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| Status |
Public on Jul 29, 2020 |
| Title |
ERBB2 drives YAP activation and EMT-like processes during cardiac regeneration |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
RNA-seq comparing WT and caERBB2 over expresising hearts with/out injury
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| Overall design |
For this experiment, 4 animals for each experimental group were used (WT Sham, ERBB2 - OE Sham, WT MI, ERBB2 - OE MI). Truseq libraries were made and barcoded, and subsequently subjected to 60bp single read solexa illumine sequencing, using the Solexa HiSeq. For RNA analysis, Adapters were trimmed using the cutadapt tool. Following adapter removal, reads that were shorter than 40 nucleotides were discarded (cutadapt option –m 40). Reads were sub-sampled randomly to have 23M Reads. TopHat (v2.0.10) was used to align the reads to the mouse genome (mm10). Counting reads on mm10 RefSeq genes (downloaded from igenomes) was done with HTSeq-count (version 0.6.1p1) . Differential expression analysis was performed using DESeq2 (1.6.3). Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
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| Contributor(s) |
Umansky K, Aharonov A, Kain D, Tzahor E |
| Citation(s) |
33046882 |
| |
| Submission date |
Jan 28, 2020 |
| Last update date |
Oct 28, 2020 |
| Contact name |
Eldad Tzahor |
| Organization name |
Weizmann Institute of Science
|
| Street address |
234 Herzl Street
|
| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA603547 |
| SRA |
SRP245626 |
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