|
| Status |
Public on May 09, 2019 |
| Title |
P12_H2AK119ub1_ChIPseq_cKO1 |
| Sample type |
SRA |
| |
|
| Source name |
Spermatogenic cells from P12 Brg1 cKO testes
|
| Organism |
Mus musculus |
| Characteristics |
strain: Mixed background
age: P12
tissue: testes
genotype: Brg1cKO
cell type: spermatogenic cells
chip antibody: Millipore -E6C5 (05-678)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Spermatogenic cells were isolated from P12 and P18 testes which were digested with collagnease and trypsin followed by filteration through a 40 micron sieve. Cells were fixed in 0.3% formaldehyde at 4 C for 30 min. The resulting chromatin was digested with Mnase prior to immunoprecipitation with antibody.
Libraries were created using Kapa hyperprep DNA library kit for Illumina sequencing
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Mnase digested chromatin
H2AK119ub1.Chp_Inp.cKO.merge.depthNorm1xCov.bw
|
| Data processing |
Alignment to the mm9 genome was performed using bowtie1 (BRG1 ChIP-seq)/bowtie2 (Histone ChIP-seq). BAM files were generated using samtools.
For H2AK119ub1 and H3K27ac ChIP-seq, PCR duplicates were filtered out using Picard tools, MarkDuplicates
BAM files were converted to bigWig format, representing log2(ChIP/Input) ratio, using Deeptools (version 2.5.2) bamCompare -bs 1 -bl mm9-blacklist.bed --normalizeto1x --scaleFactors --extend reads =150
Replicates were merged using UCSC tools bigWigMerge
Peaks called using macs2 call peak --broad --broad-cutoff 0.05. Differential peak analysis performed using macs2 bdgdiff
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of log2(ChIP/Input) tracks and bed files of ChIP peaks.
|
| |
|
| Submission date |
Aug 29, 2018 |
| Last update date |
May 09, 2019 |
| Contact name |
Terry Magnuson |
| E-mail(s) |
trm4@med.unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Genetics
|
| Lab |
Terry Magnuson
|
| Street address |
120 Mason Farm Road, Genetics Medicine Bldg.,
|
| City |
Chapel hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE119177 |
Mammalian SWI/SNF collaborates with a polycomb-associated protein to regulate germ line transcription in the mouse [ChIP-seq] |
| GSE119179 |
Mammalian SWI/SNF collaborates with a polycomb-associated protein to regulate germ line transcription in the mouse |
|
| Relations |
| BioSample |
SAMN09930839 |
| SRA |
SRX4620650 |
