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Sample GSM1254259 Query DataSets for GSM1254259
Status Public on Dec 11, 2015
Title HEK293-CT
Sample type SRA
 
Source name HEK293 cells
Organism Homo sapiens
Characteristics cell type: embryonic semi-differentiated kidley cells
cell line: HEK293
Treatment protocol HEK-BAHD1 were generated by integration of a single copy of the BAHD1 cDNA under the control of the human cytomegalovirus (CMV) immediate-early enhancer/promoter in the HEK293 genome. In the isogenic control line (HEK293-CT), the β-galactosidase DNA sequence was inserted in place of BAHD1, albeit out-of-frame to avoid translation into protein.
Growth protocol Cells were grown at 37°C, in a humidified 10% CO2 incubator, in Dulbecco's modified Eagle's medium with GlutaMAX (Gibco) supplied with 10%FBS (Gibco) and 200 ug/ml Hygromycin B (10687-010-Invitrogen).
Extracted molecule genomic DNA
Extraction protocol High molecular weight genomic DNA was isolated using the conventional proteinase K/organic extraction method. DNA was reduced into 100-300 bp fragments by sonication and treated with DNA-end repair, 3’-dA overhang and ligation of methylated sequencing adapters. Samples underwent bisulfite treatment with the ZYMO EZ DNA Methylation-Gold kit.
Desalted, size-selected, PCR amplified fragments were size-selected and qualified libraries were selected for Illumina sequencing according to BGI tech protocol.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Description methylated DNA
Data processing Basecalls performed using CASAVA version 1.8
data were filtered with BGI programs, Low-quality reads include two types, and the read which could be accord with anyone of the two types will be removed: (1) The ratio of N in whole read was over 10%; (2) The ratio of base whose quality was less than 20 was over 10%.
SOAP aligner mapping as described in Li Y, Zhu J, Tian G, Li N, Li Q, et al. (2010) The DNA Methylome of Human Peripheral Blood Mononuclear Cells. PLoS Biol 8(11): e1000533.
cout: methylation information of cytosines in whole genome wide
Genome_build: hg19
Supplementary_files_format_and_content: cout (BGI); each line contains: Chromosome ID 2.Position 3. strand 4. Cytosine pattern (CG/CHH/CHG) 5. Cytosine sequence context 6. Copynumber 7. Methyl-reads num 8. Non-methyl-reads num 9. Binomial distribution expected values
 
Submission date Oct 29, 2013
Last update date May 15, 2019
Contact name Helene Bierne
E-mail(s) helene.bierne@inrae.fr
Phone 33134652289
Organization name INRA
Department Micalis Institute
Lab EPIMIC
Street address Domaine de Vilvert, bat 442, INRA Micalis
City Jouy-en-Josas
ZIP/Postal code 78350
Country France
 
Platform ID GPL11154
Series (2)
GSE51867 whole-genome bisulfite sequencing (BS-seq) of HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1)
GSE51868 HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1)
Relations
BioSample SAMN02388197
SRA SRX370354

Supplementary file Size Download File type/resource
GSM1254259_HEK293-CT.cout.txt.gz 5.7 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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