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Sample GSM7389994 Query DataSets for GSM7389994
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

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

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