|
| Status |
Public on May 19, 2016 |
| Title |
CKO-5DPR-02 |
| Sample type |
SRA |
| |
|
| Source name |
heart ventricles of pitx2CKO mouse at 5-day-post-resection
|
| Organism |
Mus musculus |
| Characteristics |
tissue: heart
tissue compartment: ventricles
surgery: cardiac apex resection at Postnatal day 2
age: postnatal day 7
genotype: MCKcre;pitx2f/f (pitx2CKO)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted form the ventricles using miRNeasy mini kit (Qiagen), and then mRNA was purified using Dynabeads mRNA DIRECT Micro Kit (Ambion, life technologies)
the libraries were prepared using Ion Total RNA-Seq Kit v2 for IonProton System (Ion Torrent, Life Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Torrent_Suite 4.0.2 for basecalling with parameters: `BaseCaller --keypass-filter on --phasing-residual-filter=2.0 --trim-qual-cutoff 15 --trim-qual-window-size 30 --trim-adapter-cutoff 16 --num-unfiltered 1000 --calibration-training=100000 --flow-signals-type scaled-residual --max-phasing-levels 2`
Sequenced reads were aligned against mouse genome mm9 using Tmap version 3.0.1 with default RNA-Seq setting `map4`
Gene expression levels were measured by counting numbers of reads in all the exons using HTSeq version 0.5.4p3 with parameters: `htseq-count -m union -s yes -t exon -i gene_symbol`
Differential gene expression was measured using DESeq version 1.16.0
Genome_build: mm9
Supplementary_files_format_and_content: comma-separated values files for raw read counts; comma-separated value file with differentially expressed genes.
|
| |
|
| Submission date |
Jun 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Min Zhang |
| E-mail(s) |
minzhang5099@gmail.com
|
| Organization name |
Baylor College of Medicine
|
| Department |
Department of Molecular Physiology
|
| Lab |
James F Martin
|
| Street address |
One Baylor Plaza Room 504E
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE70413 |
Pitx2 promotes heart repair by transcriptionally activating the antioxidant response after cardiac injury |
|
| Relations |
| BioSample |
SAMN03801639 |
| SRA |
SRX1077590 |
