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Sample GSM3377780 Query DataSets for GSM3377780
Status Public on Sep 27, 2019
Title LR35_H3K4me3
Sample type SRA
 
Source name Muscle
Organism Sus scrofa
Characteristics tissue: Muscle
breed: Landrace
antibody: H3K4me3 (Millipore, 05-745R)
Stage: 35 dpc
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Data processing Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the Sus scrofa genome assembly using EasyAlign version 3.2.
Data were filtered using Sickle
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: Sus scrofa reference genome buid 10.23
Supplementary_files_format_and_content: wig files were generated using Bigwig
 
Submission date Sep 06, 2018
Last update date Sep 28, 2019
Contact name Delin Mo
E-mail(s) wangxy635@mail2.sysu.edu.cn
Organization name Sun Yat-sen University
Street address Xingang Road
City Guangzhou
ZIP/Postal code 510006
Country China
 
Platform ID GPL9126
Series (1)
GSE119566 ChIP-seq of embryonic muscle sample of two pig breeds
Relations
BioSample SAMN09983110
SRA SRX4647080

Supplementary file Size Download File type/resource
GSM3377780_LR35K4_treat_afterfiting.tar.gz 73.4 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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