012500008771-F-A03)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

value: bone

value: Mutant


title: 8Mo naïve (F), C57BL/6 control CC, rep 1

description:
CC-10
Supple_Chronic_Expression Data-CC-10

tag: strain

value: F

tag: genotype


title: Batch1_AP_combination_rep1

description: sample 1-1-6

value: combination of albiflorin 5 uM and paeoniflorin 5 uM


title: RNAseq.RevDKO.KC.ZT16.req3

tag: tissue

value: liver

value: Liver macrophage

value: ReverbhDKO

value: 4-week high fat and sucrose diet, D12492i


title: Batch1_Vehicle(DMSO)_rep2

description: sample 1-2-1

value: 0.1% DMSO


title: Batch1_AP_combination_rep2

description: sample 1-2-6


title: Batch1_Paeoniflorin_rep2

description: sample 1-2-5

value: Paeoniflorin 10 uM


title: FB_input_rep3


title: CPZ-12+12wk-1 (F), C57BL/6, CC, rep 2

description:
CC-9
Supple_Chronic_Expression Data-CC-9

value: brain corpus callosum

value: Cuprizone-Chronic

value: 12wk+12 wk recovery


title: CPZ-12+12wk-1 (F), C57BL/6, CC, rep 1

description:
CC-8
Supple_Chronic_Expression Data-CC-8

value: wild type


title: CPZ-12+8wk-1 (M), C57BL/6, CC, rep 3

description:
CC-7
Supple_Chronic_Expression Data-CC-7

value: M

value: 12wk+8 wk recovery


title: Batch1_Vehicle(DMSO)_rep1

description: sample 1-1-1


title: Batch1_Albiflorin_rep1

description: sample 1-1-4

value: Albiflorin 10 uM


title: RNAseq.RevDKO.KC.ZT10.req3

value: male


title: FB_input_rep1

value: skin fibroblasts


title: CPZ-12+8wk-1 (F), C57BL/6, CC, rep 2

description:
CC-6
Supple_Chronic_Expression Data-CC-6

value: F


title: Human melanocyte, UV-irradiated, 3

city: Suwon

first: Jin Cheol

last: Kim

address: 206, World cup-ro, Yeongtong-gu

institute: Ajou University School of Medicine

description: counts.Senecent melanocytes-steady-state.txt

data_processing:
Altanalyze v2.1.4.3
The default recommended settings by Altanalyze was used to analyze the data
Raw data files were imported into Altanalyze software, which uses the embedded software Kallisto and Ensembl 72 annotations
Generating table of RPKM values for each sample
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: Primary normal human melanocytes (HEMn-MP, Gibco, C1025C)

extract_protocol:
Total RNA was isolated from tissue using TRI reagent based method. Total RNA (500 ng) was processed for preparing whole transcriptome sequencing library.
Enrichment of whole transcriptome RNA by depleting ribosomal RNA (rRNA) was processed for preparing whole transcriptome sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.

value: Melanocyte

value: UV


title: 8Mo naïve (F), C57BL/6 control CC, rep 2

description:
CC-11
Supple_Chronic_Expression Data-CC-11

value: untreated-Chronic


title: CPZ-12+8wk-1 (F), C57BL/6, CC, rep 1

description:
CC-5
Supple_Chronic_Expression Data-CC-5


title: CH_H3K27ac_rep3

source_name: CH

value: chondrocytes

value: Anti-H3K27ac (Diagenode c15410174)


title: Batch1_Paeoniflorin_rep1

description: sample 1-1-5


title: FB_H3K4me1_rep1

value: anti-H3K4me1 (Abcam ab8895)


title: RNAseq.RevDKO.KC.ZT16.req2

value: liver

value: Liver macrophage

value: ReverbhDKO

value: 4-week high fat and sucrose diet, D12492i


title: RNAseq.RevDKO.KC.ZT4.req3


title: RNAseq.RevDKO.KC.ZT10.req1


title: CH_H3K27ac_rep2


title: CPZ-12+4wk-1 (F), C57BL/6, CC, rep 2

description:
CC-4
Supple_Chronic_Expression Data-CC-4

value: brain corpus callosum

value: wild type

value: Cuprizone-Chronic

value: 12wk+4 wk recovery


title: Human melanocyte, sham-irradiated, 3

value: Primary normal human melanocytes (HEMn-MP, Gibco, C1025C)

value: Sham


title: RNAseq.RevDKO.KC.ZT16.req1

value: male


title: CH_H3K27ac_rep1


title: CPZ-12+4wk-1 (M), C57BL/6, CC, rep 1

description:
CC-3
Supple_Chronic_Expression Data-CC-3

value: M


title: Human melanocyte, UV-irradiated, 1

value: Melanocyte

value: UV


title: FB_input_rep2

value: skin fibroblasts


title: RNAseq.RevDKO.KC.ZT4.req2


title: CH_H3K4me3_rep3

value: chondrocytes

value: anti-H3K4me3 (Millipore 07-473)


title: RNAseq.RevDKO.KC.ZT10.req2

value: liver


title: CPZ-12wk-1 (M), C57BL/6, CC, rep 2

description:
CC-2
Supple_Chronic_Expression Data-CC-2


title: Human melanocyte, sham-irradiated, 2


title: CH_H3K4me3_rep2


title: RNAseq.RevDKO.KC.ZT4.req1

value: Liver macrophage


title: Human melanocyte, sham-irradiated, 1


title: CPZ-12wk-1 (F), C57BL/6, CC, rep 1

description:
CC-1
Supple_Chronic_Expression Data-CC-1

value: F


title: RNAseq.Control.KC.ZT22.req3

value: Control

value: 4-week high fat and sucrose diet, D12492i


title: 8Mo naïve (M), C57BL/6 control HP, rep 3

description:
hip-13
Supple_Chronic_Expression Data-HP-13

source_name: brain hippocampus

value: brain hippocampus

value: wild type

value: untreated-Chronic


title: Human melanocyte, UV-irradiated, 2

value: Primary normal human melanocytes (HEMn-MP, Gibco, C1025C)


title: RNAseq.Control.KC.ZT22.req2


title: 8Mo naïve (F), C57BL/6 control HP, rep 2

description:
hip-12
Supple_Chronic_Expression Data-HP-12


title: CH_H3K4me1_rep2

value: anti-H3K4me1 (Abcam ab8895)


title: RNAseq.Control.KC.ZT22.req1

value: male


title: RNAseq.Control.KC.ZT16.req3


title: 8Mo naïve (F), C57BL/6 control HP, rep 1

description:
hip-11
Supple_Chronic_Expression Data-HP-11


title: CH_H3K4me1_rep1


title: CPZ-12+12wk-1 (F), C57BL/6, HP, rep 2

description:
hip-10
Supple_Chronic_Expression Data-HP-10

value: Cuprizone-Chronic

value: 12wk+12 wk recovery


title: RNAseq.Control.KC.ZT16.req1


title: RNAseq.Control.KC.ZT16.req2


title: CH_input_rep3


title: CPZ-12+8wk-1 (M), C57BL/6, HP, rep 2

description:
hip-8
Supple_Chronic_Expression Data-HP-8

value: M

value: 12wk+8 wk recovery


title: CH_input_rep1

value: chondrocytes


title: CPZ-12+12wk-1 (F), C57BL/6, HP, rep 1

description:
hip-9
Supple_Chronic_Expression Data-HP-9


title: CH_input_rep2


title: RNAseq.Control.KC.ZT10.req2


title: PDXTUH110_vivo_GILT_6

city: paris

first: Jerome

last: Tamburini

address: 22 rue mechain

institute: Cochin Institute

hyb_protocol: cDNA were hybridized to GeneChip® Clariom S Human (Affymetrix) at 45°C for 17 hours, then washed on the fluidic station FS450 (Affymetrix)

scan_protocol: GCS3000 7G (Thermo Fischer Scientific)

data_processing: Raw fluorescence intensity values were normalized using Robust Multiarray Average (RMA) algorithm in R to generate the normalized data matrix by performing background correction, quantile normalization and log2 transformation of raw fluorescence intensity values of each gene. All quality controls and statistics were performed using Partek® Genomics Suite software (Partek, St. Louis, MO, USA). Data were normalized using custom brainarray CDF files (v20 ENTREZG). To identify differentially expressed genes, we applied a classical analysis of variance (ANOVA) with a FDR permutation-base for each gene. We created a matrix with only the significant ANOVA site and performed Z-scoring of rows. Hierarchical clustering by Pearson's dissimilarity and average linkage and principal components analysis (PCA) were conducted in an unsupervised fashion to control for experimental bias or outlier samples.

label: biotin

source_name: AML cell line

label_protocol: 100 ng of total RNA was reverse transcribed using the GeneChip® WT Plus Reagent Kit

growth_protocol: Human AML cells were harvested from mice after 7 days of treatment in vivo with vehicle or GILT, then sorted using human anti-CD45 antibody and directly processed for RNA extraction and analysis.

extract_protocol: RNA was extracted using a RNeasy Mini Kit (Qiagen, Redwood City, CA, USA) and quality was evaluated with a Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit)

value: patient-derived xenograft (PDX) AML cells

tag: disease

value: patient with AML

tag: agent

value: gilteritinib


title: BM_H3K27ac_rep3

source_name: BM MSC

value: bone marrow derived mesenchymal stromal cells

value: Anti-H3K27ac (Diagenode c15410174)


title: CPZ-12+8wk-1 (F), C57BL/6, HP, rep 1

description:
hip-7
Supple_Chronic_Expression Data-HP-7

value: F

tag: treatment


title: BM_H3K27ac_rep2


title: RNAseq.Control.KC.ZT10.req1

value: liver

value: Liver macrophage

value: Control

value: 4-week high fat and sucrose diet, D12492i


title: PDXTUH86_vivo_GILT_4

tag: cell line


title: CPZ-12+4wk-1 (M), C57BL/6, HP, rep 3

description:
hip-6
Supple_Chronic_Expression Data-HP-6

value: brain hippocampus

value: wild type

value: 12wk+4 wk recovery


title: PDXTUH110_vivo_vehicle_5

value: vehicle


title: BM_H3K27ac_rep1


title: RNAseq.Control.KC.ZT4.req3

value: male

tag: diet


title: CH_H3K4me3_rep1

value: anti-H3K4me3 (Millipore 07-473)


title: RNAseq.Control.KC.ZT4.req2


title: RNAseq.Control.KC.ZT10.req3


title: PDXTUH86_vivo_vehicle_3


title: PDXTUH73_vivo_vehicle_1


title: PDXTUH93_QUIZ_6

growth_protocol: AML cells were cultured in minimum essential medium (MEM)-α Glutamax (Life Technology, Carlsbad, CA, USA) supplemented with bovine serum albumin (BSA, Sigma-Aldrich, Saint Louis, MO, USA), 100 IU/mL penicillin and 100 µg/mL streptomycin (Life Technology) at 37°C under a 5% CO2 atmosphere.

value: quizartinib


title: BM_H3K4me3_rep3


title: RNAseq.Control.KC.ZT4.req1


title: CPZ-12wk-1 (M), C57BL/6, HP, rep 3

description:
hip-3
Supple_Chronic_Expression Data-HP-3

value: M

value: Cuprizone-Chronic


title: BM_H3K4me3_rep1


title: PDXTUH73_vivo_GILT_2

value: patient-derived xenograft (PDX) AML cells

value: patient with AML

value: gilteritinib


title: BM_H3K4me1_rep2

value: bone marrow derived mesenchymal stromal cells

value: anti-H3K4me1 (Abcam ab8895)


title: PDXTUH93_vehicle_5


title: PDXTUH84_QUIZ_4


title: PDXTUH06_QUIZ_2


title: RNAseq.RevScapTKO.Hep.ZT22.req2

value: liver

value: hepatocyte

value: Reverb/ScaphTKO


title: CPZ-12+4wk-1 (F), C57BL/6, HP, rep 2

description:
hip-5
Supple_Chronic_Expression Data-HP-5

value: brain hippocampus

value: F


title: Input, 3

source_name: Culture

value: Culture

tag: group

value: S. gordonii transposon library (Input)

tag: coinfection

value: No


title: BM_H3K4me3_rep2

value: anti-H3K4me3 (Millipore 07-473)


title: PDXTUH84_vehicle_3

value: vehicle


title: PDXTUH06_vehicle_1


title: scRNA_seq_ReverbScaphTKO

library_source: transcriptomic single cell

data_processing:
Cell Ranger (3.0.2) software (10x Genomics) was run on the raw data using mm10. Output from Cell Ranger was loaded into R package Seurat (version 3.0) (37). Unique sequencing reads for each gene were normalized to total Unique Molecular Identifiers (UMIs) in each nucleus to obtain normalized UMI values. Unsupervised clustering was applied after aligning the top 20 dimensions resulting from the PCA space using a resolution of 0.5. The identity for each cluster was assigned based on the prior knowledge of marker genes. The differentially expressed genes in each cluster were defined using a cutoff of p-value < 0.01 and fold change > 1.2. The UMAP plots, violin plots, Venn diagrams, and heat maps were generated by R.
Supplementary files format and content: mm10
Supplementary files format and content: .rds and .R file includes R object file specific to gene expression count data per cell and cell cluster information.

source_name: liver

extract_protocol:
Mice were anesthetized, and the livers were perfused with calcium-free Hank’s Balanced Salt Solution (HBSS) containing 0.2mg/mL EDTA, followed by sequential digestion with HBSS with 0.5mg/ml collagenase type II,  0.04mg/ml trypsin inhibitor, and 1.37mM calcium for 3 minutes at 37 °C through the portal vein. The liver was dissociated and the cell suspension was centrifuged at 30g for 5 min. The NPCs were enriched in the suspension and washed with MACS buffer (1X PBS pH 7.2, 0.5% BSA and 2mM EDTA). The pellet was resuspended in chilled (4 °C) nuclei wash and resuspension buffer (1X PBS, 1.0% BSA, and 0.2 U/μl RNase Inhibitor) with a cell concentration of 1000 nuclei/ul. 10,000 nuclei were immediately proceeded with the 10X Genomics Chromium Single-Cell 3.1’ according to the manufacturer’s instructions.
The libraries from control, ReverbhDKO, and Reverb/ScaphDKO liver were constructed based on the 10X Genomics Chromium Single-Cell 3.1’ manufacturer’s instructions and sequenced by NovaSeq 6000.

value: male

value: live tissue

value: 4-week high fat and sucrose diet, D12492i


title: CPZ-12+4wk-1 (F), C57BL/6, HP, rep 1

description:
hip-4
Supple_Chronic_Expression Data-HP-4

value: wild type

value: Cuprizone-Chronic

value: 12wk+4 wk recovery


title: RNAseq.RevScapTKO.Hep.ZT16.req3


title: scRNA_seq_ReverbhDKO

value: ReverbhDKO


title: BM_H3K4me1_rep1

value: bone marrow derived mesenchymal stromal cells

value: anti-H3K4me1 (Abcam ab8895)


title: bone_WT (DSP-1012500008771-F-B11)

description:
All_Data_WTA.xlsx
Mm_R_NGS_WTA_v1.0.pkc

data_processing:
FASTQ files were processed using the NanoString GeoMx NGS Pipeline v2.0 or v2.2
Reads were trimmed to remove low quality bases and adapter sequences
Paired end reads were aligned and stitched, and the barcode and UMI sequences were extracted. Barcodes were matched to known probe barcodes with maximum 1 mismatch allowed. Reads matching the same barcode were deduplicated by UMI. All analyses used UMI deduplicated counts to correct for any PCR amplification bias.
Segment and Probe QC with the NanoStringNCTools, GeomxTools and GeoMxWorkflows R/Bioconductor packages
Create gene-level count data and filter genes based on detection rate with the NanoStringNCTools, GeomxTools and GeoMxWorkflows R/Bioconductor packages
Differential expression analysis with the DESeq2 and RUVSeq R/Bioconductor packages
Assembly: Sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Mm_R_NGS_WTA_v1.0.pkc)
Supplementary files format and content: Excel spreadsheet with segment information, raw and normalized counts for each probe
Supplementary files format and content: Digital Count Conversion (DCC) scan attributes, one for each ROI
Supplementary files format and content: Probe Kit Configuration (PKC) file containing probe assay metadata describing the gene targets present in the data (GeoMx Mouse Whole Transcriptome)
Library strategy: Nanostring GeoMx

value: bone

tag: status

value: WT

tag: roi

tag: roi type

value: Full


title: BM_input_rep2


title: RNAseq.RevScapTKO.Hep.ZT16.req2

value: liver

tag: Sex

value: hepatocyte

value: Reverb/ScaphTKO


title: CPZ-12wk-1 (F), C57BL/6, HP, rep 2

description:
hip-2
Supple_Chronic_Expression Data-HP-2

value: brain hippocampus

value: F

tag: treatment period


title: MOLM14_shCEBPA1_+DOX_n3_6

value: patient with AML

tag: transduction


title: BM_input_rep3

tag: cell type

tag: chip antibody

tag: donor id


title: BM_input_rep1


title: CPZ-12wk-1 (F), C57BL/6, HP, rep 1

description:
hip-1
Supple_Chronic_Expression Data-HP-1

tag: tissue

tag: strain

tag: genotype


title: RNAseq.RevScapTKO.Hep.ZT16.req1

value: male


title: RNAseq.RevScapTKO.Hep.ZT22.req1

value: 4-week high fat and sucrose diet, D12492i


title: MARS3

city: La Jolla

first: Paul

last: Schimmel

state: California

address: 10550 North Torrey Pines Road, BCC379

department: Molecular Medicine

institute: The Scripps Research Institute

description: stable MetRS knock down

data_processing:
Reads were trimmed with trimgalore and aligned to grch37 with STAR (Dobin et al., 2013).
(Dobin et al., 2013). Exon usage analysis was performed with DEXSeq (Anders et al., 2012). Annotations and counts were generated using Subread (Liao et al., 2014; Bhardwaj, 2018).
Differentially expressed genes were identified with DESeq2 (Love et al., 2014).
Genome_build: grch37
Supplementary_files_format_and_content: count

growth_protocol: 2.5x106 HepG2 cells were seeded on 10 cm tissue culture dishes two days prior to RNA isolation.

extract_protocol:
RNA was isolated by using a mirVana miRNA isolation kit (Invitrogen) with phenol extraction following the manufacturer’s instruction for total RNA isolation.
Poly-A RNA-seq libraries were prepared and sequenced by the Genomic Sequencing and Analysis Facility at the University of Texas at Austin.
RNAs were selected by using a Poly(A) Purist MAG Kit (Thermo Fisher, AM1922) using the manufacturer’s protocol followed by library preparation using a NEBNext Ultra II Directional RNA Library Kit for Illumina (New England Biolabs, E7760), also following the manufacturer’s protocol.

treatment_protocol: Cells were expressing either a non-targeting shRNA control or a shRNA directed against ArgRS (gene name: RARS) or a shRNA directed against MetRS (gene name MARS) or a shRNA against SRRM2.

tag: shRNA

value: shMARS


title: MOLM14_shCEBPA1_+DOX_n2_4

tag: cell line

tag: disease


title: RNAseq.RevScapTKO.Hep.ZT10.req3

tag: diet


title: MOLM14_shCTL_+DOX_n3_5

value: shCTL


title: MOLM14_shCEBPA1_+DOX_n1_2


title: 19340X2 Female, 6-week Adrenal Gland, SF1-Cre+;Znrf3Fx/Fx

city: Salt Lake City

first: Kaitlin

last: Basham

state: UT

address: 2000 Circle of Hope Dr.

department: Oncological Sciences

institute: Huntsman Cancer Institute, University of Utah

description: 10X Genomics

data_processing:
The Fastq files were aligned to the refdata-gex-mm10-2020-A.tar mouse reference dataset from 10X genomics using cellranger count version 6.0.1 with 10000 expected cells.
The filtered gene barcode matrices were loaded into the Seurat package in R and merged into a single matrix.
Cells with more than 10% mitochondrial reads were removed and counts were normalized using the sctransform method.
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrices from cellranger

source_name: Adrenal Gland

growth_protocol: Adrenal glands were obtained from mice following rapid decapitation to mimize stress. Adrenals were placed in ice-cold 1X Hank's Balanced Salt Solution containing calcium and magnesium.

extract_protocol:
Tissues were finely chopped and digested enzymatically using enzymes and reagents from the Neural Tissue Dissociation Kit (Mitenyi Biotec, 130-092-628). All steps were carried out at 4oC, including centrifugation. All tubes and pipette tips used to handle cell suspensions were pre-coated with 3% BSA in HBSS to prevent cell loss. During the dissociation, the cell suspension was gently agitated with mechanical pipetting every 10 minutes and visually assessed under a stereo microscope until the tissue was fully digested. The suspension was then filtered through 70-micron filters to obtain a single cell suspension and enzymes were neutralized using HBSS containing 10% Fetal Bovine Serum (FBS). Red blood cells were removed using Red Blood Cell Lysis buffer (Roche, 11814389001) according to manufacturer guidelines, and the cells were washed twice in HBSS containing 2% FBS before counting using a Countess Automated Cell Counter (Thermo Fisher). Immediately following dissociation, cells were stained with 0.1 mg/mL DAPI and 5mM Vybrant DyeCycle Ruby (Invitrogen, V10309). Viable Ruby-positive, DAPI-negative single cells were sorted based on fluorescent properties using the BD FACSAria III Cell Sorter at the University of Utah Flow Cytometry Shared Resource. Cells were collected in 1XPBS (calcium- and magnesium-free) containing 0.04% BSA and kept on ice.
Chromium Next GEM Single Cell 3’ Gene Expression Library Construction Kit v3.1

value: Adrenal Gland

value: Female

tag: treatment


title: 19340X1 Female, 9-week Adrenal Gland, SF1-Cre+;Znrf3Fx/Fx

description: 10X Genomics


title: MARS2

description: stable MetRS knock down


title: RNAseq.RevScapTKO.Hep.ZT10.req2


title: 19306X27 Male, Adrenal Gland, 9-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 4

data_processing:
Mouse FASTA and GTF files were downloaded from Ensembl release 102 and a reference database was created using STAR version 2.7.6a.
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16.
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using RSEM version 1.6.3.
Expected gene counts were filtered to remove features with zero counts and features with fewer than 10 reads in any sample.
Assembly: Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1.
Supplementary files format and content: GRCm38
Supplementary files format and content: raw counts from featureCounts combined into a single tab-delimited matrix

growth_protocol: Adrenal glands were obtained from mice following rapid decapitation to mimize stress. Adrenals were places in ice-cold phosphate buffered saline, cleaned of excess fat and snap frozen in liquid nitrogen.

extract_protocol:
RLT lysis buffer (Qiagen, 74104) containing 1% b-mercaptoethanol was added to thawed adrenal tissue in high impact zirconium 1.5mm bead tubes (Benchmark Scientific, D1032-15). Samples were homogenized for 30 seconds using the Beadbug™ 3 (Benchmark Scientific, D1030), returned to ice, and homogenized for an additional 30 seconds. Total RNA isolation was completed using the RNeasy® Kit (Qiagen, 74104) according to manufacturer guidelines. DNases were removed using the RNase-Free DNase Set (Qiagen, 79254) and subsequently purified using the RNeasy MinElute Cleanup Kit (Qiagen, 74204) according to manufacturer guidelines
NEBNext Ultra II Directional RNA Library Prep with poly(A)mRNA Isolation

value: Male

value: SF1-Cre+; Znrf3 Fx/Fx

tag: time


title: MARS1

description: stable MetRS knock down


title: scRNA_seq_Control

value: live tissue

value: Control


title: RNAseq.RevScapTKO.Hep.ZT10.req1


title: 19306X26 Male, Adrenal Gland, 9-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 3


title: SRRM3

description: stable SRRM2 knock down


title: RNAseq.RevScapTKO.Hep.ZT4.req3


title: SRRM2

description: stable SRRM2 knock down


title: 19306X22 Male, Adrenal Gland, 9-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 2


title: 19306X21 Male, Adrenal Gland, 9-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 1


title: RNAseq.RevScapTKO.Hep.ZT4.req2


title: MOLM14_shCTL_+DOX_n1_1


title: MOLM14_shCTL_+DOX_n2_3


title: RNAseq.RevScapTKO.Hep.ZT4.req1


title: U5PA

description: stable ArgRS knock down

value: shRARS


title: 19306X35 Male Adrenal Gland, 9-week, Control, biol rep 4

value: SF1-Cre negative


title: SRRM1

description: stable SRRM2 knock down


title: MOLM14_shCEBPA#1_n3_12

value: shCEBPA


title: 19306X34 Male Adrenal Gland, 9-week, Control, biol rep 3


title: U3PA

description: stable ArgRS knock down


title: RNAseq.RevDKO.Hep.ZT22.req2

value: liver

value: hepatocyte

value: ReverbhDKO


title: MOLM14_shCEBPA#1_n1_8

value: patient with AML


title: RNAseq.RevDKO.Hep.ZT22.req1

value: male


title: 19306X20 Male Adrenal Gland, 9-week, Control, biol rep 2


title: MOLM14_shCEBPA#1_n2_10


title: U1PA

description: stable ArgRS knock down


title: S5PA

description: control

value: ctrl


title: MOLM14_shCTLconsti_n3_11

value: shCTLconsti


title: 19306X19 Male Adrenal Gland, 9-week, Control, biol rep 1


title: 19306X16 Male, Adrenal Gland, 6-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 4


title: RNAseq.RevDKO.Hep.ZT16.req3

value: 4-week high fat and sucrose diet, D12492i


title: RNAseq.RevDKO.Hep.ZT16.req2


title: S3PA

description: control


title: 19306X15 Male, Adrenal Gland, 6-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 3

value: Adrenal Gland


title: RNAseq.RevDKO.Hep.ZT16.req1


title: S1PA

description: control


title: RNAseq.RevDKO.Hep.ZT22.req3


title: MOLM14_shCTLconsti_n1_7


title: MOLM14_shCTLconsti_n2_9


title: MOLM14_siCEBPA_2_n1_14

value: siCEBPA


title: MOLM14_siCEBPA_2_n3_18


title: 19306X14 Male, Adrenal Gland, 6-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 2

value: Male


title: PD+human menstrual blood-derived endometrial stem cells5-Serum

type: protein

city: Xinxiang

first: Han

address: 601 Jinsui Road, Hongqi District, Xinxiang City, Henan Province

institute: Xinxiang Medical University

description: Secreted proteins

hyb_protocol: Centrifuge the Cy3-streptavidin tubule, then add 1.4 ml of sample diluent, mix well, and then quickly centrifuge again. Add 80 µ l of Cy3-streptavidin to each well, wrap the slide in aluminum foil and incubate it in a dark place. Incubate it on a shaking table at room temperature for 1 hour.

scan_protocol: The signals (532 nm excitation, 635 nm emission) were scanned and extracted using an InnoScan 300 scanner (Innopsys, Carbonne, France).

data_processing:
Individual array spots were background subtracted locally by subtracting the median background across spot replicated in each sample, and then normalized using two positive controls.
QAR-INF-1 software was used to analyze the data

molecule: protein

organism: Rattus norvegicus

source_name: Serum of rat

label_protocol: Cy3-conjugated streptavidin

extract_protocol: none provided

value: Serum

tag: gender

value: PD+MenSCs-Treated


title: MOLM14_siCEBPA_2_n2_16


title: RNAseq.RevDKO.Hep.ZT10.req3


title: RNAseq.RevDKO.Hep.ZT10.req2


title: PD+human menstrual blood-derived endometrial stem cells4-Serum

description: Secreted proteins


title: 19306X33 Male Adrenal Gland, 6-week, Control, biol rep 4


title: PD+human menstrual blood-derived endometrial stem cells3-Serum

description: Secreted proteins


title: RNAseq.RevDKO.Hep.ZT10.req1


title: MOLM14_siCTL_n3_17

value: siCTL


title: 19306X32 Male Adrenal Gland, 6-week, Control, biol rep 3


title: RNAseq.RevDKO.Hep.ZT4.req3


title: PD+human menstrual blood-derived endometrial stem cells1-Serum

description: Secreted proteins


title: RNAseq.RevDKO.Hep.ZT4.req2


title: PD+human menstrual blood-derived endometrial stem cells2-Serum

description: Secreted proteins


title: PD+PBS5-Serum

description: Secreted proteins

value: PD+PBS-Treated


title: MOLM14_siCTL_n1_13


title: MOLM14_siCTL_n2_15


title: 19306X25 Male Adrenal Gland, 6-week, Control, biol rep 1

value: SF1-Cre negative


title: RNAseq.RevDKO.Hep.ZT4.req1


title: MV411_QUIZ_n3_11

tag: agent

value: QUIZ


title: 19306X13 Male, Adrenal Gland, 6-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 1

tag: Sex

value: SF1-Cre+; Znrf3 Fx/Fx


title: MV411_QUIZ_n2_10


title: RNAseq.Control.Hep.ZT22.req3

value: liver

value: hepatocyte

value: Control


title: 19306X8 Male, Adrenal Gland, 4-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 4


title: 19306X7 Male, Adrenal Gland, 4-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 3


title: RNAseq.Control.Hep.ZT22.req2

value: male


title: PD+PBS2-Serum

description: Secreted proteins


title: 19306X6 Male, Adrenal Gland, 4-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 2


title: RNAseq.Control.Hep.ZT22.req1


title: 19306X5 Male, Adrenal Gland, 4-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 1


title: 19306X31 Male Adrenal Gland, 6-week, Control, biol rep 2


title: PD+PBS1-Serum

description: Secreted proteins


title: RNAseq.Control.Hep.ZT16.req3


title: 19306X30 Male Adrenal Gland, 4-week, Control, biol rep 4


title: PD+PBS4-Serum

description: Secreted proteins


title: RNAseq.Control.Hep.ZT16.req2


title: Sham5-Serum

description: Secreted proteins

value: Untreated


title: MV411_vehicle_n5_9

value: patient with AML

value: vehicle


title: MV411_QUIZ_n5_12


title: PD+PBS3-Serum

description: Secreted proteins


title: Sham4-Serum

description: Secreted proteins


title: RNAseq.Control.Hep.ZT16.req1

value: 4-week high fat and sucrose diet, D12492i


title: Sham3-Serum

description: Secreted proteins


title: RNAseq.Control.Hep.ZT10.req3


title: Sham1-Serum

description: Secreted proteins


title: Sham2-Serum

description: Secreted proteins


title: RNAseq.Control.Hep.ZT10.req2


title: MV411_vehicle_n2_7


title: MV411_shFLT3_n3_5


title: 19306X29 Male Adrenal Gland, 4-week, Control, biol rep 3

value: Adrenal Gland


title: 19306X28 Male Adrenal Gland, 4-week, Control, biol rep 2

value: Male


title: MV411_shFLT3_n4_6


title: 19306X3 Male Adrenal Gland, 4-week, Control, biol rep 1


title: RNAseq.Control.Hep.ZT10.req1


title: MV411_shFLT3_n1_4


title: 19128X24 Female, Adrenal Gland, 12-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 4

value: Female


title: 19128X23 Female, Adrenal Gland, 12-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 3


title: PD+human menstrual blood-derived endometrial stem cells4-CSF

description: Secreted proteins

source_name: Cerebrospinal fluid of rat

value: Cerebrospinal fluid

value: PD+MenSCs-Treated


title: RNAseq.Control.Hep.ZT4.req3


title: 19128X21 Female, Adrenal Gland, 12-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 1


title: RNAseq.Control.Hep.ZT4.req2


title: PD+human menstrual blood-derived endometrial stem cells3-CSF

description: Secreted proteins


title: MV411_shCTL_n4_3

value: shCTL


title: MV411_shCTL_n1_1


title: MV411_vehicle_n3_8


title: MV411_shCTL_n3_2


title: RNAseq.RevScapTKO.Hep.ZT22.req3

value: Reverb/ScaphTKO


title: RNAseq.Control.Hep.ZT4.req1


title: PD+human menstrual blood-derived endometrial stem cells5-CSF

description: Secreted proteins


title: 19128X22 Female, Adrenal Gland, 12-week, SF1-Cre+;Znrf3Fx/Fx, biol rep 2


title: PD+human menstrual blood-derived endometrial stem cells2-CSF

description: Secreted proteins


title: 19128X20 Female Adrenal Gland, 12-week, Control, biol rep 4

value: SF1-Cre negative


title: MOLM14_QUIZ_n5_18

value: QUIZ


title: ATAC-seq Col10a1-mCherry Proximal Femur E15.5

city: Stanford

first: Daniel

last: Richard

address: 290 Jane Stanford Way

department: Genetics

institute: Stanford University

description: ATAC-seq on growth plate chondrocytes sorted using Col10a1-mCherry

data_processing:
alignment to mm10; Bowtie2 version 2.3.2; default parameters for mm10 alignment
filter for duplicates; MACS2 version 2.1.1.2; macs2 filterdup -i file -g hs --keep-dup 1 -o outfile
peak calling; MACS2 version 2.1.1.2; macs2 callpeak -B -t rep1file -n name --nomodel --shift -100 --extsize 200
peak consolidation; bedtools version 2.30.0;
Genome_build: mm10; ;
Supplementary_files_format_and_content: COL10_distalfemur_replicates_common_peak_calls_overlapped_REQ2_consolidated_clean.bed; bed format; contains the coordinates of the peaks called and filtered as described for the DF ATAC-seq experiment;
Supplementary_files_format_and_content: COL10_proximalfemur_replicates_common_peak_calls_overlapped_REQ2_consolidated_clean.bed; bed format; contains the coordinates of the peaks called and filtered as described for the PF ATAC-seq experiment;

source_name: Proximal femoral growth plates E15.5 – Col10a1

growth_protocol: In-vivo collected E15.5 growth plate chondrocytes

extract_protocol:
The samples were collected in microcentrifuge tubes containing 200ul 5% FBS/DMEM. To generate a single cell chondrocyte suspension, each pooled sample was then subjected to 1% Collagenase II (VWR 80056-222) digestion for 2hrs at 37C rocking, mixing every 30 minutes. After placing on ice, samples were filtered using a micro-centrifuge filter set-up by gently mashing the residual tissues through the filter followed by rinsing with 5% FBS/DMEM. Samples were then spun down at 500g at 4C for 5 min. We next performed cell counting methods using trypan blue and a hemacytometer and performed subsequent ATAC-seq steps on those samples that had cell death rates well below 25%. On average we acquired 500,000-1,000,000 living cells per harvest. Next, cells were resuspended in concentrations of 50,000 cells in 1x PBS.  Cell samples then subjected to the ATAC-seq protocol as described in Buenrostro et al., 2015, modifying the protocol by using 2 ul of transposase per reaction. The transposase reaction product was then purified using the Omega MicroElute DNA Clean Up Kit following manufacturers protocols, eluted in 10 ul of warmed ddH20, and stored at -20C.
Samples were subjected to PCR amplification and barcoding following Buenrostro et al., 2015. 10 ul of transposed DNA was then placed in a reaction containing NEBNext High-Fidelity PCR Master Mix, ddH20, and primers. After amplification, samples were transferred to micro-centrifuge tubes and subjected to the OMEGA Bead Purification Protocol following manufacturers protocol. The samples were eluted in 30 ul of TE, run on a nanodrop, diluted to 5 ng/ul and run on a bioanalyzer. Prior to sequencing sample concentrations were determined using the KAPA Library Quantification Complete Kit (KK4824). Samples were then sent out to the Harvard University Bauer Core Facility for sequencing on one lane of the Illumina NextSeq 500

treatment_protocol: All experiments were performed following protocols approved by the Harvard University IACUC committee. Timed matings were established between Col10a1-mCherry (as well as FVBNJ) mice, and pregnant females were euthanized at E15.5 in order to acquire embryonic long bone growth plates. Embryos were dissected in PBS1X on ice under a dissection scope and the proximal and distal growth zones of the right and left femur were stripped clear of soft tissues. Each proximal or distal cartilaginous end was then micro-dissected from the bony diaphysis and separately pooled from a single litter, consisting on average of 8 animals. Four biological replicates for each bone-end were obtained.

value: chondrocytes

tag: reagent

value: tn5 transposase


title: PD+human menstrual blood-derived endometrial stem cells1-CSF

description: Secreted proteins


title: PD+PBS5-cerebrospinal fluid

description: Secreted proteins

value: PD+PBS-Treated


title: 19128X19 Female Adrenal Gland, 12-week, Control, biol rep 3


title: MOLM14_QUIZ_n3_17


title: MOLM14_vehicle_n5_15


title: DN1 + DN2

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

data_processing:
Th Illumina sequencing files were demultiplexed and aligned to Mus musculus genome (mm10) using the CellRanger pipeline (10X Genomics) to generate a feature barcode matrix from the raw bcl file.
Using R software (v3.6.3 and v4.1.0 ) with Seurat (v2.3 and v3.2.2), low-quality cells were filtered with based on genes and mitochondria gene expression.
The data was then normalised using VST selection method
Downstream analysis was performed (Principal componennt analysis, DoubletFinder, Clustering, Trajectory inference and differential expression analysis)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files for each Sample
Supplementary_files_format_and_content: tab-delimited text files for each Sample (compressed by the standard GNU Zip compression algorithm)
Supplementary_files_format_and_content: A matrix of counts per gene for every cell

source_name: Early T cell development

growth_protocol: C57BL/6 mice at 6-8-week of age were euthanised by asphyxiation with CO2 and the thymi were excised and placed in RPMI 1640 medium. Thymi were passed through a 70µm stainless steel mesh to produce single cell suspensions of thymocytes.

extract_protocol:
Library was generated by Chromium™ Single Cell 3’ Library Construction (10x Genomics).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four thymi were pooled for each sample and then depleted of CD4 or CD8 expression cells (DP, CD4SP and CD8SP) using anti-CD4 and CD8 MACS magnetic beads (Miltenyi Biotec). The depleted samples were then sorted for DN1 (CD4-CD8-CD25-CD44+), DN2 (CD4-CD8-CD25+CD44+), DN3 (CD4-CD8-CD25+CD44-), DN4 (CD4-CD8-CD25-CD44-), or gammadelta (CD4-CD8-TCRgd+) thymocytes on a FACSAria (BD Biosciences).

value: thymus

tag: age

value: week 6


title: PD+PBS4-cerebrospinal fluid

description: Secreted proteins


title: 19128X18 Female Adrenal Gland, 12-week, Control, biol rep 2


title: ATAC-seq Col10a1-mCherry Distal Femur E15.5

source_name: Distal femoral growth plates E15.5 – Col10a1

tag: cell type


title: PD+PBS3-cerebrospinal fluid

description: Secreted proteins


title: DN + gammadelta thymocytes


title: 19128X16 Female, Adrenal Gland, 9-week SF1-Cre+;Znrf3Fx/Fx, biol rep 4

value: SF1-Cre+; Znrf3 Fx/Fx


title: MOLM14_QUIZ_n2_16

value: patient with AML


title: Wildtype megakaryocytes from male mice replicate #4

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

data_processing:
Basecalling with NextSeq Control/RTA v2 and FastQ conversion with Bcl2fastq v2.20.0.422
Adapter clipping and trimming using Cutadapt version 2.1 with default parameters. In addition, Cutadapt was given the –nextseq-trim=20 switch to handle two color sequencing chemistry and reads that were trimmed to length 0 were discarded.
Mapping to mouse genome (GRCm38.p6) with  STAR v2.7.2b and raw read on counting gene level bases with featureCounts v1.6.4  using the RefSeq annotation.
Differential Expression analysis with DESeq2 (v1.24.0) with log fold change shrinkage using betaPrior
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: mRNA abundance measurements

source_name: Wildtype megakaryocytes from male mice

growth_protocol: native murine megakaryocytes isolated from bone marrow and purified by magnetic separation with anti-CD61-antibodies

extract_protocol:
Whole mRNA extraction using TRIzol reagent and the RNeasy Mini Extraction Kit (Qiagen) according to the manufacturers’ protocol.
DNA libraries suitable for sequencing were prepared from 50 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions

treatment_protocol: untreated

tag: strain background

value: wt

value: male

value: bone marrow megakaryocytes


title: PD+PBS2-cerebrospinal fluid

description: Secreted proteins

value: Male


title: MOLM14_vehicle_n2_13

value: vehicle


title: MOLM14_vehicle_n3_14


title: 19128X14 Female, Adrenal Gland, 9-week SF1-Cre+;Znrf3Fx/Fx, biol rep 2

value: Adrenal Gland

value: Female


title: Wildtype megakaryocytes from male mice replicate #3


title: PD+PBS1-cerebrospinal fluid

description: Secreted proteins

value: Cerebrospinal fluid


title: Wildtype megakaryocytes from male mice replicate #2


title: 19128X13 Female, Adrenal Gland, 9-week SF1-Cre+;Znrf3Fx/Fx, biol rep 1


title: 19128X17 Female Adrenal Gland, 12-week, Control, biol rep 1

value: SF1-Cre negative