|
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 |