|
| Status |
Public on Jun 01, 2016 |
| Title |
3dpa mRNA |
| Sample type |
SRA |
| |
|
| Source name |
pectoral fin
|
| Organism |
Polypterus senegalus |
| Characteristics |
days post amputation: 3
library type: mRNA
amputation site: pectoral fin
|
| Treatment protocol |
Pectoral fins were amputated with scalpels following anesthesia (0.6mM MS222).
|
| Growth protocol |
FIsh from the Maine Pet and Aquarium (Ellsworth, ME) were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) following manufacturer’s protocol.
Illumina TruSeq small RNA and PolyA+ mRNA libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
PsenD3
Polypterus_mRNA_assembly.fa.gz
Polypterus_mRNA_logCPM.txt
|
| Data processing |
Reads were adapter clipped and quality filtered using FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) for small RNA, and Trimmomatic (Bolger et al. Bioinformatics (2010)) for mRNA.
Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner (Wheeler et al. Evol. Dev. (2009)) and miRBase v. 21 (Kozomara et al. Nucleic Acids Res (2014)).
MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR (Robinson et al. Bioinformatics (2010)).
Trimmed mRNA reads were digitally normalized using khmer (http://khmer-protocols.readthedocs.org/en/v0.8.4/).
Digitally normalized mRNA reads were assembled using Trinity (Haas et al. Nat Protoc. (2013)).
Reads counts per transcript were generated using RSEM (Li and Dewey BMC Bioinformatics (2011)).
Differentially expressed transcripts were determined using R/edgeR.
Genome_build: The de novo transcriptome assembly is linked as a supplementary file on the Series record.
Supplementary_files_format_and_content: Tab-delimited text file with read counts per transcript per sample.
|
| |
|
| Submission date |
Oct 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin L King |
| E-mail(s) |
benjamin.l.king@maine.edu
|
| Phone |
207-581-2803
|
| Organization name |
University of Maine
|
| Department |
Molecular and Biomedical Sciences
|
| Street address |
5735 Hitchner Hall
|
| City |
Orono |
| State/province |
ME |
| ZIP/Postal code |
04469 |
| Country |
USA |
| |
|
| Platform ID |
GPL21070 |
| Series (1) |
| GSE74374 |
Small RNA and mRNA expression profiling during Polypterus senegalus (bichir) pectoral fin regeneration |
|
| Relations |
| BioSample |
SAMN04216988 |
| SRA |
SRX1386645 |
