 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 19, 2017 |
| Title |
N37-Stomach |
| Sample type |
SRA |
| |
|
| Source name |
stomach
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: normal
tissue: stomach
|
| Treatment protocol |
n/a
|
| Growth protocol |
n/a
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 200 ng of genomic DNA of primary tissues (N37) obtained from the Li Lab was sheared into an average size of 400 bp in a Covaris micro TUBE with Covaris E210 ultrasonicator. Fragmented genomic DNA was constructed into Illumina paired-end sequencing libraries using KAPA Library Preparation kit (KAPA Biosystems) following manufacturer’s instruction with modifications. After end-repair and dA-tailing, ligation with methylated adapters was performed at 20 ˚C for 15 min in the presence of 10-fold molar excess of Illumina methylated adapters (Illumina). The ligation mixture was purified with an equal volume of Agencourt AMPure XP beads (Beckman Coulter) and eluted with 23 µL of 10mM Tris-HCl, pH8.5. Next, 20 µL of adaptor ligated DNA was bisulfite converted using EZ DNA Methylation-Lightning kit (Zymoresearch) following manufacturer’s protocol and eluted with 30 µL of 10mM Tris-HCl, pH8.5. Bisulfite converted DNAs were amplified using iQ SYBR Green Supermix (Bio-Rad) with 200 nM each of PCR primer PE1.0 and multiplexing PCR primer for 10 cycles in 100 µL total volume. PCR products were purified with 0.8X volume of Agencourt AMPure XP beads (Beckman Coulter) and eluted with 50 µL of 10mM Tris-HCl, pH8.5, pooled in equimolar ratios, and size selected using 6% TBE gels for 400-600 bp. The concentration of sequencing libraries was quantified by qPCR using KAPA Library Quantification kit (KAPA Biosystems). Libraries were sequenced on both GAIIx for SE 36 cycles and HiSeq Run for PE 100 cycles.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
base-calling
quality trimming of fastq reads
alignment with BWA/bisReadMapper
trim overlapping pair-ends
generate methylation haplotype counts from BAM
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values: column 1 - genomic locus, column 2 - methylation haplotype call, column 3 - number of reads supporting methylation haplotype, column 4 - list of CpG positions included in methylation haplotype
|
| |
|
| Submission date |
Mar 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, San Diego
|
| Department |
Bioengineering
|
| Lab |
Integrative Genomics Laboratory
|
| Street address |
9500 Gilman Dr Mailcode: 0412
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE79215 |
Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tissue-of-origin mapping from plasma DNA [WGBS] |
| GSE79279 |
Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tissue-of-origin mapping from plasma DNA |
|
| Relations |
| BioSample |
SAMN04557049 |
| SRA |
SRX1631745 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2088211_N37-Stomach.mhbs.hapInfo.bed.gz |
3.3 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
