|
| Status |
Public on May 16, 2016 |
| Title |
CC H3K9me3 ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
CC H3K9me3 ChIP-seq
|
| Organism |
Mus musculus |
| Characteristics |
strain background: B6D2F1 (C57BL/6 X DBA/2)
development stage: 6-8 weeks post natal
genotype/variation: wild type
tissue: cumulus cell
chip antibody: H3K9me3
chip antibody vendor: active motif
chip antibody cat. #: 39161
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
500-1000 cells were washed three times in 0.5% BSA-PBS solution. Lysates were clarified from micrococcal nuclease treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to illumina TruSeq DNA LT Sample Prep Kit( FC-121-2001, FC-121-2002)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bwa mem command, reads that have map quality score less than 30 were removed from downstream analysis.
Peaks were called using masc2(v 2.0.10.20131216) with the parameters "macs2 callpeak –n Sample -g mm -B -q 0.05 --nomodel --broad --shiftsize=73 --SPMR" relative to input samples.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using macs2 pileup function and normlized to one million reads per sample using --SPMR option. Scores represent normalized tag counts per million reads.
|
| |
|
| Submission date |
Jul 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Shaorong Gao |
| Organization name |
Tongji University
|
| Department |
School of life science and technology
|
| Lab |
Gaolab
|
| Street address |
1239 Siping Road, Yangpu District
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE70606 |
Single Cell Sequencing Identifies Key Epigenetic Regulators in Nuclear Transfer Mediated Reprogramming [ChIP-seq] |
| GSE70608 |
Single Cell Sequencing Identifies Key Epigenetic Regulators in Nuclear Transfer Mediated Reprogramming. |
|
| Relations |
| BioSample |
SAMN03842764 |
| SRA |
SRX1084904 |
