|
| Status |
Public on May 04, 2021 |
| Title |
ChIPseq_CTCF_ZT12_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
C57BL/6
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
age: 8 week old
Sex: male
strain: C57BL/6
genotype: wilde type
time point: ZT12
|
| Growth protocol |
Mice were under a 12 hours light 12 hours dark cycle. Fed ad libitum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, liver tissue for two biological replicates at ZT0 and ZT12 was dissected as processed as for Hi-C and then fixed in 1% formaldehyde for 5 minutes. Chromatin immunoprecipitation was performed as described (Rubin et al., 2017) using 10 _g of _-CTCF (Millipore, 07-729). DNA was purified using Zymo Research DNA purification columns. Sequencing libraries were prepared with the NEBNext ChIP-seq library prep kit (NEB) according to manufacturer's instructions. DNA was purified using AMPure beads (Agencourt).
NEBnext library preparation protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ZT12 2nd biological replicate
ChIPseq_CTCF_ZT12_peaks_fimo_both_replicates.bed
|
| Data processing |
Raw sequencing data files for all samples were first processed with FastQC for general quality controls. Sequencing reads were mapped against the mouse genome (NCBIM37/mm9) using Bowtie2 (Langmead and Salzberg, 2012) with default parameters for single and paired reads.
Mapped reads were filtered by map quality (-q 30) using samtools (samtools view). Bam files were sorted (samtools sort) and indexed (samtools index). Duplicates were removed with Pickard. Bam files were imported to deeTools v3.3.1 (Ram’rez et al., 2016) to create signal tracks with bamCoverage. Signal tracks for all data were visualized using IGV (Thorvaldsd—ttir et al., 2013).
Peak calling was performed using MACS2 callpeak function with default parameters (Zhang et al., 2008). Peak overlap analysis was performed using the Venn module of Intervene (Khan and Mathelier, 2017).
The MEME-ChIP tool (Ma et al., 2014) was used for motif analysis using the fasta sequences from peaks detected by MACS2 with default parameters.
Genome_build: Mus musculus mm9
Supplementary_files_format_and_content: Bed files with the genomic positions of the CTCF peaks detected from both replicates
|
| |
|
| Submission date |
Jul 27, 2020 |
| Last update date |
May 04, 2021 |
| Contact name |
Mayra Furlan-Magaril |
| E-mail(s) |
[email protected]
|
| Phone |
525512291890
|
| Organization name |
IFC-UNAM
|
| Department |
Molecular Genetics
|
| Lab |
Genome Topology
|
| Street address |
Circuito exterior s/n
|
| City |
Mexico City |
| State/province |
Mexico City |
| ZIP/Postal code |
04510 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE155149 |
The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle [ChIP-seq] |
| GSE155161 |
The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle |
|
| Relations |
| BioSample |
SAMN15650085 |
| SRA |
SRX8829846 |
