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Sample GSM1462886 Query DataSets for GSM1462886
Status Public on Aug 01, 2014
Title P14 (RNA-Seq) replicate1
Sample type SRA
Source name Cardiac left ventricle - neonatal day 14
Organism Mus musculus
Characteristics gender: Male
age: P14
tissue: cardiac left ventricle
strain: C57BL/6
Treatment protocol N/A
Growth protocol Experimental Animals and Tissue Collection: All protocols were approved by The University of Queensland Animal Ethics Committee. Male C57BL/6 mice (The Jackson Laboratory, ME) were used for genome-wide DNA methylation and mRNA expression profiling during post-natal development (P1 and P14). For DNA and RNA analysis, atrial tissues were removed from ventricles (septum intact) and ventricles were blotted and weighed before snap-freezing in liquid nitrogen for storage at -80C.
Extracted molecule total RNA
Extraction protocol Cardiac ventricles were harvested at P1 and P14 (n=9 per group) from C57BL6/J mice as described above and were homogenised in PBS. Three individual hearts were pooled per replicate. RNA was isolated by TRIzol extraction (Ambion) followed by QiaQuick MinElute cleanup including on-column DNase digestion. RNA quality was verified with MultiNA bioanalyzer (Shimadzu, Kyoto). Purified mRNA was prepared using Dynabeads® Oligo (dT)25 (Ambion) enrichment.
Libraries were generated using the NEBNext® mRNA Library Prep Reagent Set for Illumina (New England Biolabs). Libraries were validated on MultiNA bioanalyzer and sequenced at a concentration of 10 pM on Genome Analyzer IIx instrument for 36 cycles. Illumina base-calling was performed off-line with OLB v1.8.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Data processing Basecalling with Illumina software (OLB v1.8)
Fastx quality trimmer was used to remove low quality bases from the 3' end of the read (base quality <30)
The mouse genome was downloaded from the Ensembl ftp site (version GRCm38.70/mm10). Reads were aligned to the mouse genome with Olego aligner with default settings.
Reads aligning to Ensembl-annotated exons with a strict mapping quality (Q≥20) were counted with BedTools and used to construct a data matrix comprising genes with an average of 10 reads or more per sample across the experiment. Differential gene expression analysis was performed using edgeR (v3.2.4).
Genome_build: GRCm38.70/mm10
Supplementary_files_format_and_content: Count matrix
Submission date Jul 31, 2014
Last update date May 15, 2019
Contact name Mark D Ziemann
Organization name Deakin University
Department Life and Environmental Sciences
Street address 75 Pigdons rd
City Waurn Ponds
State/province VIC
ZIP/Postal code 3216
Country Australia
Platform ID GPL11002
Series (2)
GSE59970 Genome-wide DNA methylation analysis reveals dynamic changes in the cardiac methylome during post-natal heart development (RNA-Seq)
GSE59971 Genome-wide DNA methylation analysis reveals dynamic changes in the cardiac methylome during post-natal heart development
BioSample SAMN02948134
SRA SRX667359

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

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