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| Status |
Public on Jun 08, 2016 |
| Title |
POLB/siFOXA1 ChIP-seq |
| Sample type |
SRA |
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| Source name |
MCF-7 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: MCF-7 cells (FOXA1- knockdown)
method: enriched with POLB antibody
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, the FOXA1-complex components and their associated DNA were extracted from the sonicated nuclei and isolated with antibody. 10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by picogreen assay and subjected to HiSeq2000 sequencing according to the manufacturer’s instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were analyzed by BGI programs. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%. After filtering, the remaining reads are called "clean reads" and stored as FASTQ format. The clean data was mapped to the reference genome by BOWTIE, and the duplication reads were removed.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record the reads coverage for ChIP-seq.
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| Submission date |
Apr 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yu Zhang |
| Organization name |
Peking University Health Science Center
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| Street address |
Xueyuan Road
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| City |
Beijing |
| ZIP/Postal code |
100191 |
| Country |
China |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE80808 |
Nucleation of DNA Repair Factors by FOXA1 Links DNA Demethylation to Transcriptional Pioneering |
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| Relations |
| BioSample |
SAMN04914831 |
| SRA |
SRX1736548 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2137771_siFOXA1_POLB.bedGraph.gz |
152.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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