|
| Status |
Public on Jan 21, 2014 |
| Title |
rIgG1 [caput epididymis, intact] |
| Sample type |
SRA |
| |
|
| Source name |
rIgG1
|
| Organism |
Mus musculus |
| Characteristics |
strain: wild type ICR
tissue: caput epididymis
age: 8-12 weeks old
treatment: intact
chip antibody: rIgG (sc-2027, SantaCruz)
|
| 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 rabbit IgG
|
| 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 |
SAMN02178574 |
| SRA |
SRX286413 |
