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Series GSE79937 Query DataSets for GSE79937
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
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.
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.
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
Organization name University College London
Street address 30 Guilford St
City London
ZIP/Postal code WC1N 1DP
Country United Kingdom
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (12)
GSM2108734 E11.5 Cre control rep1
GSM2108735 E11.5 Cre control rep2
GSM2108736 E11.5 Cre control rep3
BioProject PRJNA317463
SRA SRP072877

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 658.0 Kb (ftp)(http) TAB 655.7 Kb (ftp)(http) TAB
GSE79937_rpkm_values.csv.gz 1.7 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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