|
| Status |
Public on Oct 07, 2017 |
| Title |
Fasted 24 hrs CREB ChIP-seq rep#2 |
| Sample type |
SRA |
| |
|
| Source name |
Fasted 24 hrs CREB ChIP-seq
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: liver
chip antibody: CREB (48H2) Rabbit mAb #9197
|
| 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. All the sequencing data were sequenced on NextSeq 500 using NextSeq High V2 chemistry single end.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
GH2107
processed data file:
hs_RC_mouseliver_ChIP_CREB_fasted_24_r13_RC_GH2106xGH2108_FDR0.csv
|
| 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 |
Oct 06, 2017 |
| 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 |
SAMN07757751 |
| SRA |
SRX3260303 |
