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| Status |
Public on Jul 18, 2017 |
| Title |
wild type retina sample 1 (WR1) |
| Sample type |
SRA |
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| Source name |
retina
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| Organism |
Danio rerio |
| Characteristics |
tissue: retina
genotype: wildtype
age: 5 dpf
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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 with cufflinks-2.2.1
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 https://gist.github.com/coralzhang/fc4e51609ff316486c1682feed6404a9/471afb15b7f7b230a38e4eedaadcf5f679412a07
Supplementary_files_format_and_content: text file with raw read counts or FPKM
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| Submission date |
Jul 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Nadejda Beliakova-bethell |
| Organization name |
University of California San Diego
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| Street address |
9500 Gilman Dr, La Jolla
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| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL14875 |
| Series (1) |
| GSE101544 |
Expression profiling of the retina of pde6c, a zebrafish model of retinal degeneration |
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| Relations |
| BioSample |
SAMN07358651 |
| SRA |
SRX3010467 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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