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| Status |
Public on Mar 07, 2012 |
| Title |
MNase-seq |
| Sample type |
SRA |
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| Source name |
NCCIT, MNase
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| Organism |
Homo sapiens |
| Characteristics |
cell line: NCCIT
cell type: embryonic carcinoma cells
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| Growth protocol |
NCCIT embryonic carcinoma cell lines on a 10cm dish were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS, Hyclone) and 1% antibiotic-antimycotic solution (Hyclone) at 37ºC in a humidified atmosphere composed of 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
MNase digestion: For the purification of mononucleosomes, PBS-washed cells were lysed in 400 μl of Lysis Buffer (18% Ficoll-400 (Sigma F2637), 10 mM KH2PO4, 10 mM K2PO4, 1 mM MgCl2, 0.25 mM EGTA, 0.1 mM PMSF) and centrifuged for 15 minutes at 13,000 rpm, 4°C. The nuclei pellets were resuspended with 1 ml of A Buffer (10 mM Tris-Cl pH 7.4, 150 mM NaCl, 5mM KCl, 1 mM EDTA, 0.1 mM PMSF) and then 5 μl of CaCl2 (final 5mM) and 1.5 μl of MNase (500unit/ 2.5μl, NEB) were added. After incubation at 37°C for 5 min, the reactions were stopped by adding 100 μl of 1% SDS and 50 μl of 0.5mM EDTA. MNase-digested nuclei were reverse-crosslinked by heating at 68ºC for O/N with 350mM NaCl. Finally, the reverse-crosslinked samples were treated with RNase A and proteinase K (Sigma), isolated by phenol/chloroform extraction, and precipitated using 3 M sodium acetate (pH 5.2) with absolute ethanol.
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
The sequence tags were mapped to the human genome (UCSC hg18) by using the Genome Analyzer data analysis pipeline. The mapped sequence reads were extended to the average size of fragment length (200bp).
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| Submission date |
Dec 21, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Inkyung Jung |
| E-mail(s) |
ijungkaist@gmail.com
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| Organization name |
KAIST
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| Department |
Biological Sciences
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| Street address |
KAIST, 291 Daehak-ro, Yuseong-gu
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| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE25882 |
Genome-wide maps of chromatin state in NCCIT cells |
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| Relations |
| SRA |
SRX037078 |
| BioSample |
SAMN00189370 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM644988_Nucleosome_2.bed.gz |
120.9 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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