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| Status |
Public on Jun 08, 2016 |
| Title |
BS siFOXA1 rep2 |
| 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 (siFOXA1- transfected)
method: bisulfite conversion
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For Bisulfite-seq, the genomic DNA was extracted and purified by phenol–chloroform.
For normal Bisulfite-seq library constructing, the DNA was fragmented by sonication using a Bioruptor (Diagenode, Belgium) to a mean size of approximately 250 bp, followed by the blunt-ending, dA addition to 3'-end, finally, adaptor ligation (in this case of methylated adaptors to protect from bisulfite conversion), essentially according to the manufacturer’s instructions. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size fragments were excised from the same lane of a 2% TAE agarose gel. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. At last, Sequencing was performed using the HighSeq4000.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| 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. For Bisulfite-seq, after filtering, the clean data was mapped to the reference genome by BSMAP, and we then removed the duplication reads and merged the mapping results according to each library. The methylation level was determined by dividing the number of reads covering each mC by the total reads covering that cytosine, which was also equal the mC/C ratio at each reference cytosine.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record the 5mCG content at each CpG site.
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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 |
SAMN04914836 |
| SRA |
SRX1736553 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2137776_siFOXA1_rep2.bedGrpah.tar.gz |
474.8 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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