|
| Status |
Public on Apr 08, 2016 |
| Title |
ZF_Ablated_Hearts_1 (TAM-1) |
| Sample type |
SRA |
| |
|
| Source name |
Whole hearts 7d post ablation
|
| Organism |
Danio rerio |
| Characteristics |
strain: EK/AB
line: g(bactin2:loxP-mCherry-STOP-loxP-DTA176); cmlc2:CreER
treatment: Tamoxifen
|
| Treatment protocol |
Animals were treated with Tamoxifen of propylene glycol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts were collected 7 days after treatment. 10 ventricles were dissected, rinsed in heparin, placed in Trizol and homogenized. RNA was then extracted.
Illumina RNA-Seq, 50 bp Single end libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
TAM-1
|
| Data processing |
Base calling with Casava
Alignment with TopHat
Counts summarized with R using TopHat output
Analysis performed with EdgeR package of Bioconductor
Genome_build: Zv9
Supplementary_files_format_and_content: "Reads_cpms.txt" is tab delimited text file. CPMs were calculated using edgeR.
Supplementary_files_format_and_content: "Raw_read_counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR.
|
| |
|
| Submission date |
Dec 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ravi Karra |
| E-mail(s) |
ravi.karra@duke.edu
|
| Organization name |
Duke
|
| Department |
Cell Biology
|
| Lab |
Poss
|
| Street address |
464 Nanaline Duke, 307 Research Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL9319 |
| Series (1) |
| GSE75894 |
Modulation of tissue repair by regeneration enhancer elements. |
|
| Relations |
| BioSample |
SAMN04330072 |
| SRA |
SRX1474050 |
