|
| Status |
Public on Mar 01, 2017 |
| Title |
Leucoraja_1_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
Ampullary receptor cells
|
| Organism |
Leucoraja erinacea |
| Characteristics |
developmental stage: Adult
tissue: Ampullary receptor cells
tissue description: electroreceptor cells
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissues were removed, preserved in RNAlater solution at -20C, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Library Sample Prep Kit (Cat#RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
All reads were trimmer for low complexity or low quality ends (Sickle version 1.3).
Forward and reverse reads were pooled. A transcriptome was assembled using Trinity (version 2.1.0)
Estimates of relative abundance for differential expression were performed using RSEM (version 1.1.17)
Genome_build: de novo assembled transcriptome Leucoraja_assembly.fasta (assembled contigs)
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each sample
|
| |
|
| Submission date |
Jan 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Duncan Leitch |
| Organization name |
University of California - San Francisco
|
| Department |
Physiology
|
| Street address |
600 16th St.
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL22922 |
| Series (1) |
| GSE93582 |
RNASeq of molecular basis of ancestral vertebrate electroreception |
|
| Relations |
| BioSample |
SAMN06227244 |
| SRA |
SRX2488463 |
