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Sample GSM3465060 Query DataSets for GSM3465060
Status Public on Nov 10, 2018
Title H3K9ac_ChIP_OE_rep2
Sample type SRA
Source name H3K9ac_ChIP_OE
Organism Mus musculus
Characteristics strain: C57BL/6J
age: 8 weeks
tissue: Olfactory epithelium
cell type: Olfactory sensory neuron
chip antibody: H3K9ac (Diagenode, pAb-177-050)
Extracted molecule genomic DNA
Extraction protocol Cross-linking was done by incubating MOE cells with 1% formaldehyde for 5 minutes. After washing off the formaldehyde, MOE cells were lysed briefly in SDS containing buffer followed by sonication for 15 minutes with 30 second intervals to shear genomic DNA using Bioruptor UCD200 (Diagenode). The sheared DNA was evaluated by electrophoresis for their size ranging between 200 bp and 300 bp. Each sheared genomic DNA preparation was split into two equal portions and incubated with either MeCP2 (Diagenode, pAb-052-050) or Histone H1 (Santa Cruz, sc-34464) or H3K27me3 (Diagenode, pAb-069-050), H3K9ac (Diagenode, pAb-177-050) or Rabbit IgG (Millipore, 12-370) for the negative control. A magnetic bar was used to pull down antibody corresponding protein-genomic DNA complex. Genomic DNA in the complex was reverse cross-linked by DNase-free Proteinase K and purified.
Histone H1, H3K27me3, and H3K9ac ChIPed or input DNA were used to prepare the ChIP-Seq library as described (NEXTflex ChIP-Seq kit, Bio Scientific, NOVA 5143-01 and NEXTflex ChIP-Seq Barcodes-6, NOVA 514120) followed by high throughput sequencing with Illumina Hi-seq.2000
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing The Histone H1, H3K27me3, and H3K9ac ChIP-seq reads were aligned to the mm9 reference genome using Bowtie 2 with the options --sensitive --score-min L,-1.5,-0.3.
PCR duplicate are removed using samtools rmdup for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bigwig files were generated using the deepTools package
Submission date Nov 09, 2018
Last update date Jan 15, 2019
Contact name Wooje Lee
Organization name Chosun University
Department Cellular and Molecular Medicine
Street address 309, Pilmun-daero, Dong-gu
City Gwangju
ZIP/Postal code 61452
Country South Korea
Platform ID GPL13112
Series (2)
GSE122363 MeCP2 regulates genome-wide gene expression through recognition of H3K27me3 [ChIP_mouse]
GSE122366 MeCP2 regulates genome-wide gene expression through recognition of H3K27me3
BioSample SAMN10405932
SRA SRX4999178

Supplementary file Size Download File type/resource 70.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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