|
| Status |
Public on Dec 20, 2016 |
| Title |
fasted 24 hr CEBPb ChIP-seq rep#3 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
chip antibody: C/EBP β (C-19), sc-150
|
| Treatment protocol |
mice were fasted for 24 or 10 hrs or fed ad lib. Hepatocytes treated with glucagon (10nM) or glucagon (10nM) + corticosterone (1.7uM) for 1hr
|
| Growth protocol |
mice maintained according to NIH guidelines under 12-hr light-dark cycles (light on at 6:00AM). Hepatocytes isolated by the two-step collagenase perfusion technique
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
crosslinked material was lyzed and sonicated. Chromatin precipitated with antibody and DNA was purified by ethanol precipitation
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
GH1932
|
| Data processing |
Illumina Casava 1.8 software was used for basecalling and alignment.
Areas of enrichment were identified using DNase2Hotspots software(htrceforge.net/projects/dnase2hotspots/) software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: comma-delimited (CSV) text files include genomic locations (Chromosome, start, end ), z-score, p-value and the maximum density of hotspots. Bedgraph files contain genomic locations and normalized tag density profiles.
|
| |
|
| Submission date |
Aug 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Songjoon Baek |
| Organization name |
NCI / NIH
|
| Department |
CCR
|
| Lab |
LRBGE
|
| Street address |
41 Library Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE72084 |
Characterization of chromatin and gene expression changes during fasting in mouse liver [ChIP-Seq] |
| GSE72087 |
Characterization of chromatin and gene expression changes during fasting in mouse liver |
|
| Relations |
| BioSample |
SAMN03994729 |
| SRA |
SRX1150369 |
