|
| Status |
Public on Sep 05, 2018 |
| Title |
oct4_gfp_esc2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells (2i)
|
| Organism |
Mus musculus |
| Characteristics |
media: 2i and LIF
flox cassette: GFP
cell type: Embryonic stem cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted using the QuiAmp® DNA Micro. The gDNA was digested with DpnI, adaptors were ligated and then digested with DpnII and pcr amplified.
DNA was sonicated to an average size of 300bp using a Diagenode Bioruptor and DamID adaptors removed with AlwI digestion. Sonicated material was end-repaired, A-tailed, sequencing adaptors ligated and PCR amplified.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
DamID
processed data file:
oct4_matada_esc_average.bedgraph
|
| Data processing |
Library strategy: DamID
FASTQ files were processed with damidseq_pipeline.
Processed data from the damidseq_pipeline software in bedgraph format were used for peak calling with MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files were generated using the damidseq_pipeline software, at GATC fragment resolution. Score represents the normalised fold enrichment of Dam-OCT4 or Dam-PRDM14 fusion protein over dam-alone. Processed files are provided as averaged bedgraphs
|
| |
|
| Submission date |
Jul 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrea Brand |
| Organization name |
The Gurdon Institute
|
| Street address |
Tennis Court Rd
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE101971 |
Targeted DamID reveals differential binding of mammalian pluripotency factors |
|
| Relations |
| BioSample |
SAMN07419704 |
| SRA |
SRX3043954 |
