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| Status |
Public on Feb 12, 2011 |
| Title |
Miguel_CMC__rep18 |
| Sample type |
SRA |
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| Source name |
iPSC clone (CMC28)
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| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC clone
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
a) Mix up all genome DNA and randomly shear into fragments of 100~500bp. b) Repair the terminal of DNA fragments, 3'-dA and attach with methylation sequencing adaptors. c) Subject whole genome DNA to bisulfite processing. d) Subject to gel electrophoresis of 2% TAE, extract fragments of 320~380bp with IAquich Gel Extraction recycling, desalination and PCR amplification. e) Construct libraries with appropriate fragments for sequencing usin standard Illumina Genome Analyzer II protocol
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
sample for paired-end library with insert size of 150 bp
library selection: different insertion size
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| Data processing |
Filter adaptors, detect possible contamination of samples, count data output(including read length, total read counts, data production), and on this basis, accomplish standardized analysis and personalized information analysis. (1) Reads alignment with reference genome Align all reads against ref.c2t and ref.g2a with SOAPaligner after converting C to T on forward strand, G to A on backward strand. Each reads mapping to an unique location with minimum mismatches and clear information of positive and negative chain will be defined as uniquely matching reads and used to determine the methylated C. (2) Combine original sequences and the soap results , according to the reads ID in soap results, find the corresponding sequences which have not converted C to T or G to A in raw data ,and then use the corresponding sequences to substitute the sequences in soap results. (3) Align the sequences against the reference, record the information of base sites, and according to these sites information , select the reads with better aligning results: align the human.fa sequence with soap results according to certain patterns, and use symbols to record the results , on the basis of the results, extract local fragment of reads with best aligning results, getting align matching results. (4) According to the align matching results, select the best results among repeat present sequences , the selection criteria being to select reads with larger sum of aligning length, and judge a chain is Watson chain or Click chain. (5) Perform a detail statistic on mappable reads and remove redundancy. (6) Methylation level of whole genome and/or different regions are deduced from the original sequence.
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| Submission date |
Feb 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Yao Qiong |
| E-mail(s) |
[email protected]
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| Phone |
+86 13632720242
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| Organization name |
BGI-SZ
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| Street address |
Beishan Industrial Zone,Yantian District
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518083 |
| Country |
China |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE27239 |
Bisulfite sequencing data of one human DNA sample |
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| Relations |
| SRA |
SRX042216 |
| BioSample |
SAMN00210941 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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