|
Status |
Public on Jun 30, 2023 |
Title |
tdTomato-_adult_thrb2tdTomato_rep3 |
Sample type |
SRA |
|
|
Source name |
Retina
|
Organism |
Danio rerio |
Characteristics |
tissue: Retina cell type: Cone photoreceptor genotype: WT treatment: FACS-sorted tdTomato- retinal cells in adult zebrafish
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted with TRIzol LS or the Machery-Nagel RNA extraction kit. For samples with a RIN score greater than 8.0, sequencing libraries were constructed according to the manufacturer’s protocol using the TruSeq® RNA Library Preparation Kit (Illumina) with 5µg total RNA as input.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
tdTm.3
|
Data processing |
Reads were trimmed using Trimmomatic v0.36. Trimmed reads were processed with fastqc v0.11.5, HTStream v1.3.2. Alignments were mapped to zebrafish reference genome GRCz11 using salmon v0.13.1. Assembly: GRCz11 Supplementary files format and content: tsv files for raw counts Supplementary files format and content: tsv files for DEG list
|
|
|
Submission date |
May 19, 2023 |
Last update date |
Jun 30, 2023 |
Contact name |
Chi Sun |
E-mail(s) |
sunchi@wustl.edu
|
Organization name |
Washington University in St. Louis
|
Department |
Ophthalmology and Visual Sciences
|
Lab |
McMillan Hospital 618
|
Street address |
4523 Clayton Ave.
|
City |
St. Louis |
State/province |
MO |
ZIP/Postal code |
63110 |
Country |
USA |
|
|
Platform ID |
GPL18413 |
Series (1) |
GSE232902 |
Transcriptomic analysis of long wavelength-sensing cones of zebrafish retina |
|
Relations |
BioSample |
SAMN35215608 |
SRA |
SRX20438368 |