|
| Status |
Public on Jun 01, 2021 |
| Title |
Input_RE_NF |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: BMAL1 Liver-RE
feeding: Night feeding
|
| Treatment protocol |
Mice of the three genotypes were given ad libitum acess to food (AL) or feeding was restricted to 12 hours during the night (NF). Samples were collected at zeiteber times ZT8 and ZT20.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq for CEBPB was performed using the ChIP-IT high Sensitivity Kit (Active Motif)
Library construction was performed using the NEBNext® Ultra DNA Library Prep for Illumina® kit (E7370) according to the manufacturer's protocol. Samples were sequenced using the Illumina HiSeq2500.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw single end reads were first quality checked with FastQC v0.11.8
Aligned to the UCSC Mus Musculus release mm9, available at https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/ using Bowtie2 v2.4.2
Mapped reads were then sorted using Samtools v1.9 and filtered with Sambamba v0.7.1 with the following settings (sambamba view -h -t 2 -f bam -F "[XS] == null and not unmapped and not duplicate").
ChIP-seq quality assessment was performed using ChIPQC v1.26.0 R Bioconductor package
Genome_build: UCSC Mus Musculus release mm9
Supplementary_files_format_and_content: Enriched regions relative to input DNA were assessed using the ENCODE recommended Irreproducibility Discovery Rate (IDR) framework. Peaks in both replicates were detected with MACS2 v2.2.7.1 with the following settings (macs2 callpeak -f BAM -g 1.87e9 -B -p 1e-3). Peak consistency between true replicates were detected with IDR v2.0.4.2 with the following settings (--input-file-type narrowPeak --rank p.value). Peak Annotation was assessed with ChIPseeker v1.26.0 R Bioconductor package using the pre-build annotation database TxDb.Mmusculus.UCSC.mm9.knownGene (tssRegion=c(-2000, 2000)). Coverage tracks for each sample was computed with Bedtools bamCoverage option, with the following settings (bamCoverage --binSize 20 --normalizeUsing BPM --smoothLength 60 --extendReads 150 –centerReads).
|
| |
|
| Submission date |
Mar 23, 2021 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Paolo Kunderfranco |
| E-mail(s) |
Paolo.Kunderfranco@humanitasresearch.it
|
| Organization name |
Humanitas Research Hospital
|
| Department |
Research
|
| Lab |
Bioinformatic Unit
|
| Street address |
Via Rita Levi Montalcini 4
|
| City |
Pieve Emanuele |
| State/province |
Milano |
| ZIP/Postal code |
20090 |
| Country |
Italy |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE169483 |
Integration of Feeding Behaviour by the Liver Circadian Clock Reveals Network Dependency of Metabolic Rhythms [ChIP-seq] |
| GSE171184 |
Integration of Feeding Behaviour by the Liver Circadian Clock Reveals Network Dependency of Metabolic Rhythms |
|
| Relations |
| BioSample |
SAMN18448452 |
| SRA |
SRX10430422 |
