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Sample GSM1403294 Query DataSets for GSM1403294
Status Public on Mar 24, 2015
Title E14.5_liver_Rlf_mutant_RNA-Seq_rep1
Sample type SRA
 
Source name E14.5 liver
Organism Mus musculus
Characteristics strain: FVB
tissue: liver
developmental stage: E14.5
genotype/variation: Rlf mutant
gender: Male
Extracted molecule total RNA
Extraction protocol Tissues were homogenized in Buffer RLT Plus (Qiagen) and RNA extracted using the AllPrep DNA/RNA Mini Kit (Qiagen)
Libraries were prepared and sequenced by the Australian Genome Research Facility (AGRF) using the Illumina TruSeq protocol from polyA-selected RNA
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing reads were mapped to the mouse genome with Tophat using the parametres -I 100000 --no-coverage-search --read-mismatches 2 --library-type fr-unstranded
Transcript read counts (obtained from Ensembl, version 67) were extracted with the script htseq-count using the options -s no -m intersection-strict
Differentially expressed genes were identified using DeSeq
Genome_build: mm9
Supplementary_files_format_and_content: Transcript read counts
 
Submission date Jun 03, 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 SAMN02837155
SRA SRX567349

Supplementary file Size Download File type/resource
GSM1403294_E14.5_liver_Rlf_KO_rep1.tab.gz 140.0 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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