|
| Status |
Public on Sep 06, 2012 |
| Title |
PR_P4_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Mouse uterus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: uterus
age: 8 week
strain: C57BL/6
chip antibody: PR
treatment: P4
|
| Treatment protocol |
treated subcutaneously with oil/P4 for 1 hr
|
| Growth protocol |
8 week old ovariectomized mice
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. ChIP and input DNA were amplified using the Illumina ChIP-Seq DNA Sample Prep Kit. Briefly, DNA ends were polished and 59-phosphorylated using T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. Addition of 3’ adenine to blunt ends using Klenow fragment (3’-5’ exo minus), Illumina genomic adapters were ligated and the sample was size-fractionated to 175–225 bp on a 2% agarose gel. After amplification for 18 cycles with Phusion polymerase, the resulting DNA libraries were tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
2_PR_P4_s_1_aligned.xls; genome build: mm9
DNA libraries were sent to Illumina Sequencing Services for sequencing on a Genome Analyzer II. Sequences (35 bases) were aligned to the mouse genome (NCBI Build 37, July 2007) using Eland software. Aligns were extended in silico at their 39-ends to a length of 110-200 bp and assigned to 32-nt bins along the genome. The resulting histograms were stored in BAR (Binary Analysis Results) files. Peak locations were determined by applying a threshold of 18 (5 consecutive bins containing .18 aligns) and storing the resulting intervals in BED files (Affymetrix TAS software). These files were analyzed using Genpathway proprietary software that provides comprehensive information on genomic annotation, peak metrics and sample comparisons for all peaks (intervals).
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
|
| |
|
| Submission date |
Jan 07, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Franco DeMayo |
| E-mail(s) |
[email protected]
|
| Organization name |
National Institute of Environmental Health Sciences
|
| Department |
Reproductive and Developmental Biology Laboratory
|
| Street address |
Building 101, Room F191 111 T.W. Alexander Drive
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE34927 |
Genome-wide Profiling of Progesterone Receptor and GATA2 Binding in the Mouse Uterus [ChIP-Seq] |
| GSE40663 |
Genome-wide Profiling of Progesterone Receptor and GATA2 Binding in the Mouse Uterus |
|
| Relations |
| SRA |
SRX114724 |
| BioSample |
SAMN00771020 |
