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| Status |
Public on Sep 15, 2016 |
| Title |
ChIP-Seq oocyte K4Me3 zebrafish |
| Sample type |
SRA |
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| Source name |
Zebrafish oocyte
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| Organism |
Danio rerio |
| Characteristics |
strain: AB
developmental stage: Zebrafish oocyte
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| Treatment protocol |
The wild-type zebrafish lines Tübingen (Tu) and AB were utilized in this study. Unfertilized oocytes were obtained by squeezing the females gently on the ventral side. Next, the oocytes were activated by adding 3ml fresh holfreter (0.05g/L KCl, 0.1g/L CaCl2, 0.025g/L NaHCO3, 3.5g/L NaCl, pH 7.0) in 35mm dishes, and then followed by standard pronase dechorionation treatment
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
In order to deyolk oocytes (where yolk mass were highly abundant), dechorionated oocytes were transferred into a 1.5ml tube and washed with PBS for several times, then disrupted with 200ul tips. The cells of oocytes were spun down at 5000rpm for 5 min at 4°C. The remaining cells 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 |
GPL18171 |
| Series (1) |
| GSE71434 |
Allelic reprogramming of the histone modification H3K4me3 in early mammalian development |
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| Relations |
| SRA |
SRX1134828 |
| BioSample |
SAMN03979662 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1845291_zebrafish_oocyte_K4me3.bed.gz |
7.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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