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Sample GSM2719825 Query DataSets for GSM2719825
Status Public on Sep 05, 2018
Title prdm14_puro_pgclc3
Sample type SRA
 
Source name Primordial germ cells
Organism Mus musculus
Characteristics media: BMP4, BMP8, SCF, EGF and LIF
flox cassette: PuroR
cell type: Primordial germ 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:
prdm14_matada_pgclc_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 SAMN07419687
SRA SRX3043971

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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