NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2028019 Query DataSets for GSM2028019
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap