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| Status |
Public on Sep 15, 2016 |
| Title |
ChIP-Seq 8-cell K27Me3 |
| Sample type |
SRA |
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| Source name |
Preimplantation embryo
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x PWK
tissue/cell type: Preimplantation embryo
chip antibody: H3K27Me3
chip antibody vendor: Diagenode
chip antibody cat. #: C15410069; pAb-069-050
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| Treatment protocol |
Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to PWK males. Each set of embryos at a particular stage was flushed from the reproductive tract at defined time periods after hCG administration: 20h (MII oocyte), 27-28h (PN5 zygote), 30h (early 2-cell), 43h (late 2-cell), 54-56 h (4-cell), 68-70 h (8-cell) and 92-94 h (blastocysts) in Hepes-buffered CZB medium. The zona pellucida of embryos selected by cell number or morphology was gently removed by treatment of 10 IU/ml pronase (Sigma P8811) for several minutes. The embryos were then manually picked and treated with the lysis buffer for STAR ChIP-seq or Smart-seq2.
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
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| 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.
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| Submission date |
Jan 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bingjie Zhang |
| Organization name |
Tsinghua University
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| Street address |
30 Shuangqing Rd
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100190 |
| Country |
China |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE76687 |
Resetting epigenetic memory by reprogramming of histone modifications in mammals |
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| Relations |
| BioSample |
SAMN04419966 |
| SRA |
SRX1533826 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2041077_8cell_K27me3_maternal.bed.gz |
9.4 Mb |
(ftp)(http) |
BED |
| GSM2041077_8cell_K27me3_paternal.bed.gz |
6.7 Mb |
(ftp)(http) |
BED |
| GSM2041077_8cell_k27me3.bed.gz |
30.1 Mb |
(ftp)(http) |
BED |
| GSM2041077_8cell_k27me3_broadpeak.bed.gz |
176.7 Kb |
(ftp)(http) |
BED |
| GSM2041077_8cell_k27me3_maternal_broadpeak.bed.gz |
216.6 Kb |
(ftp)(http) |
BED |
| GSM2041077_8cell_k27me3_paternal_broadpeak.bed.gz |
116.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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