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| Status |
Public on Dec 15, 2016 |
| Title |
Chow 40U, rep1 (DHS-Seq) |
| Sample type |
SRA |
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| Source name |
Chow 40U, liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
age: 19 weeks
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| Treatment protocol |
C57BL/6J mice (Jackson Laboratory) were fed either a HFD (D12327, Research Diet, 40% fat by calories) or chow diet (NIH-31, Zeigler Brothers Inc., 8% fat by calories) for seven weeks from 12 weeks of age (groups termed HFD and Chow, respectively). After seven weeks, half of the mice where sacrificed by CO2 narcosis followed by cervical dislocation, livers were dissected and processed for RNA purification, nuclei isolation or frozen in liquid nitrogen for subsequent studies. Blood samples were taken as indicated and processed for metabolic measurements. The other half of the animals continued on a chow diet (termed HFD-chow and Chow-chow) for an additional five weeks
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Livers were isolated from mice and nuclei were immediately purified. DNase digestions were performed by adding digestion buffer containing 40U of DNase I (Sigma). DNase I digestion efficiency was evaluated by quantitative PCR53 and samples with optimal digestion efficiency were incubated RNase A (Sigma) before 50–500 bp DNA fragments were purified using ultracentrifugation. DNase-seq libraries were constructed according to manufacturer´s (Illumina) instructions 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 either polydT-enriched cDNA synthesis before sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq and libraries of H3K27ac-enriched DNA and DHS-seq libraries 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).
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
SM1635
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| Data processing |
Aligment to mm9 using STAR
Differential gene expression and H3K27ac binding identified using DESeq2.
Gene ontology analysis using PANTHER.
To quantify exon and intron RNA reads the iRNA pipeline was used (Madsen, J. G. et al. iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data. Nucleic acids research, doi:10.1093/nar/gku1365 (2015).
Pathway analysis of intron-regulated genes using the curated reactome database (Croft, D. et al. The Reactome pathway knowledgebase. Nucleic acids research 42, D472-477, doi:10.1093/nar/gkt1102 (2014).Fabregat, A. et al. The Reactome pathway Knowledgebase. Nucleic acids research 44, D481-487, doi:10.1093/nar/gkv1351 (2016)).
H3K27ac ChIP-seq binding sites identified using HOMER
Enriched motif analysis using DNA motifs for TFs curated by HOMER
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph
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| Submission date |
Oct 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Lars Grøntved |
| E-mail(s) |
larsgr@bmb.sdu.dk
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| Phone |
+45 24 60 14 06
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| Organization name |
University of Southern Denmark
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| Department |
Biochemistry and Molecular Biology
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| Street address |
Campusvej 55
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| City |
Odense |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE87565 |
High fat diet-induced changes of mouse hepatic transcription and enhancer activity can be reversed by subsequent weight loss |
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| Relations |
| BioSample |
SAMN05860359 |
| SRA |
SRX2208091 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2333845_SM1635_DHS40U_Chow_rep1.bedgraph.gz |
32.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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