|
| Status |
Public on Feb 06, 2015 |
| Title |
K562-400mM-GCH and HCG |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
Sex: male
|
| Growth protocol |
K562 cells were cultured in McCoy5A media supplemented with 10% FBS and penicillin/streptomycin at 37C/5%CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were trypsinized and washed with PBS. Nuclei were isolated and treated with 300 U of M.CvIPI, a GpC methyltransferase which can methylate accessible GpC sites without affecting CpG information (Kelly et al 2012)
WGBS libraries were prepared based on previously described (Berman et al 2012) and according to Illumina's recommendation.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: WGBS/whole-genome NOMe-seq
genomic alignment for paired-end reads were done using MAQ with the -c bisulfite mode
Low quality reads and improperly paired reads were filtered out
Methylation calling of CpG and GpC was done using Bis-SNP (Liu et al 2011)
Genome_build: hg19
Supplementary_files_format_and_content: Methylation value of CG and GC sites were extacted and bigwig files were generated
|
| |
|
| Submission date |
Jan 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Fides D Lay |
| E-mail(s) |
fidlay@ucla.edu
|
| Organization name |
UCLA
|
| Department |
MCDB
|
| Street address |
615 Charles E Young Drive South, BSRB 457
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE64929 |
The role of DNA methylation on the organization of the cancer epigenome |
|
| Relations |
| BioSample |
SAMN03283204 |
| SRA |
SRX840167 |
| Named Annotation |
GSM1583567_K562_400_merge_C33YCACXX_C3JK7ACXX_C4JVWACXX_KEL656A315_GCH.hg19_rCRSchrm.fa.realign.mdups.recal.cytosine.filtered.sort.GCH.bw |
| Named Annotation |
GSM1583567_K562_400_merge_C33YCACXX_C3JK7ACXX_C4JVWACXX_KEL656A315_HCG.hg19_rCRSchrm.fa.realign.mdups.recal.cytosine.filtered.sort.HCG.bw |
