|
| Status |
Public on Dec 11, 2015 |
| Title |
HEK293-CT MeDIP R1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: embryonic semi-differentiated kidney cells
treatment: control
cell line: HEK293
sample type: MeDIP enrichment
|
| 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 |
DNA was isolated using the conventional proteinase K/organic extraction method and sheard to obtain 100 to 500bp fragments. Fragments were size selected and purified by separating on agarose gel followed by gel-purification using gel-extraction kit (Qiagen)
the fragments were subjected for library preparation using Illumina paired-end sample preparation kit, using manufactures protocol.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
methylated DNA
|
| Data processing |
Basecalls performed using CASAVA version 1.8
reads were filtered with custom Python scripts
MeDIP-seq reads were aligned to the hg19 genome assembly using MAQ with default parameters
reads were assigned to genomic windows of 300 bp using MEDIPS
counts were normalized with edgeR per effective library size
Genome_build: hg19
Supplementary_files_format_and_content: WIG files, library size normalized counts per 300 bp genomic window
|
| |
|
| 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) |
| GSE51864 |
Methylated DNA immunoprecipitation-sequencing 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 |
SAMN02388134 |
| SRA |
SRX370329 |
