|
| Status |
Public on Oct 18, 2013 |
| Title |
ChipSeq_antiTH2B_total_male_germ_cells |
| Sample type |
SRA |
| |
|
| Source name |
Male germ cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Total male germ cells from adult mice
chip antibody: anti TH2B
genotype: wild type
|
| Treatment protocol |
Total spermatogenic cell suspensions were prepared from wt mice and used for ChIP with an anti-TH2B antibody exactly as previously reported in (Tan et al, 2011; PMID: 21925322).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard Applied Biosystems Life Technologies protocols were followed for the creation of short-insert bar-coded, paired-end libraries (insert length ~150 bp) according to the ChIP-seq Kit Guide from the manufacturer (cms_079323.pdf) and library preparation guide (cms_081748.pdf).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
Sequence reads of 75+35 bp reads were produced with a SOLiD hq5500xl sequencer, according to standard Life Technologies protocols. The sequence reads were analyzed with the LifeScopeâ„¢ software suite (cms_4448431.pdf).
After sequence read mapping to version 9 build 37 of the mouse genome allowing up to 4 mismatches, only reads mapping once to the genome were retained for subsequent analyses, to prevent spurious calls in repetitive regions.
two BAM files were generated by the LifeScope pipeline, corresponding to the two biological conditions ChIP-seq antiTH2B and its input
BAM files were transformed into SAM format (Li et al, 2009; PMID: 19505943).
Genome_build: mm9
Supplementary_files_format_and_content: Bed and wig files were generated using SICERÂ with following parameters : W200, G600, FDR 0.01 (for WIG) and 0.01 (for BED)
|
| |
|
| Submission date |
Jul 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Sophie Rousseaux |
| Organization name |
INSERM-UGA
|
| Department |
IAB
|
| Lab |
U1209
|
| Street address |
Bd de la Chantourne
|
| City |
La Tronche |
| ZIP/Postal code |
38706 |
| Country |
France |
| |
|
| Platform ID |
GPL15907 |
| Series (2) |
| GSE45915 |
Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B [ChIP-Seq] |
| GSE46137 |
Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B |
|
| Relations |
| BioSample |
SAMN02222157 |
| SRA |
SRX317032 |
