NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1146487 Query DataSets for GSM1146487
Status Public on Jan 21, 2014
Title AP2a_Cast1b [caput epididymis, castrated+vehicle]
Sample type SRA
 
Source name AP2a_Cast1b
Organism Mus musculus
Characteristics strain: wild type ICR
tissue: caput epididymis
age: 8-12 weeks old
treatment: castrated+vehicle
chip antibody: AP2a (ab52222, Abcam)
Treatment protocol Tissues were harvested from intact adult male mice or from castrated male mice after 2-h testosterone- or vehicle-treatment.
Growth protocol Mice were housed in standard 12-h light-dark cycle and were fed ad libitum.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and DNA-protein complexes were isolated with respective antibodies. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 20 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description Chromatin IP against AP2a
Data processing Alignment: Sequence reads were obtained, purity filtered using the Illumina Genome Analyzer Pipeline and mapped to the mouse (mm9) genomes using BOWTIE with parameters -n0, -k1, -l30.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/). The technical replicate lanes assigned as a and b for each sample and IgG were concataned wherever required before peak calling. Overlapping peaks present in both biological replicates with a 2% FDR cutoff were used in downstream analysis. The peak files from MACS are submitted as tab-delimited text files.
Genome_build: mm9
Supplementary_files_format_and_content: Processed peak files in tab-delimited text format
 
Submission date May 22, 2013
Last update date May 15, 2019
Contact name Olli A. Jänne
E-mail(s) olli.janne@helsinki.fi
Phone +358919125040
Organization name University of Helsinki
Department Inst. of Biomedicine/Physiology
Lab Androgen Receptor Laboratory
Street address Haartmaninkatu-8
City Helsinki
ZIP/Postal code FI-00014
Country Finland
 
Platform ID GPL11002
Series (2)
GSE47192 Tissue-specific pioneer factors associate with androgen receptor cistromes and transcription programs. [ChIP-Seq]
GSE47194 Tissue-specific pioneer factors associate with androgen receptor cistromes and transcription programs
Relations
BioSample SAMN02178569
SRA SRX286408

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap