|
| Status |
Public on Apr 18, 2013 |
| Title |
shCONT-IgG-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Control mouse ES cells
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: IgG
cell type: embryonic stem
genotype/variation: control
|
| Treatment protocol |
Around 1x10^5 ES cells/well in 24-well plates are infected with lentiviral vectors at 10 MOI. 48 hours after transduction, puromycin (2ug/ml) is added to the medium for selecting transduced cells.
|
| Growth protocol |
E14 mESCs are cultured on the 0.1% gelatin coated plates in the DMEM medium (Sigma) supplemented with 100U/ml penicillin/streptomycin, 15% fetal bovine serum (Sigma), 1x nonessential amino acid, 1x sodium pyruvate, 1x GlutaMax, 1x beta-mercaptoethanol (Invitrogen) and 1000 units/ml leukemia inhibitory factor (ESGRO, EMD Millipore).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB) following manufacture's instructions.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls were performed using OLB-1.8.0
Sequenced reads were de-multiplexed, trimmed and mapped to mm9 whole genome using bowtie v0.12.7
Peak calling were performed using MACS 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: wiggle files (IgG signal subtracted; scores represent tag numbers per 10 million reads)
|
| |
|
| Submission date |
Apr 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Li Shen |
| Organization name |
HHMI/Boston Children's Hospital/Harvard Medical School
|
| Street address |
200 Longwood Ave
|
| City |
Boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE42250 |
Genome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics |
| GSE46111 |
Genome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics [MeDIP-Seq] |
|
| Relations |
| SRA |
SRX266847 |
| BioSample |
SAMN02045845 |
