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| Status |
Public on Feb 04, 2015 |
| Title |
vector_rep 2 |
| Sample type |
SRA |
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| Source name |
lung cancer cell line A549
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| Organism |
Homo sapiens |
| Characteristics |
cell line: lung cancer A549 cells
genotype/variation: vector control
chip antibody: Oct4 (Abcam, catalog# ab19857)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Empty vector control and Oct4 stably-expressing A549 cells (1 × 10^7 cells) were cross-linked with 1% formaldehyde, followed by preparation of nuclear lysates using Magna ChIP protein G Kit (Millipore, Billerica, MA, USA) according to the protocols provided by the manufacturer. Nuclear lysates were sonicated for shearing crosslinked DNA to around 200~300 bps using Covaris-S2 machine (Covaris Inc., Woburn, MA, USA). Chromatin was immunoprecipitated with anti-Oct4 antibody (Abcam, #ab19857).
Purified chromatin-immunoprecipitated DNA was subjected to preparation of fragment libraries using 5500 SOLiD Fragment Library Core Kit (Applied Biosystems, Foster City, CA, USA) according to the protocols provided by the manufacturer.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500xl Genetic Analyzer |
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| Description |
Sample 2
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| Data processing |
High-throughput sequencing was performed by SOLiD 5500xl sequencer (Applied Biosystems) and abound 24~29 million raw reads were obtained from samples.
The raw reads were further analyzed using LifeScopeTM Genomic Analysis Software (version 2.5), and mapped to human genome (hg19) released from UCSC database.
To find the significant peak, the mapped profiles were analyzed using the ChIP-seq tool in CLC Genomics Workbench (version 4.9). The peak-finding algorithm included the following four steps: 1) Calculate the null distribution of the background sequencing signal; 2) Scan the mappings to identify candidate peaks with a higher read count than expected from the null distribution; 3) Merge overlapping candidate peaks; 4) Refine the set of candidate peaks based on the count and the spatial distribution of forward and backward reads within the peaks. The estimate for the null distribution of coverage and the calculation of the false discovery rate (FDR) were based on the window size and maximum FDR (%) parameters. In this study, the window size and FDR were set to 200 bp and 5%, respectively.
To determine the high confidence Oct4 binding loci, the ChIP-region was identified by scanning the peaks with significantly higher read count in Oct4 stably-expressing cells compared to those in the vector control cells.
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are BED files which are Oct4 ChIP-seq reads peaks in vector control and stable Oct4 expressing A549 cells.
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| Submission date |
Jun 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yi-Ching Wang |
| E-mail(s) |
ycw5798@mail.ncku.edu.tw
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| Phone |
+886-6-2353535
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| Organization name |
National Cheng Kung University
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| Department |
Department of Pharmacology, College of Medicine
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| Street address |
No.1, University Road, Tainan 70101, Taiwan, R. O. C.
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| City |
Tainan |
| ZIP/Postal code |
70101 |
| Country |
Taiwan |
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| Platform ID |
GPL16288 |
| Series (1) |
| GSE58462 |
Genome-wide Oct4 binding profile in lung cancer A549 cells |
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| Relations |
| BioSample |
SAMN02867739 |
| SRA |
SRX612572 |
| Named Annotation |
GSM1412054_vector_reads_peaks_2.bed.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1412054_vector_reads_peaks_2.bed.gz |
28.3 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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