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Sample GSM1122516 Query DataSets for GSM1122516
Status Public on Apr 17, 2013
Title Adx_liver_veh_DNase_rep1
Sample type SRA
 
Source name Male C57BL/6, adrenalectomized
Organism Mus musculus
Characteristics genetic background: C57BL/6
gender: male
tissue: liver
treatment: veh
replicate: rep1
chip antibody: DNase
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 GH305
Adx_liver_veh_DNase_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 SRX265310
BioSample SAMN02045736

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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