GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2705948 Query DataSets for GSM2705948
Status Public on Jul 18, 2017
Title pde6c mutant retina sample 2 (PR2)
Sample type SRA
Source name retina
Organism Danio rerio
Characteristics tissue: retina
genotype: pde6c mutant
age: 5 dpf
Extracted molecule total RNA
Extraction protocol Total RNAs was extracted from the biological replicates by an optimized procedure that combined TRIzol (Life Technologies, Grand Island, NY) and RNeasy Micro kit (Qiagen, Valencia, CA). The quality of the extracted total RNAs were evaluated by Bioanalyzer electrophoresis (Agilent Technologies, Santa Clara, CA).
Libraries were prepared according to Illumina's instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Generating genome index using STAR-2.5.3a using the Danio_rerio.GRCz10.dna.toplevel.fa and Danio_rerio.GRCz10.89.gtf from ensemble ftp
Alignment using STAR-2.5.3a
Read counting using featureCounts v1.5.2
Generating normalized expression measurements
Quantifying differential expression
Genome_build: Danio_rerio.GRCz10.dna.toplevel.fa and Danio_rerio.GRCz10.89.gtf from ensemble ftp
For more analysis done, see
Supplementary_files_format_and_content: text file with raw read counts or FPKM
Submission date Jul 17, 2017
Last update date May 15, 2019
Contact name Nadejda Beliakova-bethell
Organization name University of California San Diego
Street address 9500 Gilman Dr, La Jolla
City San Diego
State/province CA
ZIP/Postal code 92093
Country USA
Platform ID GPL14875
Series (1)
GSE101544 Expression profiling of the retina of pde6c, a zebrafish model of retinal degeneration
BioSample SAMN07358655
SRA SRX3010471

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap