|
| Status |
Public on Sep 15, 2016 |
| Title |
ChIP-Seq growing oocyte 7days K27Me3 |
| Sample type |
SRA |
| |
|
| Source name |
Growing oocyte
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
tissue/cell type: Growing oocyte
chip antibody: H3K27Me3
chip antibody vendor: Diagenode
chip antibody cat. #: C15410069; pAb-069-050
|
| Treatment protocol |
Follicles were isolated from 10-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min. Oocytes were then incubated in lysis buffer after removing the zona pellucida by pronase treatment.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. (PMID: 25223787) with slightly modification.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The bed files include RPKM values in 100bp bins for each ChIP-seq sample. Bed files labeled maternal or paternal contain RPKM values for two parental alleles, allelic reads were normalized to total reads number. Tab-delimited text files include FPKM values RNA-seq sample.
|
| |
|
| Submission date |
Jan 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bingjie Zhang |
| Organization name |
Tsinghua University
|
| Street address |
30 Shuangqing Rd
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100190 |
| Country |
China |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE76687 |
Resetting epigenetic memory by reprogramming of histone modifications in mammals |
|
| Relations |
| BioSample |
SAMN04419956 |
| SRA |
SRX1533816 |
