|
Status |
Public on Mar 01, 2017 |
Title |
Leucoraja_4_RNASeq |
Sample type |
SRA |
|
|
Source name |
Liver
|
Organism |
Leucoraja erinacea |
Characteristics |
developmental stage: Adult tissue: Liver tissue description: 4 mg sample from liver
|
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 |
SAMN06227241 |
SRA |
SRX2488466 |