|
| Status |
Public on Apr 04, 2011 |
| Title |
Set ABCD, DMC1 |
| Sample type |
SRA |
| |
|
| Source name |
adult testis
|
| Organism |
Mus musculus |
| Characteristics |
strain: 13R/9R and 9R/13R crosses
genotype/variation: Hop2 -/-
chip antibody: DMC1 (C-20)
antibody catalog number: sc 8973
antibody lot: G0909
antibody vendor: Santa Cruz
|
| Growth protocol |
Cells were extracted from testis (or liver) of euthanized mice and immediately subjected to immunoprecipitation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates from mice testis cells were sonicated, clarified and DNA protein complexes were isolated with anti Dmc1 or anti Rad51 or H3K4Me3 antibodies. DNA purified from proteins and libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample preparing kit part number 1000181. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenowpolymerase) 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 18 cycles and library fragments of 150~250 bp were 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 II |
| |
|
| Description |
Chromitin IP against DMC1. Pool of Sets A, B, C, D.
|
| Data processing |
Sequencing reads were aligned to the mm9 mouse genome annotation using ELAND and the Illumina Genome Analizer pipeline. The resulting export.txt files were converted to the BAM format with Samtools/Picard.
Peak finding was performed with MACS 1.3.7 (http://liulab.dfci.harvard.edu/MACS/) with a p-value threshold of 0.0001 and the. The resulting peaks were kept only if the MCAS-estimated FDR was 50% or less. In the case of Dmc1, the peaks were resized to 3.4kb.
|
| |
|
| Submission date |
Sep 29, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Ivan Gregoretti |
| E-mail(s) |
ivangreg@gmail.com
|
| Phone |
1-301-496-1016
|
| Fax |
1-301-496-9878
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Diabetes and Digestive and Kidney Diseases
|
| Street address |
5 Memorial Dr, Building 5, Room 205.
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE24438 |
Genome wide maps of Dmc1 in testis of Hop2 null mice. |
|
| Relations |
| SRA |
SRX027441 |
| BioSample |
SAMN00113762 |
| Named Annotation |
GSM602194.bed.gz |
