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| Status |
Public on Mar 07, 2012 |
| Title |
NCC-Rb-WT paired-end seq |
| Sample type |
SRA |
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| Source name |
NCCIT
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| Organism |
Homo sapiens |
| Characteristics |
cell line: NCCIT
cell type: embryonic carcinoma cells
chip antibody: anti-H2Bub
catalog/vendor: Cell Signaling (5546) with lot number #1
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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 |
Genomic DNA extraction: Cross-linking was performed by incubating cells in 1% formaldehyde (Sigma) for 20 min at 25 C. Cells were quenched with 125 mM Glycine. PBS-washed cells were lysed in 400 l of SDS Lysis Buffer, and DNA was sonicated to create fragments of 400-500 nucleotides in length using a Sonic Dismembrator (Model 500, Fisher).
Chromatin immunoprecipitation: Chromatin cleared by centrifugation for 15 minutes at 13,000 rpm, 4 C were subjected to immunoprecipitation using antibodies of interest with a mixture of protein A and G agarose (GE Healthcare) for 2 hr at 4 C. Protein A and G agarose/antibody/chromatin complexes then were washed for 10 minutes with each of the following solutions: Low Salt Wash Buffer (150 mM NaCl lysis buffer without 0.2% SDS), High Salt Wash Buffer (500 mM NaCl lysis buffer without 0.2% SDS), LiCl buffer (10 mM Tris-Cl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Sodium deoxycholate), and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). The chromatin complexes were then eluted twice in 250 l elution buffer (1% SDS, 0.1M NaHCO3) by incubation at 25 C for 15min with rotation and were reverse-crosslinked by heating at 68 C for O/N with 400mM NaCl.
The purified ChIP DNA fragments were ligated to a pair of adaptors for sequencing on the HiSeq2000.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
H2BUb1-Rb-NCCIT-WT.bed; genome build: hg18
The sequence tags were mapped to the human genome (UCSC hg18) by using Bowtie.
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| Submission date |
Jan 03, 2012 |
| 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 |
GPL11154 |
| Series (1) |
| GSE25882 |
Genome-wide maps of chromatin state in NCCIT cells |
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| Relations |
| SRA |
SRX115873 |
| BioSample |
SAMN00773096 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM855979_H2BUb1-Rb-NCCIT-WT.bed.gz |
118.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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