|
| 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 |
INRAE - University PARIS SACLAY
|
| Department |
Micalis Institute
|
| Lab |
Epigenetics and Cellular Microbiology
|
| 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 |
