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| Status |
Public on Jun 20, 2013 |
| Title |
FAM10-01 Human peiripheral blood |
| Sample type |
SRA |
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| Source name |
Human peiripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
gender: Male
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from peripheral blood of 22 pedigrees, and approximately 1 µg of genomic DNA was bisulfite converted with EZ-96 Zymo DNA Methylation-Gold kit
Bisulfite padlock probes capture and sequencing (Diep et al, 2012). Briefly, approximately 250ng of bisulfite converted genomic DNAs were mixed with normalized amount of genome-wide scale padlock probes and oligo suppressors. The padlock probes annealing to targets were polymerized and ligated resulting in circularized DNA. The bisulfite sequencing libraries were generated by library-free BSPP protocol as described (Dinh et al. 2012). Two-thirds of the circularized DNA of each captured reaction were directly amplified and barcoded. The bisulfite sequencing libraries were purified with AMPure magnetic beads, pooled in equimolar ratios, size selected with 6% polyacrylamide gel, and sequenced by Illumina HiSeq and GAIIx sequencers. We firstly sequenced the 96 pooled libraries with Illumina HiSeq. For those samples with number of reads than 22 millions (53 samples), we did 3 additional sequencings on the same libraries as indicated in the two columns below (HiSeq, GAIIx, and Hiseq).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The libraries were sequenced by Illumina HiSeq and GAII. Illumina OLB was used for base-calling.
Adaptor sequences (27bp from 5' end) were trimmed from bisulfite reads prior to mapping
Bisulfite reads were mapped using the protocol from Diep et al, Nature Methods 2012. Briefly, all 'C's were replaced by 'T's in reads and mapped to a reference with all 'C's converted to 'T's. After mapping, the modified reads were replaced by the original reads then pileup files were generated using SAMTOOLS
Methylation levels were calculated as the number of cytosines over the total thymines and cytosines for CpGs where at least 90% of base called were thymines and cytosines
CpG sites with at least 10 depth of coverage were reported in final processed file (BED format)
Genome_build: hg19
Supplementary_files_format_and_content: BED formated (tab-delimited) text files include chromosome position and methylation fraction value for each CpG in each subject
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| Submission date |
Jun 03, 2013 |
| Last update date |
Jun 20, 2013 |
| Contact name |
Nongluk Plongthongkum |
| E-mail(s) |
nongluk6665@gmail.com
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| Organization name |
University of California, San Diego
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| Department |
Bioengineering
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| Lab |
Zhang Lab
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| Street address |
9500 Gilman Drive, MC0412, PFBH402
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| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE47614 |
Characterization of genome-methylome interactions in 22 nuclear pedigrees |
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| Relations |
| BioSample |
SAMN02189965 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1153234_FAM10-01.BED.txt.gz |
7.9 Mb |
(ftp)(http) |
TXT |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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