|
Status |
Public on Sep 05, 2018 |
Title |
oct4_gfp_esc3 |
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 |
SAMN07419703 |
SRA |
SRX3043955 |