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Sample GSM3465058 Query DataSets for GSM3465058
Status Public on Nov 10, 2018
Title Histone_H1_ChIP_OE_rep2
Sample type SRA
 
Source name Histone_H1_ChIP_OE
Organism Mus musculus
Characteristics strain: C57BL/6J
age: 8 weeks
tissue: Olfactory epithelium
cell type: Olfactory sensory neuron
chip antibody: Histone H1 (Santa Cruz, sc-34464)
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 Nov 10, 2018
Contact name Wooje Lee
E-mail(s) ntinamu001@gmail.com
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
Relations
BioSample SAMN10405934
SRA SRX4999176

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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