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| Status |
Public on Aug 12, 2016 |
| Title |
Mesp1Cre;Hira-/fl and Mesp1Cre;Hira+/fl in heart at E11.5 and E12.5 |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The goals of this study are to compare transcriptome profiling (RNA-seq) resulting from a Mesp1Cre driven ablation of Hira in the heart at E11.5 and E12.5.
Methods: RNA extraction was done in triplicate from Mesp1Cre;Hira-/fl and Mesp1Cre;Hira+/fl embryonic hearts at E11.5 and E12.5 using the QIAGEN RNeasy mini kit. RNAseq was processed by the ICH genomics facility, reads were aligned and normalised using BOWTIE and DEseq R package. Strand NGS 2.5 software was used to re-analyse the aligned files (.bam). By applying the Mann Whitney unpaired test, Benjamini Hochberg False discovery rate (FDR) and filtering the genes using adjusted p-value ≤ 0.05 and absolute fold change ≥ 1.5, 95 % of the results were identical to the DEseq package used by the UCL Genomics facility.
Results: We identified 360 coding transcripts changed in the mutant hearts (Mann Whitney unpaired test, Benjamini Hochberg FDR, p ≤ 0.05, FC ≥ 1.5) with no trend towards up- or down-regulation of global transcription (48.8% down vs 51.2% up) at E12.5.
Conclusions: This work analyses the role of HIRA in mouse cardiac development. It was found that Tnni2 is the most upregulated gene in the absence of Hira. qRT-PCR validation of 25 targets. Little (<5%) or no variation of fold change between RNAseq and qRT-PCR data were observed.
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| Overall design |
Cardiac mRNA profiles of 11-day and 12-day embryonic days Mesp1Cre control (Ctrl) and Mesp1Cre;Hira-/fl (mut) were generated by deep sequencing, in triplicate, using Illumina GAIIx.
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| Contributor(s) |
Dilg D, Brooks T, Scambler P, Chapgier A |
| Citation(s) |
27518902 |
| Submission date |
Apr 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Dilg |
| E-mail(s) |
daniel.dilg@gmail.com
|
| Organization name |
University College London
|
| Street address |
30 Guilford St
|
| City |
London |
| ZIP/Postal code |
WC1N 1DP |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA317463 |
| SRA |
SRP072877 |
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