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| Status |
Public on Sep 15, 2016 |
| Title |
ChIP-Seq 2-cell late K27Me3 with ActiveMotif antibody |
| Sample type |
SRA |
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| Source name |
Preimplantation embryo
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x PWK
developmental stage: Preimplantation embryo
chip antibody: H3K27Me3
chip antibody vendor: ActiveMotif
chip antibody cat. #: 61017
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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. with slightly modification (Peng, Xu, et al. "TELP, a sensitive and versatile library construction method for next-generation sequencing." Nucleic acids research (2014): gku827.)
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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 |
Jun 02, 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 |
SAMN05196278 |
| SRA |
SRX1816625 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2184778_2cell_late_K27Me3_ActiveMotif.bed.gz |
23.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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