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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 15, 2016 |
| Title |
ChIP-Seq 500 mESC K27Ac |
| Sample type |
SRA |
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| Source name |
Embryonic stem cell
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| Organism |
Mus musculus |
| Characteristics |
strain: R1
developmental stage: Embryonic stem cell
chip antibody: custom-made H3K4Me3 antibody (Abmart)
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| Treatment protocol |
Mouse ES cells were cultured without irradiated mouse embryonic fibroblasts (MEFs) in DMEM containing 15% FBS, leukemia inhibiting factor (LIF), penicillin/streptomycin, L-glutamine, β-mercaptoethanol, and non-essential amino acids. After digestion with 0.05% trypsin, counted cells were lysed for STAR ChIP-seq or Smart-seq2.
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| Growth protocol |
mESCs were cultured routinely in LIF and serum medium.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
After washing with PBS, mESCs were incubated in lysis buffer
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. 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 |
Aug 06, 2015 |
| 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) |
| GSE71434 |
Allelic reprogramming of the histone modification H3K4me3 in early mammalian development |
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| Relations |
| SRA |
SRX1134827 |
| BioSample |
SAMN03979661 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1845290_500_mESC_K27ac.bed.gz |
24.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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