run_metadata: 49762

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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
49762	SRR8040438	SRX4870950	SRS3925932	SRP165277	PRJNA495917	Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish	GSE121163	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. 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			t28lps1 RNA seq	GSM3427220		tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28lps1 RNA 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 mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 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	GSM3427220	GSM3427220: t28lps1 RNA seq; Danio rerio; RNA Seq	GSM3427220		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427220	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277					2219433000.0	29592440.0	GSM3427220 r1	0:75 1:0	A:559427934;C:519857518;G:513429485;T:626687457;N:30606	75	0			559427934	519857518	513429485	626687457	30606	SRX4870950	SRS3925932	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.89861		0.09731		0.76889		0.4978		75		B		usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown		Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System