|
| Status |
Public on Jan 21, 2014 |
| Title |
H3K27ac_Kid |
| Sample type |
SRA |
| |
|
| Source name |
H3K27ac_Kid
|
| Organism |
Mus musculus |
| Characteristics |
strain: wild type ICR
tissue: kidney
age: 8-12 weeks old
treatment: castrated+testosterone
chip antibody: H3K27ac (ab4729, 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 H3K27ac histone modification
|
| 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 wiggle files from MACS are submitted as processed data files for H3K4me1 and H3K27ac ChIP-seq.
Genome_build: mm9
Supplementary_files_format_and_content: Processed wiggle files from MACS
|
| |
|
| Submission date |
Nov 05, 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 |
SAMN02393624 |
| SRA |
SRX373261 |
