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Sample GSM1968790 Query DataSets for GSM1968790
Status Public on Jan 01, 2016
Title H3K27ac of cell sample sD (MiSeq)
Sample type SRA
Source name Erythrocyte cell
Organism Gallus gallus
Characteristics strain: Bovan
develomental stage: G0 phase Immature erythrocyte cells
layer: White leghorn
antibody information: H3K27ac (abcam 4729, lot 124541)
Extracted molecule genomic DNA
Extraction protocol Chicken immature erythrocyte nuclei were treated with 0.5% formaldehyde and chromatin was sheared into 200bp fragments. Immunoprecipitation was performed with respective antibody.
ChIPSeq library preparation was performed according to the NEBNext ChIP-Seq library preparation protocol. 20 ng of ChIP DNA was end-repaired and dA-tailed. Ligation products were size selected and PCR enriched. Libraries were quantified by qPCR,normalized and pulled to 10 nM before sequencing.ChIP DNA and Input libraries were sequenced using the MiSeq platform and v3 sequencing reagents.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
Data processing XSQ files generated from SOLiD machine were mapped on reference genome gal3 using LifeScope v2.5.1 software
Fastq sequences with 76bp generated by Miseq were trimmed off the first 3 bases and the last 2 bases and mapped onto reference genome by bowtie-0.12.8.
ChIPseq workflow of LifeScope was used
Adaptor and barcode sequences were removed
peaks were called using the bed files by MACS1.4 program
peak pvalue cutoff = 1.00e-05
Genome_build: galGal3
Supplementary_files_format_and_content: peaks.xls, chr, start, end, length, summit, tags, -10*log10(pvalue),fold_enrichment FDR(%)
Submission date Dec 09, 2015
Last update date Jan 16, 2023
Contact name James Ronald Davie
Phone 2042723174
Organization name University of Manitoba
Department Biochemistry and Medical Genetics
Street address 745 Bannatyne Avenue, RM 333A
City Winnipeg
State/province Manitoba
ZIP/Postal code R3E 0J9
Country Canada
Platform ID GPL19064
Series (2)
GSE75845 Genome-wide mapping of H3K4me3 and H3K27ac in chicken immature erythrocyte cells
GSE75955 The chicken erythrocyte epigenome
BioSample SAMN04327490
SRA SRX1472823

Supplementary file Size Download File type/resource
GSM1968790_H3K27ac_2.xls.gz 43.8 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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