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| Status |
Public on Jan 25, 2019 |
| Title |
GSM1827607 Input_WT_rep2 |
| Sample type |
SRA |
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| Source name |
Olfactory epithelium
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| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6J
genotype/variation: Wild-type, MeCP2(+/y)
age: 8 weeks
cell type: Olfactory sensory neuron
chip antibody: None
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was done based on methods established previously (Li, Y et al. 2014). Two independent chromatin immunoprecipitation assays were performed using MAGnify chromatin immunoprecipitation kit (Life Technologies, Grand Island, NY). Specifically, main olfactory neuroepithelia (MOE) were dissected from the nasal cavity and dissociated mechanically via trituration in phosphate buffer saline (PBS). Equal number of cells was used for subsequent steps. Protein-DNA complexes were cross linked by incubating dissociated MOE cells with 1% formaldehyde for 5 minutes on a rocker at room temperature. The cross-linking was quenched by adding Glycine. After washing off the media, MOE cells were lysed briefly in SDS containing buffer followed by sonication for 15 minutes with 30 second intervals to shear genomic DNA using a BioruptorTM 300 (Diagenode, Denville, NJ). Sheared DNA was evaluated by 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and selected for sizes ranging between 200 bp and 300 bp. Each sheared genomic DNA preparation was split into two equal portions and incubated with MeCP2 antibody (Diagenode, pAb-052-050) or Rabbit IgG (Millipore, Cat# 12-370) for the negative control. MeCP2-genomic DNA complexes were pulled down and reverse cross-linked by DNase-free Proteinase K and subsequently purified. MeCP2 ChIP-seq and input DNA library were prepared according to manufacturer’s instruction (Bioo Scientific, Austin, TX) using 5143-01 NEXTflex ChIP-Seq kit and 514120 NEXTflex ChIP-Seq Barcodes-6. ChIP and Input DNAs were PCR amplified, cleaned up and sequenced on Illumina Hi-Seq 2000 at QB3 Vincent J. Coates Genomics Sequencing Laboratory in the UC Berkeley.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
processed data file: Input_OE_merge.bw
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| Data processing |
The Input, MeCP2 ChIP-seq, and MNase-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.
Supplementary_files_format_and_content: The bed files were generated using the PING program. For the MNase-seq analysis, “MNase” as the default of the datatype in the postPING() option (alpha2=98; beta2=200000) were used. For MeCP2 ChIP-seq analysis, the combined MeCP2 ChIP-seq data from the two biological replicates were analyzed with “sonicated” in the postPING() option (alpha2=100; beta2=100000).
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| Submission date |
Jan 24, 2019 |
| Last update date |
Jan 26, 2019 |
| Contact name |
Wooje Lee |
| E-mail(s) |
ntinamu001@gmail.com
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| Organization name |
Chosun University
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| Department |
Cellular and Molecular Medicine
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| Street address |
309, Pilmun-daero, Dong-gu
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| City |
Gwangju |
| ZIP/Postal code |
61452 |
| Country |
South Korea |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE122366 |
MeCP2 regulates genome-wide gene expression through recognition of H3K27me3 |
| GSE125585 |
MeCP2 regulates genome-wide gene expression through recognition of H3K27me3 [ChIP, MNase] |
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| Relations |
| Reanalysis of |
GSM1827607 |
| BioSample |
SAMN10808223 |
| SRA |
SRX5287317 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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