|
| Status |
Public on Jun 03, 2014 |
| Title |
Setdb1_WT_5hmC_capture-seq |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wildtype
cell type: mouse embryonic stem cells
|
| Treatment protocol |
Setdb1 CKO cells were treated with 800nM of 4-OHT for 4 days and further cultured without treatment for 2 days to induce Setdb1 deletion
|
| Growth protocol |
mESCs were grown on gelatinized plates in DMEM supplemented with 15% FBS (HyClone), 20 mM Hepes, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 100 U/mL penicillin, 0.05 mM streptomycin, leukemia inhibitory factor (1000 U/ml), and 2 mM glutamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Genomic DNA was fragmented by sonication of harvested mESCs and size selected (~300bp). The purified DNA was treated with β-glucosyltransferase (β-GT), which transfers an azide-glucose to 5-hmC. The purified products are then biotinylated by click chemistry. This allows the labelled 5hmC containing DNA fragments to be captured by using streptavidin beads. The DNA is purified and sequenced following standard protocols from Illumina.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
hmC capture and sequencing
|
| Data processing |
Basecalls performed using CASAVA version 1.4
hmC reads were aligned to the mm9 genome assembly using Bowtie keeping only uniquely mapping reads (max number of mismatches is 2)
Non-monoclonal reads were filtered out using the Picard software
Wig files c generated by caclulating reads per 100bp bin and per million reads.
Genome_build: mm9
|
| |
|
| Submission date |
Jun 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ulrich Wagner |
| Organization name |
Uiversity Hospital Zurich
|
| Street address |
Schmelzbergstrasse 12
|
| City |
Zurich |
| ZIP/Postal code |
8091 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE47892 |
Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (K9 KO 5hmC-capture-seq) |
| GSE47894 |
Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases |
|
| Relations |
| BioSample |
SAMN02202327 |
| SRA |
SRX305014 |
