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| Status |
Public on Mar 11, 2024 |
| Title |
acuteCtrl289 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
Sex: male
cell type: acute
genotype: C57/Bl6
treatment: Ctrl
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| Treatment protocol |
The mice were stressed with our Cvs protocol as previously described (doi:https://doi.org/10.1016/j.molmet.2018.06.012). In brief, the Cvs protocoll consists of five different stressors (warm swim, cold exposure, shaking, restraint and overnight isolation) applied in a random manner 2 per day for 15 days. the first cohort was analysed immediately after the stress protocoll, a recovery cohor was analysed 3 month later. Age matched unstressed animals were used as control pe cohort.
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| Growth protocol |
C57/Bl6 male mice were bred and maintained in a regular 12h light/dark cycle (22°C ± 1°C, 50% ± 5% humidity). All mice were group housed (max. 5 mice per cage) with ad libitum access to standard chow (58% carbohydrates, 9% fat, 33% protein, R/M-H Extrudat, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water. Animal protocols were approved by the Landesamt für Natur, Umwelt und Verbraucherschutz (LANUV), NRW, Germany (81-02.04.2017.A421) and performed according to the ‘Principle of laboratory animal care’ (NIH publication No. 85-23, revised 1996) and the German law on the protection of animals.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen, Dneasy Blood & tissue Kit
500 ng of DNA were shared by ultrasound to an average length of 200 nt (Bioruptor® Pico; Diagenode SA, Seraing, Belgium). DNA was then processed in two steps and subsequently analyzed by Next-Generation Sequencing. Sample complexity was reduced by enrichment of DNA fragments with methylated cytosines using the EpiXplore™ Methylated DNA Enrichment Kit (Takara Bio Inc., Japan). NEB Ultra-II Library kit (NewEngland BioLabs® Inc.) was used according to manufacturer's instructions. Libraries were paired-end sequenced on the NextSeq550™ instrument with automated FastQ raw data analyses (Illumina, San Diego, USA).
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| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
NextSeq 550 |
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| Data processing |
FastQ files were analyzed using the Illumina Dragen® (Dynamic Read Analysis for Genomics) Bio-IT platform v 3.9.5 (Edico Genome, Illumina San Diego) on the Illumina cloud providing predesigned analysis pipelines.
Runs were prepared and quality checked using Fast Q toolkit pipeline (v1.0.0.) with a minimum length of 32 bp adapter trimming using the TRUESEQ HT/LT adapters sequence (Illumina San Diego, USA). Settings were: trimming strength: 4 and a quality score < 10 to trim bases at 5’ and 3’ sites prior to mapping.
Paired read FastQ files were then mapped using a Hash table generated by DRAGEN Reference builder (v.3.10.4) based on the mouse genome (GRCm38.p6.genome.fa). Fragments with a minimum read quality of at least 20 and a minimum read coverage of at least 5, as well as a maximum coverage of 99.9%, were considered for analysis. Deduplication, sorting, and alignment mapping to reference genome was performed using the DRAGEN Germline pipeline (version v3.2.8).
Outputs of sequence alignment/mapped Bam files were merged per condition using SamTools and analyzed using the R package MeDIP (Settings were: extend: 300; paired: TRUE; shift: 0; uniq: 0.001, window size: 100) (Lienhard et al, 2014).
Assembly: GRCm38.p6.genome.fa
Supplementary files format and content: Dragen (TM) germline pipeline bam file (bam)
Supplementary files format and content: corresponding Dragen (TM) germline pipeline bam.bai file (bam.bai)
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| Submission date |
Jun 21, 2023 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Birgit Knebel |
| Organization name |
German Diabetes Center
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| Department |
Cinical Biochemistry and Pathobiochemistry
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| Street address |
Auf'm Hennekamp 65
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| City |
Duesseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
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| Platform ID |
GPL21626 |
| Series (2) |
| GSE235423 |
Chronic stress alters hepatic metabolism and thermodynamic respiratory efficiency affecting epigenetics in C57BL/6 mice [MeDIP-seq] |
| GSE235424 |
Chronic stress alters hepatic metabolism and thermodynamic respiratory efficiency affecting epigenetics in C57BL/6 mice |
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| Relations |
| BioSample |
SAMN35818825 |
| SRA |
SRX20735423 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7502284_acuteCtrl289cut13sitetoolkit_.bigwig |
73.4 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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