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| Status |
Public on Jun 01, 2024 |
| Title |
bcas2-KO biol rep 3 |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Danio rerio |
| Characteristics |
tissue: embryo
genotype: bcas2-KO
age: 3 dpf
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| Extracted molecule |
total RNA |
| Extraction protocol |
After genotyping, for each WT and bcas2-KO sample, 10 zebrafish embryos were used to isolate total RNA using the TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.
Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s technical guide.
The library preparations were then sequenced on an Illumina Hiseq platform using the 2 x 150 bp paired-end configuration according to the manufacturer’s protocol. For each cDNA library, 6 G base paired-end raw reads were generated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
B3
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| Data processing |
Raw reads in fastq format were firstly processed by Cutadapt (v1.15) to remove adapters, reads containing ploy-N, and low-quality reads. The resulting clean reads were used for all downstream analyses.
Clean reads were mapped to the zebrafish reference genome (DanRer11) using STAR (v2.6.1a) according to the user manual with the default parameters. featureCounts (v1.6.0) was adopted to count the mapped reads. Stringtie (v1.3.3b) was executed to calculate the FPKM values of genes.
Differential expression analysis was performed by DESeq2 R package (v1.22.1). The significantly DEGs between WT and Bcas2-KO embryos were identified by using the threshold fold change > 2 and adjusted p-values < 0.05.
Alternative splicing patterns were identified and calculated by rMATs python package (v4.0.2). The threshold of inclusion level change > 0.10 and adjusted p-values < 0.05 was used to identify significant DSEs.
GO and KEGG enrichment analysis was performed by using the RDAVIDWebService R package.
Assembly: GRCz11 (GCA_000002035.4)
Supplementary files format and content: raw_counts.txt is a tab-delimited text file for read count numbers of each gene.
Supplementary files format and content: FPKMs_allsamples.txt is a tab-delimited text file for quantitative expression (FPKM) of each gene.
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| Submission date |
Oct 26, 2023 |
| Last update date |
Jun 01, 2024 |
| 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 |
GPL14875 |
| Series (1) |
| GSE246374 |
RNA-seq analysis of the WT and bcas2-KO zebrafish embryos at 3 dpf |
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| Relations |
| BioSample |
SAMN37999806 |
| SRA |
SRX22240819 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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