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| Status |
Public on Jan 25, 2019 |
| Title |
GSM1827608 MNase_WT |
| 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
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For MNase digestion, olfactory neuroepithelia were harvested from Mecp2 WT littermate adult mice and resuspended in PIPES buffer (5mM PIPES, 85mM KCl, 0.5% NP-40, pH 8.0) at 4 °C. After disruption with a dounce homogenizer, nuclei were collected by centrifugation. Collected nuclei were washed once, resuspended in the MNase buffer and digested with 0.5 units of MNase (New England Biolabs, Ipswich, MA) per microliter volume for 15 min at 37 °C. MNase digestion was stopped by putting the samples on ice and adding EDTA to a concentration of 10 mM. After digestion with 0.1 µg/µl RNase A (Fermentas, Pittsburgh, PA), DNAs were purified with DNA Purification Magnetic Beads (Life Technologies, Grand Island, NY), and pellets were dissolved in H2O. DNA fragments corresponding to mononucleosomes (about 150 bp) were confirmed by using 2100 Bioanalyzer (Agilent Technologies Santa Clara, CA). MNase-seq libraries were prepared as described (Bioo Scientific, Austin, TX) using 5140-01 NEXTflex DNA Sequencing kit and 514101 NEXTflex DNA Barcodes-6. High throughput sequencing was done with Illumina Hi-Seq 2000.
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
processed data file: MNase_seq_OE.bw
processed data file: MNase_Peaks_by_PING.bed
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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 |
GSM1827608 |
| BioSample |
SAMN10808220 |
| SRA |
SRX5287320 |
| 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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