run_metadata: 59484
This data as json
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| 59484 | SRR11922870 | SRX8468584 | SRS6769272 | SRP265910 | PRJNA637219 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes | GSE151770 | Transcriptome Analysis | Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf | pubmed:32980661 | zebrafish embryo Aldh3a1 KO rep2 | GSM4590768 | source name:zebrafish embryo|genotype:aldh3a1 KO|tissue:embryo|age:48 hpf | zebrafish embryo Aldh3a1 KO rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | zebrafish embryo | Not applicable | Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation | genotype:aldh3a1 KO|tissue:embryo|age:48 hpf | GSM4590768 | GSM4590768: zebrafish embryo Aldh3a1 KO rep2; Danio rerio; RNA Seq | GSM4590768 | 1 | Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM4590768 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP265910 | 8_aldh3a1----homo-48hpf-2_1.fq.gz 8_aldh3a1----homo-48hpf-2_2.fq.gz | fastq fastq | 5097901600.0 | 50979016.0 | GSM4590768 r1 | 0:100 1:100 | A:1487281075;C:1055394796;G:1035616985;T:1519608744;N:0 | 100 | 100 | 1487281075 | 1055394796 | 1035616985 | 1519608744 | 0 | SRX8468584 | SRS6769272 | SRA1083013 | GEO | ZMF, University Heidelberg | 1 | 0.92556 | 0.18622 | 0.73026 | 0.5187 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2020-06-04 | Hatching | Embryo | Embryo Imprecise | All anatomical structures |