|
| Status |
Public on Jul 07, 2020 |
| Title |
Female_CTCFchip_Repl4_G100_M1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: Crl:CD1(ICR) (Charles River, strain code #022)
chip antibody: Millipore anti CTCF (cat# 07-779)
Sex: Female
age: 8 weeks
|
| Growth protocol |
Male and female CD1 mice, 8-9 weeks of age, were purchased from Charles River Laboratories (Crl:CD1(ICR)).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated by ultracentrifugation in a high sucrose buffer then crosslinked with 0.8% formaldehyde for 9 minutes. Samples were sonicated with a Bioruptor Twin (Diagenode, UCD-400) until the majority of DNA fragments were between 100-400bp (60-70 cycles total, 30 sec ON 30 sec OFF). Chromatin was quantified and 70 ug of chromatinized DNA was incubated with the indicated ChIP antibody.
Samples were prepared for sequencing with NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's directions for low input samples (New England Biolabs, #E7645). All samples were subjected to double-sided SPRI size selection prior to PCR amplification (Agencourt AMPure XP; Beckman Coulter: A63882). Samples were barcoded using New England Biolabs NEBNext Multiplex Oligos for Illumina (#E7335) with 8 rounds of PCR per the manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ChIP-seq Library
|
| Data processing |
READ MAPPING: ChIP-seq reads were aligned using Bowtie2 (Langmead et al 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
PEAK CALLING: Peaks were called using Macs2 (Zhang et al 2008, Genome Biology) with default parameters without filtering for PCR duplicates. Peaks were filtered to remove blacklisted regions (www.sites.google.com/site/anshulkundaje/projects/blacklists) and also regions called as peaks that contain only PCR duplicated reads.
Genome_build: mm9
Supplementary_files_format_and_content: Replicate merged peak lists for CTCF (Female_CTCF_merged.bed) and cohesin/Rad21 (Female_Rad21_merged.bed). Samples were combined at the fastq level and processed through a standard ChIP-seq pipeline as described. Columns are in BED6+4 format from MACS2 narrowPeak defaults. Specifically, columns 1-3 represent genomic coordinates of the indicated peak; column 4 is the peak name (unique identifier); column 5 is an integer score for display calculated as -10*log10(qvalue); column 6 indicates the strand; column 7 indicates the fold-change over background; column 8 indicates -(log10pvalue); column 9 indicates -log10(qvalue); and column 10 indicates the summit position relative to the 5' end of the peak.
|
| |
|
| Submission date |
May 08, 2019 |
| Last update date |
Jul 07, 2020 |
| Contact name |
David J. Waxman |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University
|
| Department |
Department of Biology and Bioinformatics Program
|
| Street address |
5 Cummington Mall
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE130908 |
CTCF and Cohesin (Rad21) ChIP-seq in female mouse liver |
| GSE131128 |
CTCF and Cohesin link sex-biased distal regulatory elements to sex-biased gene expression in mouse liver |
|
| Relations |
| BioSample |
SAMN11605324 |
| SRA |
SRX5807313 |
