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Sample GSM839875 Query DataSets for GSM839875
Status Public on Apr 01, 2012
Title KO library 3
Sample type SRA
Source name Total fetal Liver Klf1-/-
Organism Mus musculus
Characteristics strain: BALB/c
genotype/variation: Klf1-/-
tissue: Fetal liver
developmental stage: Embryonic day 14.5
Growth protocol Fetal livers were collected from E14.5 timed matings (Klf1+/- x Klf1+/-) by dissection, mechanically dissociated and passed through a 40 micron cell strainer to obtain a single cell suspension. Fetal livers were collected from 3 Klf1-/- embryos and 3 Klf1+/+ embryos from 2 independent litters and genotypes confirmed by PCR.
Extracted molecule total RNA
Extraction protocol Total RNA was collected from homogenized E14.5 fetal livers using TRIzol (Invitrogen) and treated with amplification grade DNaseI (Invitrogen). 12μg of total RNA for each sample was treated with the mouse GlobinClear kit (Ambion) to remove the majority of globin RNA. Libraries were prepared from this RNA starting with 8μg per sample and using the mRNA-seq Sample Prep Kit (Illumina) as per recommended instructions. Cluster generation and sequencing was performed as per standard Illumina GAIIx protocols to generate single end reads of 76bp. Each library was sequenced in an individual lane of the GAIIx flow cell. A single Klf1+/+ library (WT library 3) was sequenced to approximately twice the depth by generating two lanes of sequence.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Data processing s_5.bam; genome build: mm9
The six files of raw mRNA-Seq reads were mapped onto the mm9 genome of UCSC ( to generate six BAM files individually using Tophat-1.3.1 (
Submission date Nov 28, 2011
Last update date May 15, 2019
Contact name Michael Robert Tallack
Phone +61 7 3346 2357
Organization name Institute for Molecular Bioscience, The University of Queensland
Lab Perkins
Street address Services Road
City St Lucia
State/province QLD
ZIP/Postal code 4072
Country Australia
Platform ID GPL11002
Series (1)
GSE33979 Novel roles for Klf1 in regulating the erythroid transcriptome revealed by mRNA-seq
SRA SRX109328
BioSample SAMN00760832

Supplementary file Size Download File type/resource
GSM839875_s_5.bam 660.5 Mb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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