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Sample GSM3165220 Query DataSets for GSM3165220
Status Public on Oct 25, 2018
Title muscle_H3K27ac
Sample type SRA
 
Source name muscle
Organism Danio rerio
Characteristics strain: AB
cell type: muscle cell
developmental stage: adult
antibody: Active Motif, Cat # 39133
Treatment protocol An wild type adult AB fish was euthanized with tricaine, and skeletal muscle was dissected carefully from trunk region after skin elimination by tweezers.
Growth protocol The wild type AB female strain were raised as standard protocol.
Extracted molecule genomic DNA
Extraction protocol The ChIP procedure (STAR ChIP-seq) was based on a previously described method with modifications to adapt it for zebrafish embryos (Gilfillan et al., 2012; Zhang et al., 2016). For oocyte and embryo samples, yolk was firstly removed as described above. After centrifuge, cell pellet was lysed in 40 µl lysis buffer (0.5% NP-40, 0.5% Tween, 0.1% SDS and proteinase inhibitor) with pipetting up and down several times. 0.1 unit of MNase (Sigma, Cat # N3755) was added for chromatin digestion at 37℃ for 5 min. The reaction was then terminated by adding 1 µl 0.5 M EGTA. IP sample was incubated with 1 µg H3K4me3 antibody (Homemade), 2 µg H3K27ac antibody (Active Motif, Cat # 39133), 2 µg H3K27me3 antibody (Active Motif, Cat # 61017), or 2 µg H3K36me3 antibody (Active Motif, Cat # 61021), overnight with rotation at 4℃. In the next day, the sample was incubated with 300 µg protein A or protein G dynabeads (Life technologies, Cat # 10001D or 10003D) for 2 hrs with rotation at 4℃. The beads were washed 5 times in 150 µl RIPA buffer and once in 150 µl LiCl buffer. After washing, spin tubes briefly and remove the supernatant. For each IP sample, resuspend beads with 27 µl ddH2O and 1 µl 10x Ex-Taq buffer (TaKaRa). 1 µl proteinase K (Roche, Cat # 10910000) was then added and the mix was incubated at 55℃ for 90 min to elute DNA from beads. The supernatant was then transferred to a new tube and the proteinase K was inactivated at 72℃ for 40 min. 1 µl rSAP (NEB, Cat # M0371) was then added to dephosphorylate 3’ end of DNA at 37℃ for 1 h. rSAP was inactivated at 65℃ for 10 min. The resulting sample was subjected to TELP library preparation as previously described (Peng et al., 2015).
The resulting sample is ready for TELP library preparation (Peng et al., 2015).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Description processed data file: muscle_H3K27ac.bw
Data processing RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low quality reads.The filtered data were then mapped to the zebrafish reference genome (danRer7) by STAR (version: STAR_2.5.3a_modified) with following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilterMultimapNmax 20 --twopassMode Basic.
All STAR ChIP-seq reads were aligned to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM).
All STEM-seq datasets were mapped to the danRer7 reference genome by Bismark (Krueger and Andrews, 2011). Reads were trimmed with cutadaptor (Martin, 2011) using parameters: --minimum-length 20 --pair-filter=any. Alignments were performed with the following parameters: -N 1 -X 600 --score_min L,0,-0.6. Multi-mapped reads and PCR duplicates were removed. bismark_methylation_extractor was used to calculate the DNA methylation level
Genome_build: danRer7
Supplementary_files_format_and_content: Bigwig for ChIP-seq and RNA-seq tracks, gene expression table for RNA-seq data
 
Submission date May 30, 2018
Last update date Oct 25, 2018
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 GPL23085
Series (1)
GSE114954 Widespread enhancer dememorization and promoter priming during parental-to-zygotic transition
Relations
BioSample SAMN09283279
SRA SRX4141848

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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