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Series GSE45760 Query DataSets for GSE45760
Status Public on Mar 26, 2014
Title Identification of dysregulated genes after deletion of miR-1-1 and miR-1-2
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The goals of this study are to identify dysregulated mRNAs in the heart after deletion of miR-1-1 and miR-1-2. Methods: Total RNAs were extracted from hearts at embryonic E15.5 (E15.5) or postnatal 2.5 days (P2.5) of miR-1s dHET and miR-1s dKO mice. mRNAs were purified using a poly-A selection approach and sequenced using Illumina HiSeq 2000. The sequence reads were aligned to the mouse reference genome (NCBI Build 37/mm9) using TopHat program (Bowtie algorithm). Transcript assembles and identification of differentially expressed genes were achieved using Cufflinks package. To account for expression bias due to transcript length, each sample transcript expression was normalized by using cufflinks algorithm with a FDR of 0.05. Results: Using 1.5-fold change as a cutoff, 997 and 653 transcripts were found to be upregulated and downregulated, respectively, in miR-1s dKO heart at P2.5. 423 transcripts were found to be upregulated and 653 were down-regulated in miR-1s dKO heart at E15.5. Many upregulated genes are directly involved in a fetal gene program. Conclusions: miR-1 directly represses a fetal gene program.
Overall design We performed RNA deep-seq using postnatal 2.5 days (P2.5) heart from miR-1-1 and miR-1-2 double knockout mice and compared it to that of littermate control.
Contributor(s) Zhao Y
Citation(s) 24481529
Submission date Apr 03, 2013
Last update date May 15, 2019
Contact name Yong Zhao
Phone 212-824-8916
Organization name Icahn School of Medicine at Mount Sinai
Department Mindich Child Health and Development Institute
Street address 1470 Madison Ave
City New York City
State/province NY
ZIP/Postal code 10029
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (4)
GSM1113840 P2.5 miR-1s dHET
GSM1113841 P2.5 miR-1s dKO
GSM1113842 E15.5 miR-1s dHET
BioProject PRJNA196236
SRA SRP020501

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Supplementary file Size Download File type/resource
GSE45760_E15.5.csv.gz 870.4 Kb (ftp)(http) CSV
GSE45760_P2.5.csv.gz 856.9 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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