|
| Status |
Public on Aug 01, 2014 |
| Title |
P14 (RNA-Seq) replicate2 |
| 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 |
| E-mail(s) |
mark.ziemann@gmail.com
|
| Organization name |
Burnet Institute
|
| Department |
Bioinformatics Working Group
|
| Street address |
85 Commercial Rd
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3004 |
| 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 |
|
| Relations |
| BioSample |
SAMN02948135 |
| SRA |
SRX667360 |
