|
| Status |
Public on Sep 27, 2013 |
| Title |
Ring1B KO |
| Sample type |
SRA |
| |
|
| Source name |
CD43 negative mouse resting B cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed
genotype/variation: RING1B KO (Homozygous Rosa26-CreERT2/Rnf2 flox)
developmental stage: adult
tissue: spleen
treated with: 250 nM 4-hydroxytamoxifen for 48hrs
chip antibody info.: Ring1B (D139-3), MBL
|
| Treatment protocol |
48 hours incubation with 4-hydroxytamoxifen for samples labeled WT or KO
|
| Growth protocol |
RPMI, 15% foetal calf serum, 0.1 U/mL penicillin, 0.1 μg/mL streptomycin, 2 mM L-Glutamine, 50 μM beta-mercaptoethanol, 6 ng/ml IL-4
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde and isolated nuclei were sonicated to the desired fragment size. Pre-coupled antibodies-beads were used to immunoprecipitated chromatin bound proteins/histone marks. After cross-link reversal and DNA purification, a total of 10 ng immunoprecipitated input was used for the library preparation with NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB) and Multiplexing Sample Preparation Oligonucleotide Kit (Illumina)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RING1B KO (Homozygous Rosa26-CreERT2/Rnf2 flox) treated for 48 hours with 250 nM 4-hydroxytamoxifen
|
| Data processing |
The reads were aligned to Mouse genome mm9 using Bowtie version 0.12.8 using '-S -n 2 -l 25 -m 1' parameters. Only reads aligned uniquely to the genome were retained for further analysis.
Reads with identical chromosomal co-ordinates and orientation (duplicates) were filtered using Picard version 1.65.
To visualise the genomic coverage of samples in UCSC genome browser, the reads were extended to estimated fragment size and converted to BigWig format. The fragment size was estimated using SISSR method (Jothi et al., 2008)
Genome_build: mm9
Supplementary_files_format_and_content: BigWig
|
| |
|
| Submission date |
Dec 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Gopuraja Dharmalingam |
| Organization name |
MRC London Institute of Medical Sciences
|
| Department |
Epigenetics section
|
| Street address |
Faculty of Medicine, Imperial College, Hammersmith Hospital Campus
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE42705 |
The Aurora B kinase and the polycomb protein Ring1B combine to regulate active promoters in quiescent lymphocytes [ChIP-seq] |
| GSE42706 |
The Aurora B kinase and the polycomb protein Ring1B combine to regulate active promoters in quiescent lymphocytes |
|
| Relations |
| SRA |
SRX208214 |
| BioSample |
SAMN01822812 |
