|
| Status |
Public on Jun 03, 2014 |
| Title |
input DNA 1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
genotype: wildtype
chip antibody: none
|
| Growth protocol |
mESCs were grown 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.
See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
ChIP-Seq reads were mapped by bowtie to mm9, keeping only uniquely mapping reads and discarding all but one of clonal reads. Wig files combining H3K9m3 ChIP-seq and the respective input were generated using the SPP package for R and binning the data into non-overlapping 100bp bins.
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq 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 were generated by combining CHIP and respective Input files using SPP for R
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 |
GPL11002 |
| Series (2) |
| GSE47878 |
Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (Dnmt3ab KO ChIP-Seq) |
| GSE47894 |
Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases |
|
| Relations |
| BioSample |
SAMN02202292 |
| SRA |
SRX304980 |
