 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 29, 2016 |
| Title |
BS-seq-P2-N |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
individual: patient2
tissue: matched normal
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA(Qiagen, Cat#: 51306) were extracted according to manufacturer’s instructions.
The DNA was directed to bisulfite conversion using the EZ DNA methylation-Gold kit (Zymo Research) according to the instruction manual. The library was sequenced using Illumina HiSeq 2000.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
BS-seq
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Paired-end TAB-seq reads were mapped against the reference by Bismark with stringent parameters: -n 2 -l 60 -e 100 -X 600. The overlapped part of paired reads is trimmed from one end to prevent counting twice from the same observation. For each CpG site, the number of CGs and the number of TGs were counted.
Paired-end BS-seq reads were mapped against the reference by Bismark with stringent parameters: -n 2 -l 60 -e 100 -X 600. The overlapped part of paired reads is trimmed from one end to prevent counting twice from the same observation. For each CpG site, the number of CGs and the number of TGs were counted.
For patient 1, in BSseq or TABseq, the CG sites covered by at least 5 reads were considered. 5mC level or 5hmC level is calculated as the number of CGs divided by the sum of the number of CGs and the number of TGs. CG sites were considered as hydromethylated, if the following three criterias were met (1.BH corrected binormial P value less than or equal to 0.05; 2. CpG sites identified both methylated and hydroxymethylated; 3. 5mC level larger than or equal to 5hmC level). For CpG sites identified both methylated and hydroxymethylated, the methylation levels of CpG sites were corrected by subtracting the 5hmC level.
For patient 2, in BSseq or TABseq, the CG sites covered by at least 1 reads were listed. 5mC level or 5hmC level is calculated as the number of CGs divided by the sum of the number of CGs and the number of TGs.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include 5mC and 5hmC level for each sample (real 5hmC level for each CG site covered by at least 5 reads, real 5mC level for each CG site covered by at least 5 reads)
|
| |
|
| Submission date |
Nov 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jing Zhang |
| E-mail(s) |
henry.jingzhang@gmail.com
|
| Organization name |
Columbia University Medical Center
|
| Street address |
1130 St Nicholas Ave ICRC, room403
|
| City |
Beijing |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE63183 |
Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer |
|
| Relations |
| BioSample |
SAMN03198265 |
| SRA |
SRX761074 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1546666_5mc-P2-N-corrected-updated.txt.gz |
185.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
