|
Status |
Public on May 07, 2021 |
Title |
CLL [G70107_GCLL-0286-T-01] |
Sample type |
SRA |
|
|
Source name |
CLL cells
|
Organism |
Homo sapiens |
Characteristics |
tissue: Chronic lymphocytic leukemia time point: Before treatment
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was isolated and quantified using previously described methods (Boyle et al., 2012). RRBS library generation was performed as previously described (Boyle et al., 2012). Genomic DNA was enzymatically sheered using MspI endonuclease (New England Biolabs, catalogue number R0106L), which exposes a CpG site at the 3’-end. Barcoded Illumina sequencing adapters were added to each end of the DNA strand. The DNA was then subjected to two rounds of sodium bisulfite conversions using the Epitect Bisulfite Conversion Kit (Qiagen, catalogue number 59104). A final, large-scale PCR was conducted on the converted DNA (which uracil is replaced by thymine) and the product was submitted for sequencing.
|
|
|
Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
Reduced Representation |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
RRBS
|
Data processing |
Libraries were sequenced and aligned to the bisulfite-converted hg19 reference genome using Bismark v0.15.0 (Krueger et al., 2011) and the original methylation sites were inferred based on cytosine-to-thymine conversion. Genome_build: hg19 (GRCh37) Supplementary_files_format_and_content: Methyl call files are in .txt format.
|
|
|
Submission date |
Jan 14, 2020 |
Last update date |
May 09, 2021 |
Contact name |
Heng Pan |
E-mail(s) |
hep2007@bjmu.edu.cn
|
Organization name |
Peking University Third Hospital
|
Street address |
49 North Garden Rd., Haidian District
|
City |
Beijing |
ZIP/Postal code |
100191 |
Country |
China |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE143673 |
Reduced representation bisulfite sequencing (RRBS) of chronic lymphocytic leukemia (CLL) samples |
|
Relations |
BioSample |
SAMN13863660 |
SRA |
SRX7563045 |