|
| Status |
Public on Apr 17, 2013 |
| Title |
Adx_adGFP_liver_dex_GR_ChIP_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Male C57BL/6, adrenalectomized
|
| Organism |
Mus musculus |
| Characteristics |
genetic background: C57BL/6
gender: male
tissue: liver
treatment: dex adGFP
replicate: rep1
chip antibody: cocktail of PA-510A and PA-511A from Affinity BioReagents and sc-1004 from Santa Cruz
|
| Treatment protocol |
Bilateral adrenalectomy was carried out via a dorsal approach under ketamine/xylazine anesthesia. Mice were intraperitoneal injection of dex-cyclodextrine complex, containing 65 mg/g of dex (1 mg/kg), or vehicle (1 mg/kg cyclodexitrine) in a total volume of 300 ul of sterile saline.
|
| Growth protocol |
Male C57BL/6 mice, eight weeks old
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
GH495
Adx_adGFP_liver_dex_GR_ChIP_rep1
|
| Data processing |
Illumina Casava 1.8 software was used for basecalling.
Areas of enrichment were identified using DNase2Hotspots software(htrceforge.net/projects/dnase2hotspots/) software with FDR 0%. Peaks with the maximum tag density lower than 10 were eliminated.
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: tab-delimited peak text files include genomic locations (Chromosome, start, end ).
|
| |
|
| Submission date |
Apr 15, 2013 |
| 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 |
GPL9185 |
| Series (1) |
| GSE46047 |
C/EBP Maintains Chromatin Accessibility in Liver and Facilitates Glucocorticoid Receptor Recruitment to Steroid Response Elements |
|
| Relations |
| SRA |
SRX265322 |
| BioSample |
SAMN02045748 |
