|
| Status |
Public on Feb 11, 2014 |
| Title |
S5ph pol2_ChIPSeq Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
S5ph pol2_ChIPSeq
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
strain: C57BL/6
age: 8 weeks
gender: male
chip antibody: S5ph pol2 (Abcam, ab5131)
|
| Treatment protocol |
Liver was dissected and washed in PBS then was snap frozen on dry ice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
30 mg of liver tissue was pulverized then incubated in 1% formaldehyde in PBS for 15 min at room temperature. Cross-linking was terminated by addition of glycine. The cells were spun down and rinsed in ice-cold PBS two times. The cell lysates were sonicated using a Bioruptor (Diagenode) to generate 150–350 bp fragments for immunoprecipitation. The following antibodies were used for ChIP: H3K36me3 (Abcam), S5ph pol2 (Abcam), S2ph pol2 (Abcam).
libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kits v1 following the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7 with parameters -m 1 -v 2
Only reads that were mapped to an unambiguous ‘best’ genomic location with no more than 2 mismatches were accepted
Duplicate reads were removed to limit PCR amplification bias, and all alignments were extended at the 3’ end to a length of 150 bases
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files were generated from these mapped, non-duplicate, extended reads for visualization of aggregate genomic coverage.
|
| |
|
| Submission date |
Oct 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
ruifang li |
| E-mail(s) |
lir4@niehs.nih.gov
|
| Organization name |
NIEHS
|
| Street address |
111 T.W. Alexander Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE41472 |
Epigenetic regulation of gene expression is instructed by promoter sequence and refined by developmental progression |
|
| Relations |
| SRA |
SRX193435 |
| BioSample |
SAMN01760819 |
