run_metadata: 49791

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
49791	SRR8040472	SRX4870984	SRS3925964	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914			t28lps2 miRNA seq	GSM3427251		tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28lps2 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427251	GSM3427251: t28lps2 miRNA seq; Danio rerio; miRNA Seq	GSM3427251		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427251	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278					1099817964.0	14471289.0	GSM3427251 r1	0:76 1:0	A:243156900;C:278653612;G:304671994;T:273326443;N:9015	76	0			243156900	278653612	304671994	273326443	9015	SRX4870984	SRS3925964	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01845		0.0012		0.99671		0.58128		76		B		usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown		Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System