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| Status |
Public on Sep 27, 2019 |
| Title |
LR28_H3K4me3 |
| Sample type |
SRA |
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| Source name |
Muscle
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| Organism |
Sus scrofa |
| Characteristics |
tissue: Muscle
breed: Landrace
antibody: H3K4me3 (Millipore, 05-745R)
Stage: 28 dpc
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| 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
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| Submission date |
Sep 06, 2018 |
| Last update date |
Sep 28, 2019 |
| Contact name |
Delin Mo |
| E-mail(s) |
wangxy635@mail2.sysu.edu.cn
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| Organization name |
Sun Yat-sen University
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| Street address |
Xingang Road
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| City |
Guangzhou |
| ZIP/Postal code |
510006 |
| Country |
China |
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| Platform ID |
GPL9126 |
| Series (1) |
| GSE119566 |
ChIP-seq of embryonic muscle sample of two pig breeds |
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| Relations |
| BioSample |
SAMN09983111 |
| SRA |
SRX4647079 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3377779_LR28K4_treat_afterfiting.tar.gz |
63.5 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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