|
| Status |
Public on Nov 24, 2011 |
| Title |
Input_ES |
| Sample type |
SRA |
| |
|
| Source name |
E14 stem cells (TNG-A)
|
| Organism |
Mus musculus |
| Characteristics |
sample type: Embryonic stem cells carrying the EGFP reporter at the Nanog locus (TNG) from Austin Smith
antibody: none
|
| Growth protocol |
Embryonic stem cells were cultured without feeders in the presence of leukaemia inhibitory factor (LIF) in DMEM containing 10% fetal calf serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MeDIP-/hMeDIP-seq: ESC genomic DNA was purified and sonicated. Illumina adapters were ligated before MeDIP/hMeDIP. Adaptor-ligated DNA was denatured and incubated with 2µg of anti-5mC or 2µg of anti-5hmC antibody at 4°C overnight. Antibody-DNA complexes were captured by magnetic beads and the immunoprecipitated DNA was purified and sequenced followed by standard Illumina protocols. MethylCap-seq: ESC genomic DNA was purified and sonicated. Capturing of methylated DNA was done by incubating 2 ug of His6-GST-MBD (Diagenode) with 1 ug of fragmented DNA. GST-MBD-DNA complexs were captured by magnetic GST-beads. Beads-GST-MBD-DNA complexes were washed and eluted using different concentrations of NaCl. The collected eluates were purified using QIAquick PCR purification spin columns (Qiagen), eluted with 100ul elution buffer and prepared following standard Illumina protocols.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
genomic DNA derived from the chromatin input
|
| Data processing |
Reads (36bp) were aligned to the NCBI build 37 (mm9) with BWA v0.5.8 allowing 0/1 mismatches and unique mapped reads were converted to BED format. The aligned reads for MethylCap-seq_medium and MethylCap-seq_high were merged in an unique bed file.
|
| |
|
| Submission date |
Aug 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
H.G. Stunnenberg |
| E-mail(s) |
h.stunnenberg@ncmls.ru.nl
|
| Phone |
+31-24-3610520
|
| Organization name |
Radboud University
|
| Department |
Department of Molecular Biology (274)
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE31343 |
5-hydroxymethylcytosine: the sixth DNA base |
|
| Relations |
| SRA |
SRX091985 |
| BioSample |
SAMN00709483 |
