NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4271931 Query DataSets for GSM4271931
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

Supplementary file Size Download File type/resource
GSM4271931_cpg.G70107_GCLL-0286-T-01.mincov10.txt.gz 7.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap