NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1400928 Query DataSets for GSM1400928
Status Public on Mar 24, 2015
Title Wildtype E14.5 liver rep1
Sample type SRA
 
Source name E14.5 liver rep1
Organism Mus musculus
Characteristics strain: FVB
genotype/variation: Wildtype
gender: Male
Treatment protocol N/A
Growth protocol N/A
Extracted molecule genomic DNA
Extraction protocol Qiagen AllPrep
Illumina
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Data processing 3' ends were trimmed for low quality bases using trim_seq with the settings (www.biopieces.org)
Reads were mapped to the mouse genome (build mm9) using Bismark and Bowtie2 with the options -N 1 -D 30
PCR duplicates were removed from mapped reads using deduplicate_bismark_alignment_output.pl
Methylation values extracted using bismark_methylation_extractor with the setttings --ignore_r2 2
CpG methylation values were finally merged into a single value per CpG
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph showing %mCG. Additionally, columns with counts for unconverted Cs and converted Cs are included.
 
Submission date May 29, 2014
Last update date May 15, 2019
Contact name Harald Oey
Organization name La Trobe University
Department Genetics
Street address Kingsbury Drive
City Bundoora
State/province Vic
ZIP/Postal code 3086
Country Australia
 
Platform ID GPL13112
Series (1)
GSE58108 Rlf, a widely-spaced zinc finger protein, is involved in maintaining epigenetic marks at CpG island shores and enhancer elements across the genome
Relations
BioSample SAMN02803949
SRA SRX555625

Supplementary file Size Download File type/resource
GSM1400928_E14.5_liver_wt_rep1.tab.gz 168.1 Mb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap