run_metadata: 69620

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
69620	SRR18959654	SRX15036813	SRS12783651	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation		pubmed:35641933		C60d 2	GSM6070548		source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	C60d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen China.	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	GSM6070548	GSM6070548: C60d 2; Danio rerio; RNA Seq	GSM6070548 r1	GSM6070548	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA ssCir DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball DNB which had more than 300 copies of one molecular DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform BGI Shenzhen China.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500		SRP372606			C60d_2_1.fq.gz C60d_2_2.fq.gz	fastq fastq	6920478600.0	46136524.0	GSM6070548 r1	0:150 1:150	A:1860288879;C:1602876302;G:1589399217;T:1867783032;N:131170	150	150			1860288879	1602876302	1589399217	1867783032	131170	SRX15036813	SRS12783651	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.95235		0.05236		0.74836		0.55427		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown		China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures