run_metadata: 63601

This data as json

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63601	SRR13951243	SRX10330040	SRS8449842	SRP310389	PRJNA713989	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes	GSE168786	Transcriptome Analysis	Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf		pubmed:34278746;pubmed:36711148		Zebrafish larvae akr1a1a KO rep3	GSM5169476		source name:Zebrafish larvae akr1a1a KO larvae\|genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	Zebrafish larvae akr1a1a KO rep3	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: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	Zebrafish larvae akr1a1a KO larvae	6 replicates were treated with acrolein from 24 hpf to 120 hpf	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation.	genotype:akr1a1a KO\|treatment:Ctrl\|tissue:Larvae	GSM5169476	GSM5169476: Zebrafish larvae akr1a1a KO rep3; Danio rerio; RNA Seq	GSM5169476		1	Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM5169476	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500		SRP310389			V300079388_L3_HK500ZEBaopEAAORAAPEI-518_1.fq.gz V300079388_L3_HK500ZEBaopEAAORAAPEI-518_2.fq.gz	fastq fastq	4978639200.0	49786392.0	GSM5169476 r1	0:100 1:100	A:1331238273;C:1143633964;G:1152228372;T:1351538591;N:0	100	100			1331238273	1143633964	1152228372	1351538591	0	SRX10330040	SRS8449842	SRA1205863	GEO	ZMF, University Heidelberg	1	0.94616		0.1007		0.66054		0.46712		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		Germany	2021-03-12	Multi-stage	Multi-stage	Undetermined	Undetermined