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| Status |
Public on Oct 27, 2020 |
| Title |
WT-R1 |
| Sample type |
SRA |
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| Source name |
Retina
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| Organism |
Danio rerio |
| Characteristics |
tissue: Retina
strain: AB
age: 2 months post fertilization
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
For each RNA sample, three eyes (lens removed) from different zebrafish were homogenized in RNAiso Plus reagent (Takara, Cat# 9108). Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies) and NanoDrop (Thermo Fisher Scientific). RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA-seq.
The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Quality control, mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. The high-quality clean data were generated by Trimmomatic (v0.30) and aligned to the reference genome of zebrafish via software Hisat2 (v2.0.1).
Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq (v0.6.1). Differential expression analysis was performed by DESeq Bioconductor package. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, the threshold of p-values was set to <0.05 to detect differentially expressed genes.
GO and KEGG enrichment analysis: GO-TermFinder was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant p-value less than 0.05. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG), which was used to enrich significant differential expression gene in KEGG pathways.
Genome_build: GRCz11 from Ensembl
Supplementary_files_format_and_content: Tab-delimited text files including the raw counts and FPKM values for each Sample
Supplementary_files_format_and_content: Tab-delimited text files showing the foldchanges and p-values of the differentially expressed genes
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| Submission date |
Oct 26, 2020 |
| Last update date |
Oct 27, 2020 |
| Contact name |
Fei Liu |
| E-mail(s) |
liufei2018@ihb.ac.cn
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| Phone |
+8613554697245
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| Organization name |
Institute of Hydrobiology, Chinese Academy of Sciences
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| Street address |
No. 7 Donghu South Road, Wuchang District
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430072 |
| Country |
China |
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| Platform ID |
GPL18413 |
| Series (2) |
| GSE160138 |
Nrl-dependent and independent rod photoreceptor development in zebrafish [RNA-Seq] |
| GSE160141 |
Nrl-dependent and independent rod photoreceptor development in zebrafish |
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| Relations |
| BioSample |
SAMN16555683 |
| SRA |
SRX9364740 |
| 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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