title: LV heart tissue, wildtype, female (wt_f_141-1)

description:
Mouse left ventricular heart tissue, wildtype, female (wt_f_141-1)
Column name in processed data files: 503


title: Mouse liver, metastatic, replicate 1, WTA

status: Public on Oct 27 2022

type: SRA

city: Zürich

first: Kristina

last: Handler

address: Winterthurerstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zürich

description: polyA RNA

library_source: transcriptomic single cell

data_processing:
zUMIs (v. 2.9.4)
genome building/assembly: GRCm38 vM25 genecode
3 UMI and 3 read count tables; gene-wise counts for exon, intron and exon+intron (.rds format)
Cell barcodes in first column and total UMI counts in second column (.txt format)

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
in-vitro digestion
BD Rhapsody: WTA kit

tag: cell type

value: Liver cells

tag: tissue

value: Liver

tag: strain

tag: treatment

value: intrasplenic injection with mouse colon cancer organoids

tag: disease state

value: metastatic liver

tag: termination

value: 2 weeks after injection

tag: age

value: 8-10 weeks old


title: LV heart tissue, Rbm20 knockout, female (ko_f_151-1)

city: Heidelberg

first: Maarten

last: van den Hoogenhof

state: (select)

address: In Neuenheimer Feld 669

country: Germany

institute: Institute of Experimental Cardiology

description:
Mouse left ventricular heart tissue, Rbm20 knockout, female (ko_f_151-1)
Column name in processed data files: 525

library_source: transcriptomic

data_processing:
BGI processed all sequenced reads using standard methods
Trimmed reads were then aligned with STAR (2.7.10a) to Gencode mm39 reference genome with parameters:STAR --genomeDir $GENOME_DIR --readFilesCommand zcat --readFilesIn $INPUT_DIR/fastq/${VAR}.txt.gz --sjdbGTFfile $GENOME_DIR/gencode.v28.annotation.gtf --sjdbOverhang 99 --quantMode GeneCounts --runThreadN 12 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${RESULTS_DIR}/Alignment/${VAR}_
DESeq2 (2.7.10a) within R (4.1.2) was then run to get to final differential expression results comparing RBM20 vs. WT mice for male and female mice.
Assembly: GRCm39.primary
Supplementary files format and content: 4 excel files with output from differential expression analysis (DESeq and DEXSeq), including STAR-generated normalized counts
Supplementary files format and content: sample numbers in the excel files can be found under 'description' in the SAMPLES section

molecule: total RNA

source_name: Heart (LV)

extract_protocol:
RNA was isolated using TRI Reagent from LV tissue
RNA libraries were prepared for sequencing using standard BGI protocols for the BGISEQ-500 Transcriptome

value: Heart (LV)

tag: Sex

value: female

tag: genotype

value: Rbm20 knockout


title: Fraction_12

city: Tokyo

first: Kotaro

last: Chihara

address: 1-23-1 Toyama

department: Research Center for Drug and Vaccine Development

country: Japan

institute: National institute of infectious diseases

data_processing:
Adapter clipping: cutadapt
Read mapping: READemption align and segemehl
Coverage calculator: READemption coverage
Assembly: NC_00913.3
Supplementary files format and content: wiggle

organism: Escherichia coli

growth_protocol: Overnight cultures of E. coli MG1655 were 100-fold diluted in 100 ml of fresh LB medium, grown to an OD600 of 2.0, cooled down in an ice-water bath, and then harvested by centrifugation.

extract_protocol:
RNA from each fraction was extratced by P/C/I while the lysate RNA was extracted by TRIzol method. The aqueous phases were precipitated with GlycoBlue and ethanol/3M sodium acetate, pH 6.5 (30:1) overnight at −20°C. The RNA was pelleted by centrifugation, washed with 70% ethanol. Thereafter, RNA was dissolved in DEPC-treated H2O and DNase-digested . The DNase-treated RNA was purified by  P/C/I. The purified, DNase-treated RNA was dissolved in DEPC-treated H2O.
RNA samples were fragmented, ligated with 3’ adapter, and reverse-transcribed with MMLV reverse transcriptase. Purified first-strand cDNA was then ligated with the 5’ Illumina TruSeq sequencing adapter, followed by PCR amplification. The cDNA samples were purified with the Agencourt AMPure XP kit and pooled with ratios according to the input samples' RNA concentrations. Finally, cDNA with a size range of 200-550 bp was gel-eluted.

treatment_protocol: The cells were resuspended in ice-cold lysis buffer and lysed by vortexing with 0.1 mm glass beads. The lysate was cleared by centrifugation. The cleared lysate was then injected into the equilibrated column connected to ÄKTA pure purification system. Each fraction was automatically collected using fraction collector F9-R at 4°C.

tag: growth phase

value: Early stationary (OD 2.0)

value: wild type

value: fractionation by superose 6 increase column


title: LV heart tissue, wildtype, male (wt_m_139-1)

description:
Mouse left ventricular heart tissue, wildtype, male (wt_m_139-1)
Column name in processed data files: 520

value: male

value: wildtype


title: LV heart tissue, wildtype, female (wt_f_140-1)

description:
Mouse left ventricular heart tissue, wildtype, female (wt_f_140-1)
Column name in processed data files: 501


title: CD45 cells_CTR_4

city: New Haven

first: Ana Luisa

last: Perdigoto

state: CT

address: 300 George Street

country: USA

institute: YALE UNIVERSITY

description: Bulk RNAseq

data_processing:
Partek Flow used for processing
Trim bases (both ends, discard before 1 and after 75, min read length 50)
Prealignment QA/QC
STAR - 2.7.3a to generate aligned read
Postalignment QA/QC
Filter alignments (filter low mapping quality section, min mapping quality 20, filter alignments with mismatched sections, remove singletons, remove unaligned reads, max mismatched bases 2)
Quantify to annotation model (Partek E/M) (strict paired-end compatibility, require junction reads to match introns, minimum read overlap with feature 100%, min reads 10)
Generate gene counts
Assembly: mm10
Supplementary files format and content: Excel files with gene counts for CD45+ cells and Islet cells from pancreatic islets

source_name: Pancreatic Islet

extract_protocol:
Cells were frozen in RLT buffer and subsequent RNA isolation was performed using Qiagen RNeasy Plus Micro Kit.
SMARTer universal low input RNA kit (Takara Bio Inc) was used to convert RNA to cDNA. Bioanalyzer 2100 was used to measure cDNA quality and concentration. Nextera DNA Library Preparation Kit was used to make libraries
Quality control of the libraries performed on an Agilent Technologies 2100 bioanalyzer using an Agilent high sensitivity chip. Multiplexed DNA libraries are normalized to 10nM and then pooled in equal volumes with each unique barcoded sample. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 4000 per the manufacturer’s protocols.

treatment_protocol: Approximately 7-week-old NOD mice were treated with anti-PD-L1 (Bio X Cell, Clone 10F.9G2) or anti-CTLA4 (Bio X Cell, Clone 9D9) every three days for 2 doses. Two days after the second dose mice were sacrificed and islets were harvested and processed into single cells. NOD control mice were sacrificed at 11 weeks old and processed similarly to antibody treated mice. CD45+ cells and CD45- cells (Islet cells) were sorted by FACS.

value: Pancreatic Islet

value: NOD

value: 11 week


title: ATAC, PPARg2-R212Q, rep2

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: ATAC, Tn5-enriched DNA

library_source: genomic

data_processing:
Alignment to mm10 genome using STAR
ChIP-seq and ATAC-seq data was deduplicated using Picard Tools (Broard Institutte http://broadinstitute.github.io/picard/)
Nucleosome-free accessible regions were extracted as fragments <120 bp using SamTools (ATAC-seq)
Tag-directories were generated using HOMER makeTagDirectories (RNA-, ChIP, and ATAC-seq)
HOMER findPeaks was used to call peaks (ChIP- and ATAC-seq)
HOMER annotatePeaks.pl was used to count tags within called peaks (ChIP- and ATAC-seq)
HOMER analyzeRepeats.pl was used to count reads within exons (RNA-seq)
DESeq2 was used to identify differential binding of HA-PPARg and Med1, acetylation of H3K27 (ChIP-seq), accessibility of chromatin (ATAC-seq), and gene expression (RNA-seq).
Assembly: mm10
Supplementary files format and content: bigwig-file: contain file for visualization of sequenced reads in the UCSC genome browser.
Supplementary files format and content: bed-file: contains positions for called peaks
Supplementary files format and content: Counts_RNA_FPLD3_mm10.txt: count matrix for exon-counts within all RNA samples

molecule: genomic DNA

source_name: PPARg-/-MEF-CAR cells

growth_protocol: PPARγ-/- MEF-CAR cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) 4.5 g/L D-glucose supplemented with 10% fetal bovine serum (Gibco), and 100 μg penicillin/ml and 100 μg streptomycin/ml (Invitrogen)

extract_protocol:
Nuclei were prepared from 100,000 cells and tagmented with 2.5 ul Tn5 for 30 min at 37°C. Tagmented DNA was prepared for sequencing according to manufacturer's instructions (Illumina).
Purified RNA was subjected to polydT-enriched cDNA synthesis before sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq libraries of HA-, Med1, and H3K27ac-enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279). ATAC-seq libraries were prepared for sequencing according to manufacturer's instructions (Illumina).

treatment_protocol: PPARγ-/- MEF-CAR cells were transduced with adenoviral vectors expressing HA-tagged mPPARγ2-WT, mPPARγ2-E379K or mPPARγ2-R212Q. Control cells were not subjected to adenovirus. After two hours of virus exposure, the medium was removed, and cells were treated with medium containing either vehicle dimethyl sulfoxide (DMSO) or 1 µM rosiglitazone (Alexis) for another 6 hours before harvest.

tag: cell line

value: PPARg-/-MEF-CAR cells

tag: transduction

tag: ligand

value: DMSO


title: CD45 cells_CTLA4_4

description: Bulk RNAseq

value: 7 week


title: YAP-M tumor_H3K27ac-ChIP-seq-1

city: Cincinnati

first: Zaili

last: Luo

state: OH

address: 3333 Burnet Ave.

institute: CCHMC

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence. HiChIP reads were aligned to mm10 using bwa mem.
We then kept paired-end reads where at least one end overlaps with the H3K27ac ChIP-seq peaks in the matched cell type, and fitted a positive Poisson regression model to remove systematic biases including restriction enzyme cutting frequency, GC content, sequence uniqueness and ChIP efficiency.
We then identified significant long-range chromatin interactions as 10 kb bin pairs with FDR<1% and normalized chromatin contact frequency >2.
Lastly, we assigned genes whose transcription start site resides in the anchor bins of MAPS-identified interactions.
Assembly: mm10
Library strategy: HiChIP

source_name: brain

growth_protocol: Mouse Neural Stem Cells (mNSC) were maintained in Neural Stem Cell (NSC) Basal Medium with NSC proliferation supplements, 10 ng/ml EGF, 20 ng/ml basic-FGF and 2 μg/ml Heparin (Stem Cell Technologies, Vancouver, Canada).

extract_protocol:
Genomic DNA was prepared using DNeasy Blood & Tissue Kit (Qiagen) as the manufatuer's guide.
HiChIP assays were performed using Dovetail® HiChIP MNase Kit according to the manufacturer’s instruction.

value: brain

value: YAP-M tumor

value: YAP-M fusion

value: H3K27ac antibody


title: YAP-M tumor_H3K27ac-ChIP-seq-2


title: CD45 cells_CTR_1

description: Bulk RNAseq


title: CD45 cells_CTLA4_3

description: Bulk RNAseq


title: mNSC_H3K27ac-ChIP-seq-1

value: neural progenitor cells

value: wile-type


title: mNSC_H3K27ac-ChIP-seq-2


title: CD45 cells_CTR_3

description: Bulk RNAseq


title: LV heart tissue, wildtype, female (wt_f_142-1)

description:
Mouse left ventricular heart tissue, wildtype, female (wt_f_142-1)
Column name in processed data files: 505

value: Heart (LV)

value: female


title: CD45 cells_CTLA4_1

description: Bulk RNAseq


title: ATAC, PPARg2-R212Q, rep1

description: ATAC, Tn5-enriched DNA


title: ATAC, Control, rep2

description: ATAC, Tn5-enriched DNA

value: Untransduced

value: 1 µM Rosiglitazone


title: ATAC, PPARg2-WT, rep2

description: ATAC, Tn5-enriched DNA


title: ATAC, PPARg2-E379K, rep1

description: ATAC, Tn5-enriched DNA


title: CD45 cells_PDL1_3

description: Bulk RNAseq


title: CD45 cells_PDL1_2

description: Bulk RNAseq


title: CD45 cells_CTR_2

description: Bulk RNAseq


title: ATAC, Control, rep1

description: ATAC, Tn5-enriched DNA


title: ATAC, PPARg2-WT, rep1

description: ATAC, Tn5-enriched DNA


title: Med1, R212Q, rep2

description: ChIP-enriched DNA

extract_protocol:
ChIP-seq libraries of Med1-enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
Purified RNA was subjected to polydT-enriched cDNA synthesis before sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq libraries of HA-, Med1, and H3K27ac-enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279). ATAC-seq libraries were prepared for sequencing according to manufacturer's instructions (Illumina).

tag: chip antibody

value: MED1; Bethyl Laboratories A300-793A


title: Islet cells_CTR_4

description: Bulk RNAseq

value: Pancreatic Islet


title: Med1, E379K, rep2

description: ChIP-enriched DNA


title: Islet cells_CTR_3

description: Bulk RNAseq

value: NOD


title: Med1, WT, rep2

description: ChIP-enriched DNA


title: ATAC, PPARg2-E379K, rep2

description: ATAC, Tn5-enriched DNA


title: Islet cells_CTR_2

description: Bulk RNAseq

value: 11 week


title: CD45 cells_CTLA4_2

description: Bulk RNAseq


title: Islet cells_CTR_1

description: Bulk RNAseq


title: CD45 cells_PDL1_1

description: Bulk RNAseq


title: Med1, E379K, rep1

description: ChIP-enriched DNA

value: PPARg-/-MEF-CAR cells


title: Med1, WT, rep1

description: ChIP-enriched DNA


title: Islet cells_CTLA4_3

description: Bulk RNAseq


title: Islet cells_CTLA4_2

description: Bulk RNAseq


title: Islet cells_CTLA4_4

description: Bulk RNAseq


title: Input, rep1

description: input genomic DNA, pool of all chromatin from rep 1

extract_protocol:
Libraries of input genomic DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
Purified RNA was subjected to polydT-enriched cDNA synthesis before sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq libraries of HA-, Med1, and H3K27ac-enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279). ATAC-seq libraries were prepared for sequencing according to manufacturer's instructions (Illumina).

value: Cells transduced with Ad-HAmPPARg2-WT, Ad-HAmPPARg2-E379K, Ad-HAmPPARgR212Q or untransduced control were pooled in equal ratio.

value: 1 µM Rosiglitazone and DMSO


title: Islet cells_CTLA4_1

description: Bulk RNAseq

value: 7 week


title: Input, rep2

description: input genomic DNA, pool of all chromatin from rep 2


title: Islet cells_PDL1_1

description: Bulk RNAseq


title: Islet cells_PDL1_3

description: Bulk RNAseq


title: H3K27ac, PPARg2-WT, rep2

description: ChIP-enriched DNA

extract_protocol:
ChIP-seq libraries of H3K27ac-enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
Purified RNA was subjected to polydT-enriched cDNA synthesis before sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq libraries of HA-, Med1, and H3K27ac-enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279). ATAC-seq libraries were prepared for sequencing according to manufacturer's instructions (Illumina).

value: H3K27ac; Abcam Ab4729


title: Med1, Control, rep1

description: ChIP-enriched DNA


title: Activated Pax7+ Satellite cells from Cxcr4 KO rep 2

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

data_processing:
The raw sequencing data (FASTQ files) with approximately 20 million reads per sample were adapter trimmed (TrimGalore 0.6.0) and mapped to the GRCm38.p6/mm10 genome with STAR (2.7.2a)
GENCODE M25 gene annotations were quantified with Rsubread (2.2.6).
FPKM values and differential gene expression were determined using DESeq2 (1.34.0).
Assembly: GRCm38/mm10
Supplementary files format and content: CSV files of raw counts and mean FPKM values for each experimental condition

source_name: skeletal muscle

extract_protocol:
Isolation of bulk satellite cells from hind limbs was performed as described previously (Arpke et al. 2013; Arpke and Kyba 2016). Briefly, hind limb muscles were carefully dissected and cut longitudinally with a razor blade parallel to the muscle fibers, using forceps each time pressing the blade to separate the fibers. The minced muscle was incubated shaking for 75 min in 0.2% collagenase type II (Gibco, Grand Island, NY) in high glucose Dulbecco’s modified Eagle’s medium (DMEM) containing 4 mM L-glutamine 4,500 mg/L glucose, and sodium pyruvate (HyClone, Logan, UT) supplemented with 1% Pen/Strep (Gibco) at 37oC. Samples were washed twice with Rinsing Solution (F-10+), Ham’s/F-10 medium (HyClone) supplemented with 10% Horse Serum (HyClone), 1% 1 M HEPES buffer solution (Gibco), and 1% Pen/Strep. Samples were centrifuged at 500 G for 5 minutes. After aspiration of supernatant, the sample was resuspended in F-10+ containing collagenase type II and dispase (Gibco), vortexed, and incubated shaking at 37⁰C for 30 min. Samples were vortexed again, drawn and released into a 10 mL syringe with a 16-gauge needle four times, then with a 18-gauge needle four times to release the cells from the muscle fibers prior to passing the cell suspension through a 40-µm cell strainer (Falcon, Hanover Park, IL). The sample was drawn and released into a 10 mL syringe with the 18-gauge needle four additional times and passed through a new 40-µm cell strainer. Samples were centrifugated for 5 min 500 G at 4 oC, and resuspended in Fluorescent-activated Cell Sorting (FACS) staining medium: Phosphate Buffered Saline (PBS, Corning, Manassas, VA) containing 2% fetal bovine serum (HyClone) and 0.5 μg/mL propidium iodide, for FACS analysis and sorting on a FACSAriaII (BD Biosciences, San Diego, CA)
Libraries were prepared from total RNA from FACS sorted cells using the NEBNext Ultra Kit by GeneWiz (South Plainfield, NJ).

treatment_protocol: Mice were treated for 5 consecutive days with 80 mg/kg IP tamoxifen (Sigma Aldrich) dissolved at a concentration of 85 mg per 1 ml ethanol 100% then mixed with sunflower oil (Sigma Aldrich) to reach a final concentration of 12.75 mg in 1ml vehicle. FACS sorted cells were cultured overnight.

value: skeletal muscle

value: Pax7+ Satellite Cells

value: CXCR4 FL/FL (Jackson 008767), Pax7-creERT2 (PMID: 25971691), Pax7-ZsGreen (PMID:18802040)


title: H3K27ac, R212Q, rep2

description: ChIP-enriched DNA

value: DMSO


title: Activated Pax7+ Satellite cells from Cxcr4 KO rep 1


title: Activated Pax7+ Satellite cells from WT rep 2

value: CXCR4 FL/FL (Jackson 008767), Pax7-ZsGreen (PMID:18802040)


title: H3K27ac, E379K, rep2

description: ChIP-enriched DNA


title: Med1, Control, rep2

description: ChIP-enriched DNA


title: H3K27ac, E379K, rep1

description: ChIP-enriched DNA


title: Activated Pax7+ Satellite cells from WT rep 1


title: H3K27ac, PPARg2-WT, rep1

description: ChIP-enriched DNA


title: H3K27ac, R212Q, rep1

description: ChIP-enriched DNA


title: H3K27ac, UT, rep2

description: ChIP-enriched DNA


title: Med1, R212Q, rep1

description: ChIP-enriched DNA


title: Islet cells_PDL1_2

description: Bulk RNAseq


title: Quiescent Pax7+ Satellite cells from Cxcr4 KO rep 4

treatment_protocol: Mice were treated for 5 consecutive days with 80 mg/kg IP tamoxifen (Sigma Aldrich) dissolved at a concentration of 85 mg per 1 ml ethanol 100% then mixed with sunflower oil (Sigma Aldrich) to reach a final concentration of 12.75 mg in 1ml vehicle.


title: H3K27ac, UT, rep1

description: ChIP-enriched DNA


title: Quiescent Pax7+ Satellite cells from Cxcr4 KO rep 3


title: Quiescent Pax7+ Satellite cells from WT rep 3


title: HA, untransduced control, rep2

description: ChIP-enriched DNA

extract_protocol:
ChIP-seq libraries of HA-enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
Purified RNA was subjected to polydT-enriched cDNA synthesis before sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq libraries of HA-, Med1, and H3K27ac-enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279). ATAC-seq libraries were prepared for sequencing according to manufacturer's instructions (Illumina).

value: HA; Abcam ab9110


title: HA, PPARg R212Q, rep2

description: ChIP-enriched DNA


title: Quiescent Pax7+ Satellite cells from Cxcr4 KO rep 2


title: Quiescent Pax7+ Satellite cells from WT rep 2


title: HA, PPARg E379K, rep2

description: ChIP-enriched DNA


title: Quiescent Pax7+ Satellite cells from Cxcr4 KO rep 1


title: HA, PPARg WT, rep2

description:
ChIP-enriched DNA
HApeaks_DESeq2.bed


title: HA, PPARg E379K, rep1

description: ChIP-enriched DNA


title: Quiescent Pax7+ Satellite cells from WT rep 1


title: Quiescent Pax7+ Satellite cells from WT rep 4


title: HA, PPARg WT, rep1

description:
ChIP-enriched DNA
HApeaks_DESeq2.bed


title: HA, untransduced control, rep1

description: ChIP-enriched DNA

value: Untransduced


title: Rat Sciatic Nerve, dissociated, CCI Day 60, Replicate 34b

city: West Point

first: Ditte

last: Lovatt

address: 770 Sumneytown Pike

institute: Merck

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Rn6.0

organism: Rattus norvegicus

source_name: Sciatic Nerve

extract_protocol:
Enzymatic digestion: About 10 mm of naïve sciatic nerve or 10 mm of the CCI ligated sciatic nerve was dissected from rats transcardially perfused with PBS for immediate enzymatic dissociation. Nerve tissues were finely chopped with scalpels and then digested in 1-2 ml enzyme cocktail comprising: trypsin (Gibco, 3 mg/ml), collagenase II (Worthington 800U/ml), hyaluronidase (Worthington, 1105 U/ml), pronase (Sigma, 240 U/ml) and dispase (Sigma, 5 U/ml) in HEPES buffered HBSS with 0.45% glucose. The digestion continued at 37°C and 5% CO2, and was terminated after 40-60 min by adding 1-2 ml dissociation medium (HBSS with HEPES, 0.45% glucose and 1% BSA) followed by trituration with a p1000 pipette. The dissociate was then filtered over a 40 um filter and into a 50 ml tube on ice and 10 ml dissociation medium was added. Cells were centrifugated (10 min, 1000rpm, 10°C) and resuspended in 1 ml dissociation medium for an additional two washes. Cells were finally resuspended in PBS with 1% BSA and counted.
Single cell RNA-sequencing was performed using the Chromium Single Cell 3′ Kit with v2 chemistry (10X Genomics) according to manufacturer instructions. We targeted 8000 cells per 10X GEM reaction. Libraries were QC’ed by verifying optimal size using the High Sensitivity DNA Agilent Bioanalyzer kit and cDNA concentration quantified using the Invitrogen Qubit HS DNA kit according to the manufacturer’s instructions. Then libraries were sequenced on an Illumina Novaseq 6000.

treatment_protocol: CCI model generation, perfusion and nerve extraction: Sprague Dawley rats weighed between 175-250 g at the time of surgery. The procedure was performed under aseptic conditions, and using standard sterile technique to perform CCI (or Sham-CCI) surgery. Anesthesia (3% Isoflurane in 100% Oxygen) was delivered by a nose cone, connected to an anesthetic machine containing a scavenging system. The skin over the back and left thigh was shaved and wiped alternately 3 times with alcohol and Betadine. The animals laid on a heating pad, temperature regulated. An incision was made to expose the left common sciatic nerve at mid-thigh level. Four loose ligatures (catgut chromic 4-0) were applied to the sciatic nerve (1 mm apart) in order to induce a local constriction injury according to the model by Bennett & Xie, 1998. The skin was closed with wound clips. For all studies conducted at the Research Labs of Merck & Co., Inc., Kenilworth, NJ, USA, experimental procedures described herein were approved by the Institutional Animal Care and Use Committees, and subjects were housed and tested in AAALAC-accredited facilities.

value: Sprague Dawley

value: Sciatic Nerve

value: Dissociated

value: Wildtype

tag: treatment/time point


title: Rat Sciatic Nerve, dissociated, CCI Day 60, Replicate 32b

description: 10x Genomics


title: Rat Sciatic Nerve, dissociated, CCI Day 60, Replicate 33a

description: 10x Genomics


title: BAT rep5 in AL mice sacrified at ZT12

city: Changsha

first: Guolin

last: Li

state: Hunan

address: 177 Lushan Road

department: College of Life Sciences

country: China

institute: Hunan Normal University

description: ad libitum (AL)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Brown adipose tissue

growth_protocol: Six-week-old male C57BL/6N mice were purchased from Beijing Vital River Laboratory Animal Technology Co., Ltd. Mice were housed in a temperature (25℃)-and light-controlled vivarium with free access to water and standard rodent chow food. All experiments were started with 8-week-old mice.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were randomly grouped to ad libitum (AL) group, acute fasting (AF) group, refeeding after acute fasting (AR) group, every-other-day fasting (EODF) group and every-other-day refeeding (EODR) group. All mice were single housed for 2 weeks prior to study initiation to allow for acclimation to the animal facility. The AL group mice were allowed unrestricted access to food. The mice of AF groups were allowed free access to food except the last day acute fasting for 4 h, 8 h, 12 h, 16 h, 20 h and 24 h, respectively, before sacrificed. The mice of AR groups were allowed free access to food except the last two days followed an acute fasting for 24 h, and then refeeding for 4 h, 8 h, 12 h, 16 h, 20 h and 24 h, respectively, before sacrificed. The mice of EODF and EODR groups were fed with 15 cycles of alternating 24 h periods of free access to food followed by 24-h fasting, then EODF mice were sacrificed after fasting for 4 h, 8 h, 12 h, 16 h, 20 h and 24 h, respectively, while EODR mice were sacrificed after refeeding for 4 h, 8 h, 12 h, 16 h, 20 h and 24 h, respectively. Considering the nocturnal eating characteristics of mice, all fasting and refeeding switches were started at Zeitgeber time 12.

value: Mice fed ad libitum


title: BAT rep3 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: BAT rep4 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: Rat Sciatic Nerve, dissociated, CCI Day 60, Replicate 32a

description: 10x Genomics


title: Rat Sciatic Nerve, dissociated, CCI Day 60, Replicate 31b

description: 10x Genomics


title: Rat Sciatic Nerve, dissociated, CCI Day 12, Replicate 3

description: 10x Genomics


title: BAT rep5 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)

value: Mice refed for 24h after 24h fasted before sacrificed


title: BAT rep1 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: Rat Sciatic Nerve, dissociated, CCI Day 60, Replicate 31a

description: 10x Genomics


title: BAT rep2 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: HA, PPARg R212Q, rep1

description: ChIP-enriched DNA

value: PPARg-/-MEF-CAR cells

value: 1 µM Rosiglitazone


title: BAT rep4 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: Rat Sciatic Nerve, dissociated, CCI Day 12, Replicate 2a

description: 10x Genomics


title: Rat Sciatic Nerve, dissociated, CCI Day 60, Replicate 34a

description: 10x Genomics


title: BAT rep3 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: Rat Sciatic Nerve, dissociated, CCI naïve, Replicate 23b

description: 10x Genomics

value: Naïve


title: BAT rep5 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: Rat Sciatic Nerve, dissociated, CCI naïve, Replicate 24b

description: 10x Genomics


title: BAT rep1 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: BAT rep4 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: Rat Sciatic Nerve, dissociated, CCI Day 60, Replicate 33b

description: 10x Genomics


title: Rat Sciatic Nerve, dissociated, CCI naïve, Replicate 22a

description: 10x Genomics


title: Rat Sciatic Nerve, dissociated, CCI naïve, Replicate 24a

description: 10x Genomics


title: Rat Sciatic Nerve, dissociated, CCI naïve, Replicate 22b

description: 10x Genomics


title: BAT rep1 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: BAT rep2 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: Rat Sciatic Nerve, dissociated, CCI Day 3, Replicate 5b

description: 10x Genomics


title: Rat Sciatic Nerve, dissociated, CCI Day 3, Replicate 6b

description: 10x Genomics


title: Rat Sciatic Nerve, dissociated, CCI Day 3, Replicate 4b

description: 10x Genomics


title: Rat Sciatic Nerve, dissociated, CCI Day 3, Replicate 1b

description: 10x Genomics


title: BAT rep4 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)

value: Mice fasted for 24h before sacrificed


title: BAT rep5 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: BAT rep2 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: BAT rep3 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: BAT rep2 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: Rat Sciatic Nerve, dissociated, CCI Day 3, Replicate 4a

description: 10x Genomics


title: Rat Sciatic Nerve, dissociated, CCI Day 3, Replicate 5a

description: 10x Genomics


title: BAT rep1 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: Rat Sciatic Nerve, dissociated, CCI Day 3, Replicate 1a

description: 10x Genomics


title: BAT rep4 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: BAT rep3 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: Rat Sciatic Nerve, dissociated, CCI Day 12, Replicate 6b

description: 10x Genomics


title: Rat Sciatic Nerve, dissociated, CCI Day 12, Replicate 7a

description: 10x Genomics


title: BAT rep3 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: Rat Sciatic Nerve, dissociated, CCI Day 12, Replicate 7b

description: 10x Genomics


title: BAT rep5 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: BAT rep1 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: Rat Sciatic Nerve, dissociated, CCI Day 12, Replicate 6a

description: 10x Genomics


title: BAT rep2 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: Rat Sciatic Nerve, dissociated, CCI Day 12, Replicate 5b

description: 10x Genomics


title: BAT rep5 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: Rat Sciatic Nerve, dissociated, CCI Day 12, Replicate 5a

description: 10x Genomics


title: BAT rep2 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: Rat Sciatic Nerve, dissociated, CCI Day 3, Replicate 6a

description: 10x Genomics


title: BAT rep3 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: Rat Sciatic Nerve, dissociated, CCI Day 12, Replicate 4a

description: 10x Genomics


title: BAT rep1 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: Rat Sciatic Nerve, dissociated, CCI Day 12, Replicate 2b

description: 10x Genomics


title: BAT rep5 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)

value: Mice refed for 20h after 24h fasted before sacrificed


title: Rat Sciatic Nerve, dissociated, CCI Day 12, Replicate 1

description: 10x Genomics


title: BAT rep4 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: BAT rep3 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: BAT rep2 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: RNAseq_polyA_lib7_pollen_mbd56CRISPR1_rep1

city: Los Angeles

first: Lucia

last: Ichino

state: CA

address: 610 Charles E Young Dr East

department: MCDB

institute: University of California, Los Angeles

data_processing:
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM).
Assembly: TAIR10
Supplementary files format and content: counts file (.count)
Supplementary files format and content: coverage tracks (.bw)

organism: Arabidopsis thaliana

source_name: mature pollen

growth_protocol: Plants were grown on soil in a greenhouse under long-day conditions (16h light / 8h dark).

extract_protocol:
Mature pollen was harvested with Galbraith Buffer method. RNA was extracted with RNeasy mini kit (Qiagen) with in column DNAse I digestion
300-500 ng of RNA was used to prepare libraries using the Illumina TruSeq Stranded mRNA Library Prep protocol, following manufacturer's instructions.

value: mature pollen

tag: ecotype

value: mbd5/6 CRISPR1


title: RNAseq_polyA_lib7_pollen_mbd56CRISPR1_rep2


title: RNAseq_polyA_lib7_pollen_mbd56CRISPR1_rep3


title: RNAseq_polyA_lib7_pollen_cmt23_rep3


title: Rat Sciatic Nerve, dissociated, CCI Day 12, Replicate 4b

description: 10x Genomics


title: RNAseq_polyA_lib7_pollen_drm12_rep3


title: BAT rep1 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: BAT rep5 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: RNAseq_polyA_lib7_pollen_cmt23_rep2


title: RNAseq_polyA_lib7_pollen_cmt23_rep1


title: RNAseq_polyA_lib7_pollen_drm12_rep2


title: BAT rep4 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: BAT rep3 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: RNAseq_polyA_lib7_pollen_nrpe1_rep3


title: BAT rep4 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: BAT rep2 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: BAT rep1 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: BAT rep4 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)

value: Mice fasted for 20h before sacrificed


title: RNAseq_polyA_lib7_pollen_nrpe1_rep2


title: RNAseq_polyA_lib7_pollen_nrpe1_rep1


title: BAT rep5 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: BAT rep3 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: RNAseq_polyA_lib7_pollen_Col0_rep3

value: wild-type


title: BAT rep2 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: RNAseq_polyA_lib7_pollen_Col0_rep2


title: RNAseq_polyA_lib7_pollen_Col0_rep1


title: BAT rep1 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: BAT rep5 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: BAT rep4 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: snRNAseq, 10X, mbd56exp7

description:
10X 3' GEX
mbd56exp6

data_processing:
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM).
For 10X data, the fatsq files were processed with CellRanger and Seurat
Assembly: TAIR10
Supplementary files format and content: For RNA-seq, processed data files are sequencing depth tracks (bigWig)  obtained using bamCoverage (deepTools) and count files obtained with Htseq-count.
Supplementary files format and content: For 10X data, we included the counts matrix for each sample, extracted from the seurat object (slot = "counts"). We also included the  meta.data file (nuclei_annotations) of the integrated seurat object, which contains all annotations for each cell (such as cluster assignment, PCA, UMAP coordinates, VN pseudotime).

source_name: mixed-stage male gametophytes

extract_protocol:
The pollen wall was disrupted by vortexing in the presence of glass beads. Nuclei were purified via DAPI sorting.
10x Genomics Chromium Single Cell 3’ Reagent Kit v3

value: mixed-stage male gametophytes

tag: genetic background


title: BAT rep3 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: snRNAseq, 10X, slnexp7

description:
10X 3' GEX
slnexp6

value: sln


title: RNAseq_polyA_lib7_pollen_drm12_rep1


title: snRNAseq, 10X, Col0exp7

description:
10X 3' GEX
Col0exp6


title: snRNAseq, 10X, morcexp6

description:
10X 3' GEX
morcexp5

value: morc hextuple


title: BAT rep1 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: BAT rep2 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: BAT rep4 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: BAT rep5 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: BAT rep3 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: BAT rep2 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: snRNAseq, 10X, Col0exp4

description:
10X 3' GEX
Col0exp3


title: BAT rep5 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)

value: Mice refed for 16h after 24h fasted before sacrificed


title: snRNAseq, 10X, ddm1exp4

description:
10X 3' GEX
ddm1exp3


title: snRNAseq, 10X, Col0exp3

description:
10X 3' GEX
Col0exp2


title: snRNAseq, 10X, met1exp5

description:
10X 3' GEX
met1exp4


title: snRNAseq, 10X, mbd56exp2

description:
10X 3' GEX
mbd56exp1


title: BAT rep3 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: snRNAseq, 10X, mom1exp3

description:
10X 3' GEX
mom1exp2


title: BAT rep4 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: snRNAseq, 10X, Col0exp2

description:
10X 3' GEX
Col0exp1


title: BAT rep2 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: BAT rep1 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: BAT rep1 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: RNAseq, polyA, lib6, pollen, mbd56, rep3

extract_protocol:
Mature pollen was harvested with vacuum method. RNA was extracted with RNeasy mini kit (Qiagen) with in column DNAse I digestion
300-500 ng of RNA was used to prepare libraries using the Illumina TruSeq Stranded mRNA Library Prep protocol, following manufacturer's instructions.

value: mbd5/6 TDNA


title: RNAseq, polyA, lib6, pollen, mbd56, rep2


title: BAT rep5 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: RNAseq, polyA, lib6, pollen, mbd56, rep1


title: BAT rep4 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: snRNAseq, 10X, Col0exp6

description:
10X 3' GEX
Col0exp5


title: BAT rep3 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: snRNAseq, 10X, Col0exp5

description:
10X 3' GEX
Col0exp4


title: RNAseq, polyA, lib6, pollen, Col0, rep2


title: BAT rep1 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: BAT rep5 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)

value: Mice fasted for 16h before sacrificed


title: BAT rep2 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: RNAseq, polyA, lib5, seedlings, mbd56h1, rep3

source_name: seedlings

extract_protocol:
RNA was extracted with Direct-zol RNA Miniprep kit (Zymo, R2052) with in column DNAse I digestion
1000 ng of RNA was used to prepare libraries using the Illumina TruSeq Stranded mRNA Library Prep protocol, following manufacturer's instructions.

value: seedlings


title: RNAseq, polyA, lib5, seedlings, h1, rep3


title: RNAseq, polyA, lib5, seedlings, mbd56h1, rep1


title: RNAseq, polyA, lib5, seedlings, h1, rep1


title: RNAseq, polyA, lib5, seedlings, mbd56, rep2


title: RNAseq, polyA, lib6, pollen, Col0, rep3


title: RNAseq, polyA, lib5, seedlings, mbd56, rep3


title: RNAseq, polyA, lib6, pollen, Col0, rep1


title: RNAseq, polyA, lib5, seedlings, mbd56, rep1


title: RNAseq, polyA, lib5, seedlings, mbd56h1, rep2


title: BAT rep4 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: BAT rep3 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: BAT rep5 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: BAT rep1 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: RNAseq, polyA, lib5, seedlings, Col0, rep3


title: BAT rep4 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: BAT rep2 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: BAT rep1 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: BAT rep3 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: RNAseq, polyA, lib5, seedlings, Col0, rep1


title: RNAseq, polyA, lib5, seedlings, Col0, rep2


title: BAT rep5 in AL mice sacrified at ZT0

description: ad libitum (AL)

value: Mice fed ad libitum


title: BAT rep4 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: RNAseq, polyA, lib4, seedlings, slnh1, rep1


title: RNAseq, polyA, lib4, seedlings, h1, rep3


title: RNAseq, polyA, lib4, seedlings, slnh1, rep3


title: BAT rep3 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: BAT rep2 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: RNAseq, polyA, lib4, seedlings, slnh1, rep2


title: BAT rep2 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: RNAseq, polyA, lib4, seedlings, h1, rep2


title: RNAseq, polyA, lib4, seedlings, h1, rep1


title: BAT rep4 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)

value: Mice refed for 12h after 24h fasted before sacrificed


title: BAT rep5 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)


title: RNAseq, polyA, lib4, seedlings, sln, rep3


title: BAT rep2 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)


title: RNAseq, polyA, lib4, seedlings, sln, rep1


title: BAT rep4 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: BAT rep1 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)


title: RNAseq, polyA, lib4, seedlings, wt, rep3


title: RNAseq, polyA, lib4, seedlings, wt, rep1


title: RNAseq, polyA, lib4, seedlings, wt, rep2


title: RNAseq, polyA, lib3, pollen, met1, rep3


title: BAT rep5 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)

value: Mice fasted for 12h before sacrificed


title: BAT rep5 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: BAT rep2 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: BAT rep1 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: RNAseq, polyA, lib4, seedlings, sln, rep2


title: BAT rep3 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: BAT rep1 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: BAT rep4 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)


title: RNAseq, polyA, lib3, pollen, met1, rep2


title: BAT rep3 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)


title: RNAseq, polyA, lib3, pollen, Col0, rep3


title: RNAseq, polyA, lib3, pollen, Col0, rep2


title: BAT rep3 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)


title: BAT rep2 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)


title: BAT rep1 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)


title: RNAseq, polyA, lib3, pollen, Col0, rep1


title: BAT rep4 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: RNAseq, polyA, lib2, pollen, sln, rep1


title: BAT rep5 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: RNAseq, polyA, lib2, pollen, sln, rep3


title: RNAseq, polyA, lib2, pollen, sln, rep2


title: BAT rep3 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: RNAseq, polyA, lib3, pollen, met1, rep1


title: RNAseq, polyA, lib2, pollen, mbd56, CRISPR2, rep3

value: mbd5/6 CRISPR2


title: BAT rep2 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: BAT rep1 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: BAT rep4 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: BAT rep5 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: BAT rep3 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: RNAseq, polyA, lib2, pollen, mbd56, CRISPR1, rep3


title: RNAseq, polyA, lib2, pollen, mbd56, TDNA, rep3


title: BAT rep2 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: BAT rep5 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)

value: Mice refed for 8h after 24h fasted before sacrificed


title: RNAseq, polyA, lib2, pollen, mbd56, TDNA, rep2


title: BAT rep1 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: RNAseq, polyA, lib2, pollen, mbd56, TDNA, rep1


title: RNAseq, polyA, lib2, pollen, mbd56, CRISPR2, rep2


title: BAT rep3 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)


title: BAT rep2 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)


title: RNAseq, polyA, lib2, pollen, mbd6, rep2


title: RNAseq, polyA, lib2, pollen, mbd6, rep3


title: BAT rep4 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)


title: RNAseq, polyA, lib2, pollen, mbd56, CRISPR1, rep2


title: RNAseq, polyA, lib2, pollen, mbd6, rep1


title: BAT rep1 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)


title: RNAseq, polyA, lib2, pollen, mbd56, CRISPR2, rep1


title: BAT rep5 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: RNAseq, polyA, lib2, pollen, mbd56, CRISPR1, rep1


title: BAT rep3 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: RNAseq, polyA, lib2, pollen, mbd5, rep1


title: BAT rep4 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: RNAseq, polyA, lib2, pollen, Col0, rep3


title: RNAseq, polyA, lib2, pollen, Col0, rep2


title: BAT rep5 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)

value: Mice fasted for 8h before sacrificed


title: BAT rep4 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)


title: RNAseq, polyA, lib1, seedlings, sln, rep2

extract_protocol:
RNA was extracted with Direct-zol RNA Miniprep kit (Zymo, R2052) with in column DNAse I digestion
600 ng of RNA was used to prepare libraries using the Illumina TruSeq Stranded mRNA Library Prep protocol, following manufacturer's instructions.


title: RNAseq, polyA, lib1, seedlings, sln, rep1


title: RNAseq, polyA, lib1, seedlings, sln, rep3


title: BAT rep2 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)


title: RNAseq, polyA, lib2, pollen, Col0, rep1

value: mature pollen


title: BAT rep1 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)


title: BAT rep5 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: RNAseq, polyA, lib1, seedlings, Col0, rep1


title: RNAseq, polyA, lib1, seedlings, Col0, rep2


title: BAT rep4 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: BAT rep1 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: RNAseq, polyA, lib2, pollen, mbd5, rep3


title: RNAseq, polyA, lib1dissections, no, anthers, sln, rep2

source_name: Dissections: no-anthers

extract_protocol:
RNA was extracted with RNeasy mini kit (Qiagen) with in column DNAse I digestion
300-400 ng of RNA was used to prepare libraries using the Illumina TruSeq Stranded mRNA Library Prep protocol, following manufacturer's instructions.


title: RNAseq, polyA, lib2, pollen, mbd5, rep2


title: BAT rep3 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: RNAseq, polyA, lib1dissections, anthers, sln, rep2

source_name: Dissections: anthers


title: BAT rep2 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: BAT rep2 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: BAT rep1 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: BAT rep5 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: RNAseq, polyA, lib1dissections, anthers, sln, rep1


title: BAT rep4 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: RNAseq, polyA, lib1dissections, no, anthers, mbd56, rep1

value: mbd5/6 CRISPR1


title: BAT rep3 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: RNAseq, polyA, lib1, seedlings, Col0, rep3


title: RNAseq, polyA, lib1dissections, anthers, mbd56, rep1


title: BAT rep2 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: RNAseq, polyA, lib1dissections, no, anthers, Col0, rep1


title: BAT rep1 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: BAT rep5 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)

value: Mice refed for 4h after 24h fasted before sacrificed


title: BAT rep3 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)


title: RNAseq, polyA, lib1dissections, anthers, Col0, rep2

value: wild-type


title: BAT rep3 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)


title: RNAseq, polyA, lib1dissections, no, anthers, Col0, rep2


title: RNAseq, polyA, lib1dissections, no, anthers, sln, rep1


title: BAT rep5 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: DM2_4

city: Guangzhou

first: Xinyan

last: Yang

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

department: Developmental Biology

institute: Southern Medical University

description:
Modified SMART-seq2
exp_TPM_log_Normal_DM.txt

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Single-cell RNA-seq raw reads were processed to remove Template Switch Oligo (TSO) sequence and polyA tail sequence. And then the reads with adapter and low-quality bases were removed to obtain clean reads.
The clean reads were aligned to human genome (GRCh38, Gencode version) using Hisat2 (v 2.1.0) with default parameters, and uniquely mapped reads according to unique molecular identifiers (UMI) numbers were counted using HTSeq (v 0.11.3).
For all 960 sequenced single cells, we quantified the numbers of genes and transcripts in each cell. Cells with either fewer than 2,000 genes or fewer than 10,000 UMI detected were removed from downstream analysis. After filtering, we obtained 441 cells from DM donor 1 and 459 cells from DM donor 2.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: exp_TPM_log_Normal_DM.txt, Info.Normal_DM.txt

organism: Homo sapiens

source_name: Human Testicular Cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly, a single cell was picked into the lysis buffer by mouth pipette. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the cells of the same sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ terminal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on Illumina HiSeq 4000 platform (sequenced by Novogene).

tag: diagnosis

value: type 2 diabetes mellitus

value: testis

tag: gender

value: male

tag: donor


title: RNAseq, polyA, lib1dissections, anthers, Col0, rep1

tag: tissue


title: BAT rep2 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)

tag: treatment


title: BAT rep1 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)


title: DM2_3


title: BAT rep4 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: RNAseq, polyA, lib1dissections, no, anthers, mbd56, rep2


title: DM2_5


title: BAT rep3 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: DM2_1


title: DM2_2


title: BAT rep1 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: RNAseq, polyA, lib1dissections, anthers, mbd56, rep2


title: DM1_10


title: DM1_9


title: BAT rep5 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)

value: Mice fasted for 4h before sacrificed


title: BAT rep4 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)


title: DM1_6


title: DM1_7


title: BAT rep2 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)


title: BAT rep3 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)


title: BAT rep4 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)


title: BAT rep1 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)


title: BAT rep2 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: BAT rep3 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: BAT rep5 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: BAT rep4 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: BAT rep1 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: BAT rep2 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: IngWAT rep4 in AL mice sacrified at ZT12

description: ad libitum (AL)

source_name: Inguinal white adipose tissue


title: WT yeast, MnCl2 and DNase treatment I, replicate 1

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

description:
WT Untreated vs MnCl and DNase Treated sumnorm.csv
MnCl Treated vs MnCl and DNase Treated sumnorm.csv

data_processing:
Base-calling was performed using bcl2fastq software (version 2.20.00).
Reads were deduplicated based on the UMI sequence via fqtrim (version 0.9.7) with the "-C" option.
Reads containing the 5' sequence and UMI 5'-AGNNNNNNNNTG-3' were identified, and this sequence was removed using cutadapt (version 3.4) with "-g -no-indels" parameters.
The 3' sequence 5'-CTGTAGGCACCAT-3' was removed with cutadapt (version 3.4) and the parameters "-a -no-indels".
STAR (version 2.7.1a) was used to align the reads to the Saccharomyces cerevisiae genome. The STAR alignIntronMax parameter was set to 1.
SAMtools (version 1.6) was used to sort and index BAM files.
Sorted BAM files were converted to BED files using BEDTools (version 2.28.0).
BEDTools (version 2.28.0) was used to generate genome coverage files, with the genomecov function and parameters "-strand" and "+strand"
Data processing and visualization was performed using R (version 4.0.2) and RStudio (1.3.959).
Assembly: S. cerevisiae R64-1-1
Supplementary files format and content: Processed data are all in a .csv file format. The header/column names specify which treatment group and replicate that the values in the table are representing.
Library strategy: NET-seq

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast was grown at 30ºC with nutation.

extract_protocol:
Extraction methods were based on previously published methods from our lab (data available at GSE142457, GSE166983, and GSE175553). In brief, cells were harvested by filtration, flash frozen, and lysed under cryogenic conditions. Samples were either left untreated or treated as described in the "treatment protocol" section. Pol I was immunoprecipitated as previously described. Finally, a total RNA extraction was performed using acidic phenol and chloroform.
DNA libraries were constructed exactly as previously published (Jacobs and Huffines et al., "The small-molecule BMH-21 directly inhibits transcription elongation and DNA occupancy of RNA polymerase I in vivo and in vitro", JBC, 2021). Briefly, a DNA linker containing a UMI sequence was ligated onto the 3' end of RNA reads. Samples were precipitated, reads were reverse transcribed, and DNA was circularized. Circular DNAs were amplified, libraries were purified with PCRClean DX beads, and sequencing was performed.

treatment_protocol: Untreated control samples were not exposed to any treatments. CaCl2 and CaCl2 + MNase samples were treated with 5 mM (final concentration) of CaCl2. CaCl2 + DNase I samples were then treated with 100 U/µL (final concentration) of MNase. Both the CaCl2 and CaCl2 + MNase samples were incubated at 37ºC for 2 minutes, a final concentration of 5 mM EDTA (pH 8.5) was added to the samples, and then the normal NET-seq protocol was followed. MnCl2 and MnCl2 + DNase I samples were treated with 10 mM (final concentration) of MnCl2. MnCl2 + DNase I samples were then treated with 100 U/mL (final concentration) of DNase I. Both the MnCl2 and MnCl2 + DNase I samples were incubated on ice for 20 minutes. EDTA at a final concentration of 5 mM was added to these samples, they were incubated on ice for an additional 30 minutes, and then the normal NET-seq protocol was followed.

tag: cell type

value: yeast

value: MnCl2 and DNase I


title: WT yeast, CaCl2 and MNase treatment, replicate 3

description:
WT Untreated vs CaCl and MNase Treated sumnorm.csv
CaCl Treated vs CaCl and Mnase Treated sumnorm.csv

value: CaCl2 and MNase


title: WT yeast, MnCl2 treatment, replicate 2

description:
WT Untreated vs MnCl Treated sumnorm.csv
MnCl Treated vs MnCl and DNase Treated sumnorm.csv
CaCl Treated vs MnCl Treated sumnorm.csv


title: WT yeast, MnCl2 and DNase treatment I, replicate 2


title: WT yeast, MnCl2 treatment, replicate 1


title: IngWAT rep5 in AL mice sacrified at ZT12

description: ad libitum (AL)

value: Mice fed ad libitum


title: IngWAT rep3 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: WT yeast, MnCl2 treatment, replicate 3


title: WT yeast, CaCl2 and MNase treatment, replicate 1


title: WT yeast, MnCl2 and DNase treatment I, replicate 3


title: WT yeast, CaCl2 and MNase treatment, replicate 2


title: WT yeast, CaCl2 treatment, replicate 3

description:
WT Untreated vs CaCl Treated sumnorm.csv
CaCl Treated vs CaCl and Mnase Treated sumnorm.csv
CaCl Treated vs MnCl Treated sumnorm.csv


title: IngWAT rep2 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: DM1_8

tag: age


title: WT yeast, CaCl2 treatment, replicate 2


title: IngWAT rep1 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: WT yeast, CaCl2 treatment, replicate 1


title: IngWAT rep5 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)

value: Mice refed for 24h after 24h fasted before sacrificed


title: IngWAT rep4 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: IngWAT rep3 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: IngWAT rep2 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: IngWAT rep1 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: IngWAT rep5 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: WT yeast, untreated, replicate 1

description:
WT Untreated vs CaCl Treated sumnorm.csv
WT Untreated vs CaCl and MNase Treated sumnorm.csv
WT Untreated vs MnCl Treated sumnorm.csv
WT Untreated vs MnCl and DNase Treated sumnorm.csv


title: IngWAT rep3 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: IngWAT rep1 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: IngWAT rep2 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: WT yeast, untreated, replicate 3


title: IngWAT rep3 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)

value: Mice fasted for 24h before sacrificed


title: IngWAT rep2 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: 24763_polyA-RNA_oligo-dT_37C_4-SU-treatment_spt20D_BY4741

city: Ithaca

first: B. Franklin

last: Pugh

state: NY

address: 465 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

data_processing:
RNAseq reads were aligned using hisat2 with the following settings: hisat2 -I 10 -X 700 --very-sensitive --no-unal --no-mixed --no-discordant and then sorted with samtools
calculate coverage of read2 5' tag using ScriptManager bam-format-converter tools (RRID:SCR_021797)
calculate a scaling factor for each sample using NCIS in ScriptManager with blacklist and control BAM files from Rossi et al, 2020
scale coverage of each sample and convert it to BigWig format
Assembly: sacCer3
Supplementary files format and content: Bigwig for forward strand -- coverage of 5' end of Read 2 across the genome
Supplementary files format and content: Bigwig for reverse strand -- coverage of 5' end of Read 2 across the genome

growth_protocol: S. cerevisiae cultures were grown in 50 mL YPDA medium to an O.D600 of 0.6-0.8 at 25 ˚C.

extract_protocol:
Cells were labeled with 4-SU for 6 minutes. Nascent RNA was biotin labeled and purified streptavidin beads. PolyA enriched species were obtained using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490S, Lot:10043249) and were used for library construction (NEBNext, #E7760S, Lot:10046628).. RS
RNA libraries were sequenced in a paired-end mode with NextSeq 500 (Read_1 40 cycles, Read_2 36 cycles).

treatment_protocol: For inducing acute heat shock at 37 ˚C, 50 mL of YPDA at 55 ˚C was added to 50 mL cultures and quickly transferred to a shaker incubator (Badjatia et al., 2021)at 37 ˚C for 6 min.

tag: sample id

tag: strain background

tag: genetic modification

tag: growth media

value: YPD

tag: treatment temperature

tag: treatment chemicals


title: 24762_polyA-RNA_oligo-dT_25C_4-SU-treatment_spt20D_BY4741

description: Cells were labeled with 4-SU for 6 minutes. Nascent RNA was biotin labeled and purified streptavidin beads. PolyA enriched species were obtained using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490S, Lot:10043249) and were used for library construction (NEBNext, #E7760S, Lot:10046628).. RS


title: 10452_Med15_9E10_25C_6uM-NAPP1_WT_yFR1636

description: 6 uM of 1-Naphthyl PP1 (NAPP1; Tocris Bioscience) for 15 min prior to crosslinking

data_processing:
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1)  -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file. using picard MarkDuplicates and samtools
calculate coverage of read1 5' tag using ScriptManager bam-format-converter tools (RRID:SCR_021797)
calculate a scaling factor for each sample using (1-TF target and 2-RNAseq samples) NCIS in ScriptManager with blacklist and control BAM files from Rossi et al, 2020, (3-Nucleosome target) tally the coverage in a 25bp region around the NFR for 03_TFO and 04_UNB gene classes (defined by Rossi et al, 2020, STable 1)
scale coverage of each sample and convert it to BigWig format
Assembly: sacCer3
Supplementary files format and content: Bigwig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: Bigwig for reverse strand -- coverage of 5' end of Read 1 across the genome

extract_protocol:
50 mL cell pellets were resuspended in 750 uL FA lysis buffer (50 mM HEPES-KOH, pH7.5, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate and complete protease inhibitor (Roche) along with 1 ml of 0.5 mm acid washed zirconia beads. Lysis was performed by bead beating for 4 cycles of 3 min on and 7 min off in a Mini-Beadbeater-96 machine (Biospec). Whole cell lysates were centrifuged at 14,000 rpm for 3 min at 4 ˚C. Cytoplasmic supernatants were discarded and nuclear pellets were resuspended in 200 uL FA lysis buffer supplemented with 0.1% SDS and 75 uL 0.1 mm zirconia beads. Nuclear samples were sonicated in a Bioruptor (Diagenode) for 4 cycles of 30 sec on and 30 sec off. Samples were centrifuged at 14,000 rpm for 10 min to collect sonicated chromatin fraction which was predominantly enriched with DNA fragments in a range of 100-500 bp in size (verified on agarose gels). Following antibodies were used according to the manufacturer’s instructions to prepare ChIP-exo libraries: anti H3K120ub (Cell Signaling, 5546S), anti-H2B (Abcam, 1790), anti-IgG (Sigma, i5006), anti-TBP (Abcam, 61411), anti-PolII (Santa Cruz Biotechnology, 8WG16), anti-H3 (Abcam, 1791), anti-H3K9ac (Millipore Sigma, 07-352), anti-H3K14ac (Abcam, ab52946). Sera against Hsf1, Taf1 and SAGA subunits (Gcn5, Sgf73 and Spt3) were obtained from David Gross (Louisiana State University), Joe Reese (Pennsylvania State University) and Tony Weil (Vanderbilt School of Medicine) respectively. Chromatin obtained from 50 mL culture was used for a single ChIP experiment. Appropriate antibodies (3-5 ug per ChIP) were conjugated to protein A/G magnetic Sepharose resin (GE Healthcare Life Sciences) at 4 ˚C for 6-8 hr. Unconjugated antibody was removed, then chromatin sample were immunoprecipitated overnight (12-16 hr) at 4 ˚C. For TAP-tagged samples, 40 uL IgG-Dynabeads slurry was used per sample. Subsequent steps were performed as described previously (Rossi et al., 2018).
ChIP-exo libraries were gel purified and were sequenced in a paired-end mode with NextSeq 500 (Read_1 40 cycles, Read_2 36 cycles).

tag: target

tag: antibody

value: WT


title: 10462_Rpb3_W0012_25C_6uM-NAPP1_Kin28as_yFR763


title: 10460_Rpb3_W0012_25C_6uM-NAPP1_WT_yFR762


title: 10456_Med7_9E10_25C_6uM-NAPP1_WT_yFR1900


title: 10461_Rpb3_W0012_25C_6uM-NAPP1_Kin28as_yFR763


title: 10455_Med7_9E10_25C_6uM-NAPP1_WT_yFR1900


title: 10451_Med15_9E10_25C_6uM-NAPP1_WT_yFR1636


title: 10459_Rpb3_W0012_25C_6uM-NAPP1_WT_yFR762


title: WT yeast, untreated, replicate 2

tag: genotype


title: IngWAT rep5 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: IngWAT rep4 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: 24754_polyA-RNA_oligo-dT_25C_4-SU-treatment_spt20D_BY4741


title: IngWAT rep5 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: 24755_polyA-RNA_oligo-dT_37C_4-SU-treatment_spt20D_BY4741


title: IngWAT rep3 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: IngWAT rep4 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: IngWAT rep4 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: IngWAT rep1 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: 28301_TBP_61411_37C_AR30_Tra1-D-tag_AB001

data_processing:
library strategy: ChIP-exo
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1)  -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file. using picard MarkDuplicates and samtools
calculate coverage of read1 5' tag using ScriptManager bam-format-converter tools (RRID:SCR_021797)
calculate a scaling factor for each sample using (1-TF target and 2-RNAseq samples) NCIS in ScriptManager with blacklist and control BAM files from Rossi et al, 2020, (3-Nucleosome target) tally the coverage in a 25bp region around the NFR for 03_TFO and 04_UNB gene classes (defined by Rossi et al, 2020, STable 1)
scale coverage of each sample and convert it to BigWig format
Assembly: sacCer3
Supplementary files format and content: Bigwig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: Bigwig for reverse strand -- coverage of 5' end of Read 1 across the genome

source_name: cell

value: cell

tag: sampleID

value: TBP

tag: assay

value: ChIP-exo


title: 28372_TBP_61411_37C_AR30_WT_AB001


title: 28953_TBP_61411_37C_AR30_WT_AB001


title: IngWAT rep1 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: RNAseq, polyA, lib5, seedlings, h1, rep2

value: seedlings

tag: ecotype

tag: genetic background


title: IngWAT rep5 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: 31324_Pol2_sc-56767_37C_AR30_Taf1-Dtag_AB001

description: Auxin and Rapamycin treatments were done for 30 min. SAGA XO

data_processing:
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1)  -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file. using picard MarkDuplicates and samtools
calculate coverage of read1 5' tag using ScriptManager bam-format-converter tools (RRID:SCR_021797)
calculate a scaling factor for each sample using (1-TF target and 2-RNAseq samples) NCIS in ScriptManager with blacklist and control BAM files from Rossi et al, 2020, (3-Nucleosome target) tally the coverage in a 25bp region around the NFR for 03_TFO and 04_UNB gene classes (defined by Rossi et al, 2020, STable 1)
scale coverage of each sample and convert it to BigWig format
Assembly: sacCer3
Supplementary files format and content: Bigwig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: Bigwig for reverse strand -- coverage of 5' end of Read 1 across the genome
Library strategy: ChIP-exo

tag: temperature


title: 31325_Pol2_sc-56767_37C_AR30_Sua7-Dtag_AB001


title: IngWAT rep4 in AL mice sacrified at ZT8

description: ad libitum (AL)

tag: treatment


title: IngWAT rep3 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: IngWAT rep2 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: 31323_Pol2_sc-56767_37C_AR30_Spt20-Dtag_AB001


title: 28955_TBP_61411_37C_AR30_Tra1-D-tag_AB001

tag: cell type


title: IngWAT rep5 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)

value: Mice refed for 20h after 24h fasted before sacrificed


title: IngWAT rep3 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: IngWAT rep4 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: IngWAT rep1 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: 31319_Pol2_sc-56767_37C_AR30_Taf1-Dtag_AB001


title: 31320_Pol2_sc-56767_37C_AR30_Sua7-Dtag_AB001


title: IngWAT rep1 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: 31322_Pol2_sc-56767_37C_AR30_Spt7-Dtag_AB001


title: IngWAT rep5 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: IngWAT rep2 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: 31321_Pol2_sc-56767_37C_AR30_WT_AB001


title: 31316_Pol2_sc-56767_37C_AR30_WT_AB001


title: 31315_Pol2_sc-56767_25C_AR30_Sua7-Dtag_AB001


title: 31314_Pol2_sc-56767_25C_AR30_Taf1-Dtag_AB001


title: 31318_Pol2_sc-56767_37C_AR30_Spt20-Dtag_AB001


title: IngWAT rep4 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: IngWAT rep2 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: 31317_Pol2_sc-56767_37C_AR30_Spt7-Dtag_AB001


title: IngWAT rep1 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: 31310_H3_ab1791_37C_AR30_Tra1-Dtag_AB001


title: 31309_H3_ab1791_37C_AR30_Spt20-Dtag_AB001


title: 31312_Pol2_sc-56767_25C_AR30_Spt7-Dtag_AB001


title: 31308_H3_ab1791_37C_AR30_Gcn5-Dtag_AB001


title: IngWAT rep3 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: IngWAT rep2 in AR mice sacrified at ZT8

description: refeeding after acute fasting (AR)


title: 31313_Pol2_sc-56767_25C_AR30_Spt20-Dtag_AB001


title: IngWAT rep3 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)

value: Mice fasted for 20h before sacrificed


title: IngWAT rep4 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: 31306_H3_ab1791_37C_AR30_Tra1-Dtag_AB001


title: IngWAT rep1 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: IngWAT rep2 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: 31307_H3_ab1791_37C_AR30_WT_AB001


title: 31305_H3_ab1791_37C_AR30_Spt20-Dtag_AB001


title: IngWAT rep5 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: IngWAT rep4 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: 31303_H3_ab1791_37C_AR30_WT_AB001


title: 31302_H3_ab1791_25C_AR30_Tra1-Dtag_AB001


title: 31304_H3_ab1791_37C_AR30_Gcn5-Dtag_AB001


title: IngWAT rep3 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: IngWAT rep2 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: 31301_H3_ab1791_25C_AR30_Gcn5-Dtag_AB001


title: 31311_Pol2_sc-56767_25C_AR30_WT_AB001


title: IngWAT rep5 in EODF mice sacrified at ZT8

description: every-other-day fasting (EODF)


title: IngWAT rep1 in AF mice sacrified at ZT8

description: acute fasting (AF)


title: IngWAT rep5 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: 31300_H3_ab1791_25C_AR30_Spt20-Dtag_AB001


title: IngWAT rep4 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: 31299_H3_ab1791_25C_AR30_WT_AB001


title: IngWAT rep3 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: IngWAT rep2 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: IngWAT rep5 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)

value: Mice refed for 16h after 24h fasted before sacrificed


title: 31297_H3_ab1791_37C_-_ahc1D_BY4741

description: SAGA XO


title: 31298_H3_ab1791_37C_-_ahc1D_BY4741

description: SAGA XO


title: IngWAT rep3 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: IngWAT rep1 in AL mice sacrified at ZT4

description: ad libitum (AL)


title: IngWAT rep2 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: 31296_H3_ab1791_37C_-_sgf73D_BY4741

description: SAGA XO


title: IngWAT rep4 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: IngWAT rep1 in EODR mice sacrified at ZT4

description: every-other-day refeeding (EODR)


title: 31293_H3_ab1791_37C_-_WT_BY4741

description: SAGA XO


title: 31295_H3_ab1791_37C_-_spt20D_BY4741

description: SAGA XO


title: 31294_H3_ab1791_37C_-_gcn5D_BY4741

description: SAGA XO


title: 31291_H3_ab1791_25C_-_ahc1D_BY4741

description: SAGA XO


title: 31290_H3_ab1791_25C_-_sgf73D_BY4741

description: SAGA XO


title: 31292_H3_ab1791_25C_-_ahc1D_BY4741

description: SAGA XO


title: 31289_H3_ab1791_25C_-_spt20D_BY4741

description: SAGA XO


title: 31288_H3_ab1791_25C_-_gcn5D_BY4741

description: SAGA XO


title: 31287_H3_ab1791_25C_-_WT_BY4741

description: SAGA XO


title: IngWAT rep2 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: IngWAT rep3 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: 29189_H3K14ac_ab52946_37C_-_ahc1D_BY4741

description: SAGA XO


title: IngWAT rep1 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: IngWAT rep5 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)

value: Mice fasted for 16h before sacrificed


title: 29188_H3K14ac_ab52946_25C_-_ahc1D_BY4741

description: SAGA XO


title: IngWAT rep4 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: 29187_H3K14ac_ab52946_37C_-_ahc1D_BY4741

description: SAGA XO


title: IngWAT rep3 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: 29186_H3K14ac_ab52946_25C_-_ahc1D_BY4741

description: SAGA XO


title: IngWAT rep2 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: 29185_H3K14ac_ab52946_37C_-_gcn5D_BY4741

description: SAGA XO


title: IngWAT rep5 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: IngWAT rep4 in AR mice sacrified at ZT4

description: refeeding after acute fasting (AR)


title: 29184_H3K14ac_ab52946_25C_-_gcn5D_BY4741

description: SAGA XO


title: IngWAT rep4 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: 29182_H3K14ac_ab52946_25C_-_gcn5D_BY4741

description: SAGA XO


title: IngWAT rep5 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: IngWAT rep1 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: IngWAT rep2 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: 29181_H3K14ac_ab52946_37C_-_WT_BY4741

description: SAGA XO


title: 29183_H3K14ac_ab52946_37C_-_gcn5D_BY4741

description: SAGA XO


title: 29178_H3K14ac_ab52946_25C_-_WT_BY4741

description: SAGA XO


title: IngWAT rep1 in EODF mice sacrified at ZT4

description: every-other-day fasting (EODF)


title: IngWAT rep3 in AF mice sacrified at ZT4

description: acute fasting (AF)


title: 29179_H3K14ac_ab52946_37C_-_WT_BY4741

description: SAGA XO


title: IngWAT rep4 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: 29167_H3K9ac_07-352_37C_-_ahc1D_BY4741

description: SAGA XO


title: IngWAT rep2 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: 29180_H3K14ac_ab52946_25C_-_WT_BY4741

description: SAGA XO


title: 29168_H3K9ac_07-352_25C_-_ahc1D_BY4741

description: SAGA XO


title: IngWAT rep1 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: IngWAT rep3 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: 29166_H3K9ac_07-352_25C_-_ahc1D_BY4741

description: SAGA XO


title: 29163_H3K9ac_07-352_37C_-_gcn5D_BY4741

description: SAGA XO


title: IngWAT rep5 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)

value: Mice refed for 12h after 24h fasted before sacrificed


title: 29169_H3K9ac_07-352_37C_-_ahc1D_BY4741

description: SAGA XO


title: IngWAT rep4 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)


title: IngWAT rep3 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)


title: IngWAT rep5 in AL mice sacrified at ZT0

description: ad libitum (AL)


title: IngWAT rep2 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)


title: IngWAT rep1 in EODR mice sacrified at ZT0

description: every-other-day refeeding (EODR)


title: 29159_H3K9ac_07-352_37C_-_WT_BY4741

description: SAGA XO


title: 29161_IgG_i5006_37C_-_WT_BY4741

description: SAGA XO

value: IgG


title: 29158_H3K9ac_07-352_25C_-_WT_BY4741

description: SAGA XO


title: IngWAT rep5 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: IngWAT rep4 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: 28999_H2BK123ub_5546S_37C_-_sgf73D_BY4741

description: SAGA XO


title: 28998_H2BK123ub_5546S_25C_-_sgf73D_BY4741

description: SAGA XO


title: IngWAT rep2 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: 28995_H2BK123ub_5546S_37C_-_gcn5D_BY4741

description: SAGA XO


title: IngWAT rep3 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: IngWAT rep1 in AR mice sacrified at ZT0

description: refeeding after acute fasting (AR)


title: 28994_H2BK123ub_5546S_25C_-_gcn5D_BY4741

description: SAGA XO


title: IngWAT rep5 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)

value: Mice fasted for 12h before sacrificed


title: IngWAT rep2 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)


title: IngWAT rep3 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)


title: 28993_H2BK123ub_5546S_37C_-_WT_BY4741

description: SAGA XO


title: 28992_H2BK123ub_5546S_25C_-_WT_BY4741

description: SAGA XO


title: 28990_H2B_ab1790_25C_-_sgf73D_BY4741

description: SAGA XO


title: 28991_H2B_ab1790_37C_-_sgf73D_BY4741

description: SAGA XO


title: IngWAT rep4 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)


title: IngWAT rep1 in EODF mice sacrified at ZT0

description: every-other-day fasting (EODF)


title: 28986_H2B_ab1790_25C_-_gcn5D_BY4741

description: SAGA XO


title: 28987_H2B_ab1790_37C_-_gcn5D_BY4741

description: SAGA XO


title: 29160_IgG_i5006_25C_-_WT_BY4741

description: SAGA XO


title: 28984_H2B_ab1790_25C_-_WT_BY4741

description: SAGA XO


title: IngWAT rep5 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: IngWAT rep3 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: IngWAT rep2 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: 28979_H3K9ac_07-352_37C_-_gcn5D_BY4741

description: SAGA XO


title: 28982_H3K9ac_07-352_25C_-_sgf73D_BY4741

description: SAGA XO


title: IngWAT rep4 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: IngWAT rep4 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: 28978_H3K9ac_07-352_25C_-_gcn5D_BY4741

description: SAGA XO


title: 28983_H3K9ac_07-352_37C_-_sgf73D_BY4741

description: SAGA XO


title: 28976_H3K9ac_07-352_25C_-_WT_BY4741

description: SAGA XO


title: IngWAT rep5 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: IngWAT rep1 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: IngWAT rep3 in AL mice sacrified at ZT20

description: ad libitum (AL)


title: 28973_H3K9ac_07-352_37C_AR30_Spt20-Dtag_AB001


title: 28974_H3K9ac_07-352_25C_AR30_Tra1-Dtag_AB001


title: 28977_H3K9ac_07-352_37C_-_WT_BY4741

description: SAGA XO


title: 28975_H3K9ac_07-352_37C_AR30_Tra1-Dtag_AB001


title: 28972_H3K9ac_07-352_25C_AR30_Spt20-Dtag_AB001


title: IngWAT rep4 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)

value: Mice refed for 8h after 24h fasted before sacrificed


title: IngWAT rep5 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)


title: IngWAT rep2 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)


title: 28970_H3K9ac_07-352_25C_AR30_Gcn5-Dtag_AB001


title: 28985_H2B_ab1790_37C_-_WT_BY4741

description: SAGA XO


title: IngWAT rep1 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)


title: 28969_H3K9ac_07-352_37C_AR30_WT_AB001


title: IngWAT rep1 in AF mice sacrified at ZT0

description: acute fasting (AF)


title: IngWAT rep5 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: 28968_H3K9ac_07-352_25C_AR30_WT_AB001


title: 28967_IgG_i5006_37C_AR30_WT_AB001


title: IngWAT rep4 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: IngWAT rep3 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: IngWAT rep2 in AL mice sacrified at ZT20

description: ad libitum (AL)

value: Mice fed ad libitum


title: 28961_Taf1_ReeseLab-B01_37C_AR30_WT_AB001


title: 28966_IgG_i5006_25C_AR30_WT_AB001


title: IngWAT rep2 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: IngWAT rep1 in AR mice sacrified at ZT20

description: refeeding after acute fasting (AR)


title: 28971_H3K9ac_07-352_37C_AR30_Gcn5-Dtag_AB001


title: 28958_TBP_61411_25C_AR30_Spt20-Dtag_AB001


title: IngWAT rep5 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)

value: Mice fasted for 8h before sacrificed


title: IngWAT rep4 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)


title: 28952_TBP_61411_25C_AR30_WT_AB001


title: IngWAT rep3 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)


title: IngWAT rep3 in EODR mice sacrified at ZT20

description: every-other-day refeeding (EODR)


title: IngWAT rep2 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)


title: 28932_Taf1_ReeseLab-B01_37C_AR30_Spt20-Dtag_AB001

description: Auxin and Rapamycin treatments were done at 37C for 30 minutes. SAGA XO


title: IngWAT rep1 in EODF mice sacrified at ZT20

description: every-other-day fasting (EODF)


title: 28931_TBP_61411_37C_AR30_Spt20-Dtag_AB001


title: IngWAT rep5 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: IngWAT rep4 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: 28926_IgG_i5006_37C_AR30_Taf1-Dtag_AB001


title: 28927_TBP_61411_25C_AR30_Spt20-Dtag_AB001

description: Auxin and Rapamycin treatments were done at 25C for 30 minutes. SAGA XO


title: 28934_IgG_i5006_37C_AR30_Spt20-Dtag_AB001


title: IngWAT rep3 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: 28928_Taf1_ReeseLab-B01_25C_AR30_Spt20-Dtag_AB001


title: 28924_Taf1_ReeseLab-B01_37C_AR30_Taf1-Dtag_AB001


title: IngWAT rep2 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: 28923_TBP_61411_37C_AR30_Taf1-Dtag_AB001


title: 28920_Taf1_ReeseLab-B01_25C_AR30_Taf1-Dtag_AB001


title: IngWAT rep5 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: IngWAT rep4 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: 28919_TBP_61411_25C_AR30_Taf1-Dtag_AB001


title: IngWAT rep3 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: 28908_Taf1_ReeseLab-B01_37C_AR30_WT_AB001


title: IngWAT rep2 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: IngWAT rep1 in AL mice sacrified at ZT16

description: ad libitum (AL)


title: 28907_TBP_61411_37C_AR30_WT_AB001


title: IngWAT rep4 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)

value: Mice refed for 4h after 24h fasted before sacrificed


title: IngWAT rep5 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)


title: 28904_Taf1_ReeseLab-B01_25C_AR30_WT_AB001


title: IngWAT rep3 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)


title: IngWAT rep2 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)


title: IngWAT rep1 in EODR mice sacrified at ZT16

description: every-other-day refeeding (EODR)


title: IngWAT rep5 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: 28306_IgG_i5006_37C_AR30_Taf1-Dtag_AB001

description: Auxin and Rapamycin treatments were done at 37C for 30 minutes. XO


title: IngWAT rep4 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: 28373_H3K9ac_07-352_37C_AR30_WT_AB001


title: 28305_Taf1_ReeseLab-B01_37C_AR30_Taf1-Dtag_AB001


title: 28298_H3K9ac_07-352_37C_AR30_Gcn5-Dtag_AB001


title: IngWAT rep1 in AF mice sacrified at ZT20

description: acute fasting (AF)


title: 28296_IgG_i5006_37C_AR30_Spt20-Dtag_AB001


title: IngWAT rep3 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: 28910_IgG_i5006_37C_AR30_WT_AB001


title: IngWAT rep1 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: IngWAT rep2 in AR mice sacrified at ZT16

description: refeeding after acute fasting (AR)


title: 28294_Gcn5_Bethyl-Labs_37C_AR30_Spt20-Dtag_AB001

value: Bethyl-Labs


title: 28295_Taf1_ReeseLab-B01_37C_AR30_Spt20-Dtag_AB001


title: IngWAT rep5 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)

value: Mice fasted for 4h before sacrificed


title: 28906_IgG_i5006_25C_AR30_WT_AB001

value: WT


title: IngWAT rep4 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)


title: IngWAT rep3 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)


title: IngWAT rep2 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)


title: 28376_Gcn5_Bethyl-Labs_37C_AR30_WT_AB001


title: IngWAT rep1 in EODF mice sacrified at ZT16

description: every-other-day fasting (EODF)


title: 28304_TBP_61411_37C_AR30_Taf1-Dtag_AB001

value: TBP


title: IngWAT rep5 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: 28283_TBP_61411_37C_AR30_WT_AB001


title: 26411_Sua7_GTX64172_25C_AR30_Taf1-Dtag_AB001

description: Auxin and Rapamycin treatments were done at 25C for 30 minutes. XO


title: 26410_TBP_61411_25C_AR30_Taf1-Dtag_AB001


title: 28287_Gcn5_Bethyl-Labs_37C_AR30_WT_AB001


title: IngWAT rep4 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: 28284_H3K9ac_07-352_37C_AR30_WT_AB001


title: IngWAT rep2 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: 26404_H3K9ac_07-352_25C_AR30_Tra1-Dtag_AB001


title: 26405_H3_ab1791_25C_AR30_Tra1-Dtag_AB001


title: 26401_H3_ab1791_25C_AR30_Gcn5-Dtag_AB001


title: Muscle rep5 in AL mice sacrified at ZT12

description: ad libitum (AL)

source_name: Skeletal muscle


title: IngWAT rep1 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: 28954_TBP_61411_25C_AR30_Tra1-Dtag_AB001


title: 28292_TBP_61411_37C_AR30_Spt20-Dtag_AB001


title: Muscle rep3 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: Muscle rep4 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: Muscle rep2 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: 26400_H3K9ac_07-352_25C_AR30_Gcn5-Dtag_AB001


title: Muscle rep1 in AL mice sacrified at ZT12

description: ad libitum (AL)


title: 26396_Gcn5_Bethyl-Labs_25C_AR30_Spt20-Dtag_AB001


title: 26417_IgG_i5006_25C_-_spt3D_BY4741

description: Strain is from Reese lab. Used for the first time.. XO


title: 26397_H3K9ac_07-352_25C_AR30_Spt20-Dtag_AB001


title: IngWAT rep3 in AF mice sacrified at ZT16

description: acute fasting (AF)


title: 26387_IgG_i5006_25C_AR30_WT_AB001


title: 26385_H3_ab1791_25C_AR30_WT_AB001


title: Muscle rep3 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)

value: Mice refed for 24h after 24h fasted before sacrificed


title: Muscle rep1 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: 26384_Gcn5_Bethyl-Labs_25C_AR30_WT_AB001


title: Muscle rep4 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: Muscle rep5 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: 26382_Hsf1_D.Gross_Lab_25C_AR30_WT_AB001


title: Muscle rep2 in EODR mice sacrified at ZT12

description: every-other-day refeeding (EODR)


title: Muscle rep4 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: Muscle rep5 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: Muscle rep2 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: 25342_Hsf1_D.Gross_Lab_37C_AR30_Tra1-Dtag_AB001

description: XO


title: 26380_H3K9ac_07-352_25C_AR30_WT_AB001


title: 26381_Sua7_GTX64172_25C_AR30_WT_AB001


title: 26378_TBP_61411_25C_AR30_WT_AB001


title: 26398_IgG_i5006_25C_AR30_Spt20-Dtag_AB001


title: Muscle rep1 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: 25340_Hsf1_D.Gross_Lab_25C_AR30_Tra1-Dtag_AB001

description: XO


title: Muscle rep5 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)

value: Mice fasted for 24h before sacrificed


title: 25341_Hsf1_D.Gross_Lab_37C_DMSO_Tra1-Dtag_AB001

description: XO

value: DMSO


title: 26393_H3_ab1791_25C_AR30_Spt20-Dtag_AB001


title: 25339_Hsf1_D.Gross_Lab_25C_DMSO_Tra1-Dtag_AB001

description: XO


title: Muscle rep4 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: 25338_IgG_i5006_37C_AR30_WT_AB001

description: XO


title: Muscle rep3 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: 25337_IgG_i5006_37C_DMSO_WT_AB001

description: XO


title: Muscle rep2 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: 25334_IgG_i5006_37C_AR30_Tra1-Dtag_AB001

description: XO


title: Muscle rep1 in EODF mice sacrified at ZT12

description: every-other-day fasting (EODF)


title: Muscle rep3 in AR mice sacrified at ZT12

description: refeeding after acute fasting (AR)


title: 25333_IgG_i5006_37C_DMSO_Tra1-Dtag_AB001

description: XO


title: Muscle rep4 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: 25328_Hsf1_D.Gross_Lab_25C_AR30_WT_AB001

description: XO


title: 25317_Sgf73_Bethyl-Labs_37C_DMSO_Hsf1-Dtag_BY4742

description: XO


title: Muscle rep3 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: 25318_Sgf73_Bethyl-Labs_37C_AR30_Hsf1-Dtag_BY4742

description: XO


title: Muscle rep1 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: 23766_IgG_i5006_37C_-_WT_AB001

description: WT parentl anchor away strain. XO


title: Muscle rep2 in AF mice sacrified at ZT12

description: acute fasting (AF)


title: 23759_Sua7_D.Gross_Lab_25C_-_WT_AB001

description: WT parentl anchor away strain. XO


title: Muscle rep3 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: Muscle rep4 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: Muscle rep5 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: Muscle rep2 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: 23761_IgG_i5006_25C_-_WT_AB001

description: WT parentl anchor away strain. XO


title: 23765_Hsf1_D.Gross_Lab_37C_-_WT_AB001

description: WT parentl anchor away strain. XO


title: Muscle rep1 in AL mice sacrified at ZT8

description: ad libitum (AL)


title: Muscle rep5 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)

value: Mice refed for 20h after 24h fasted before sacrificed


title: Muscle rep4 in EODR mice sacrified at ZT8

description: every-other-day refeeding (EODR)


title: 23453_H2BK123ub_5546S_37C_-_spt20D_BY4741

description: SPT20 gene is knocked out. XO


title: 23751_IgG_i5006_25C_-_WT_BY4741

description: WT BY. XO


title: 23756_IgG_i5006_37C_-_WT_BY4741

description: WT BY. XO