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Sample GSM1845291 Query DataSets for GSM1845291
Status Public on Sep 15, 2016
Title ChIP-Seq oocyte K4Me3 zebrafish
Sample type SRA
Source name Zebrafish oocyte
Organism Danio rerio
Characteristics strain: AB
developmental stage: Zebrafish oocyte
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
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
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 Aug 06, 2015
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 GPL18171
Series (1)
GSE71434 Allelic reprogramming of the histone modification H3K4me3 in early mammalian development
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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