|
| Status |
Public on Apr 08, 2016 |
| Title |
ZF_Uninjured_Fin_1 |
| Sample type |
SRA |
| |
|
| Source name |
Uninjured fins
|
| Organism |
Danio rerio |
| Characteristics |
strain: EK
line: Wild type
treatment: None
|
| Treatment protocol |
Fins were amputated to 50% of their original length using razor blades
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Either uninjured fins or fins at 4 days post amputation were collected. 10 fins were dissected, rinsed in PBS, 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 |
Un1
|
| 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: "Regenerate_fin_counts.txt" and "Uninjured_fin_Control_counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR.
|
| |
|
| Submission date |
Jan 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Junsu Kang |
| Organization name |
University of Wisconsin - Madison
|
| Department |
Department of Cell and Regenerative Biology
|
| Lab |
Kang lab
|
| Street address |
1111 Highland Avenue, Room 4451, WIMR II, Kang lab, CRB
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL9319 |
| Series (1) |
| GSE76564 |
Transcription profiling of zebrafish fin regeneration |
|
| Relations |
| BioSample |
SAMN04385834 |
| SRA |
SRX1518388 |
