metadata: run_metadata: 32 rows where experiment.library_selection = "size fractionation" and tissue_curation

32 rows where experiment.library_selection = "size fractionation" and tissue_curation_coarse = "Hematopoietic System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.title	sample.alias	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.study_ref	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
49778	49778	SRR8040485	SRX4870997	SRS3925977	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	t32lps7 miRNA seq	GSM3427264	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps7 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	GSM3427264	GSM3427264: t32lps7 miRNA seq; Danio rerio; miRNA Seq	GSM3427264		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:GSM3427264	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			2979410976.0	39202776.0	GSM3427264 r1	0:76 1:0	A:680890914;C:823795284;G:813206458;T:661494032;N:24288	76	0	680890914	823795284	813206458	661494032	24288	SRX4870997	SRS3925977	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00172	0.00036	0.99659	0.5774	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49779	49779	SRR8040484	SRX4870996	SRS3925976	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	t32lps5 miRNA seq	GSM3427263	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps5 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	GSM3427263	GSM3427263: t32lps5 miRNA seq; Danio rerio; miRNA Seq	GSM3427263		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:GSM3427263	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			3748512888.0	49322538.0	GSM3427263 r1	0:76 1:0	A:827904249;C:957754082;G:980630416;T:982193588;N:30553	76	0	827904249	957754082	980630416	982193588	30553	SRX4870996	SRS3925976	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00336	0.00087	0.99657	0.58597	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49780	49780	SRR8040483	SRX4870995	SRS3925975	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	t32lps3 miRNA seq	GSM3427262	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps3 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	GSM3427262	GSM3427262: t32lps3 miRNA seq; Danio rerio; miRNA Seq	GSM3427262		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:GSM3427262	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			738838712.0	9721562.0	GSM3427262 r1	0:76 1:0	A:153616530;C:205779426;G:206416216;T:173020629;N:5911	76	0	153616530	205779426	206416216	173020629	5911	SRX4870995	SRS3925975	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01547	0.00084	0.99614	0.65654	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49781	49781	SRR8040482	SRX4870994	SRS3925974	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	t32lps2 miRNA seq	GSM3427261	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps2 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	GSM3427261	GSM3427261: t32lps2 miRNA seq; Danio rerio; miRNA Seq	GSM3427261		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:GSM3427261	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			826032068.0	10868843.0	GSM3427261 r1	0:76 1:0	A:173874245;C:231864336;G:237091534;T:183195515;N:6438	76	0	173874245	231864336	237091534	183195515	6438	SRX4870994	SRS3925974	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00642	0.00032	0.99799	0.64507	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49782	49782	SRR8040481	SRX4870993	SRS3925973	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	t32lps1 miRNA seq	GSM3427260	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps1 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	GSM3427260	GSM3427260: t32lps1 miRNA seq; Danio rerio; miRNA Seq	GSM3427260		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:GSM3427260	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			939595752.0	12363102.0	GSM3427260 r1	0:76 1:0	A:208106865;C:264360671;G:242572550;T:224548001;N:7665	76	0	208106865	264360671	242572550	224548001	7665	SRX4870993	SRS3925973	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00675	0.00042	0.99776	0.6162	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49783	49783	SRR8040480	SRX4870992	SRS3925972	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	t32ct9 miRNA seq	GSM3427259	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32ct9 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	GSM3427259	GSM3427259: t32ct9 miRNA seq; Danio rerio; miRNA Seq	GSM3427259		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:GSM3427259	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			2182814316.0	28721241.0	GSM3427259 r1	0:76 1:0	A:538572480;C:545202669;G:589186456;T:509834541;N:18170	76	0	538572480	545202669	589186456	509834541	18170	SRX4870992	SRS3925972	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00546	0.00069	0.99466	0.54142	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49784	49784	SRR8040479	SRX4870991	SRS3925971	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	t32ct8 miRNA seq	GSM3427258	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32ct8 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	GSM3427258	GSM3427258: t32ct8 miRNA seq; Danio rerio; miRNA Seq	GSM3427258		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:GSM3427258	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			1782092536.0	23448586.0	GSM3427258 r1	0:76 1:0	A:374737718;C:453267098;G:524775360;T:429298160;N:14200	76	0	374737718	453267098	524775360	429298160	14200	SRX4870991	SRS3925971	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01211	0.00262	0.99322	0.61785	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49785	49785	SRR8040478	SRX4870990	SRS3925970	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	t32ct7 miRNA seq	GSM3427257	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32ct7 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	GSM3427257	GSM3427257: t32ct7 miRNA seq; Danio rerio; miRNA Seq	GSM3427257		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:GSM3427257	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			1276775908.0	16799683.0	GSM3427257 r1	0:76 1:0	A:293029271;C:327721470;G:322223336;T:333791186;N:10645	76	0	293029271	327721470	322223336	333791186	10645	SRX4870990	SRS3925970	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00721	0.00121	0.99691	0.60335	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49786	49786	SRR8040477	SRX4870989	SRS3925969	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	t32ct6 miRNA seq	GSM3427256	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32ct6 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	GSM3427256	GSM3427256: t32ct6 miRNA seq; Danio rerio; miRNA Seq	GSM3427256		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:GSM3427256	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			865696012.0	11390737.0	GSM3427256 r1	0:76 1:0	A:176770645;C:244509184;G:239312533;T:205096390;N:7260	76	0	176770645	244509184	239312533	205096390	7260	SRX4870989	SRS3925969	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01202	0.00047	0.99685	0.63568	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49787	49787	SRR8040476	SRX4870988	SRS3925968	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	t32ct3 miRNA seq	GSM3427255	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32ct3 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	GSM3427255	GSM3427255: t32ct3 miRNA seq; Danio rerio; miRNA Seq	GSM3427255		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:GSM3427255	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			682433716.0	8979391.0	GSM3427255 r1	0:76 1:0	A:124505314;C:191879438;G:199861760;T:166181598;N:5606	76	0	124505314	191879438	199861760	166181598	5606	SRX4870988	SRS3925968	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00115	0.00016	0.99766	0.63905	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49788	49788	SRR8040475	SRX4870987	SRS3925966	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	t28lps8 miRNA seq	GSM3427254	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28lps8 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	GSM3427254	GSM3427254: t28lps8 miRNA seq; Danio rerio; miRNA Seq	GSM3427254		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:GSM3427254	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			1616866180.0	21274555.0	GSM3427254 r1	0:76 1:0	A:318698931;C:431888920;G:467466474;T:398799027;N:12828	76	0	318698931	431888920	467466474	398799027	12828	SRX4870987	SRS3925966	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00516	0.00033	0.99805	0.60541	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49789	49789	SRR8040474	SRX4870986	SRS3926099	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	t28lps5 miRNA seq	GSM3427253	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28lps5 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	GSM3427253	GSM3427253: t28lps5 miRNA seq; Danio rerio; miRNA Seq	GSM3427253		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:GSM3427253	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			685130044.0	9014869.0	GSM3427253 r1	0:76 1:0	A:157108408;C:176642434;G:187178331;T:164195292;N:5579	76	0	157108408	176642434	187178331	164195292	5579	SRX4870986	SRS3926099	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01486	0.00126	0.99547	0.61029	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49790	49790	SRR8040473	SRX4870985	SRS3925965	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	t28lps4 miRNA seq	GSM3427252	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28lps4 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	GSM3427252	GSM3427252: t28lps4 miRNA seq; Danio rerio; miRNA Seq	GSM3427252		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:GSM3427252	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			1939474552.0	25519402.0	GSM3427252 r1	0:76 1:0	A:360469874;C:575927354;G:555750389;T:447311541;N:15394	76	0	360469874	575927354	555750389	447311541	15394	SRX4870985	SRS3925965	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00727	0.00123	0.9948	0.57604	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49791	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
49792	49792	SRR8040471	SRX4870983	SRS3925963	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	t28lps1 miRNA seq	GSM3427250	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28lps1 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	GSM3427250	GSM3427250: t28lps1 miRNA seq; Danio rerio; miRNA Seq	GSM3427250		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:GSM3427250	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			448779772.0	5904997.0	GSM3427250 r1	0:76 1:0	A:90816279;C:135297788;G:114875760;T:107786041;N:3904	76	0	90816279	135297788	114875760	107786041	3904	SRX4870983	SRS3925963	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.03409	0.00322	0.99371	0.59951	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49793	49793	SRR8040470	SRX4870982	SRS3925961	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	t28ct7 miRNA seq	GSM3427249	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28ct7 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	GSM3427249	GSM3427249: t28ct7 miRNA seq; Danio rerio; miRNA Seq	GSM3427249		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:GSM3427249	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			385887644.0	5077469.0	GSM3427249 r1	0:76 1:0	A:87709108;C:102972334;G:97802557;T:97400488;N:3157	76	0	87709108	102972334	97802557	97400488	3157	SRX4870982	SRS3925961	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.03137	0.00448	0.99354	0.64505	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49794	49794	SRR8040469	SRX4870981	SRS3925960	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	t28ct5 miRNA seq	GSM3427248	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28ct5 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	GSM3427248	GSM3427248: t28ct5 miRNA seq; Danio rerio; miRNA Seq	GSM3427248		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:GSM3427248	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			530506600.0	6980350.0	GSM3427248 r1	0:76 1:0	A:116331973;C:147098854;G:132744863;T:134326464;N:4446	76	0	116331973	147098854	132744863	134326464	4446	SRX4870981	SRS3925960	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.0176	0.0022	0.99586	0.65278	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49795	49795	SRR8040468	SRX4870980	SRS3926000	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	t28ct3 miRNA seq	GSM3427247	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28ct3 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	GSM3427247	GSM3427247: t28ct3 miRNA seq; Danio rerio; miRNA Seq	GSM3427247		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:GSM3427247	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			854083592.0	11237942.0	GSM3427247 r1	0:76 1:0	A:207803970;C:226907346;G:210770016;T:208595483;N:6777	76	0	207803970	226907346	210770016	208595483	6777	SRX4870980	SRS3926000	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00898	0.00088	0.99685	0.55397	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49796	49796	SRR8040467	SRX4870979	SRS3925959	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	t28ct2 miRNA seq	GSM3427246	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28ct2 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	GSM3427246	GSM3427246: t28ct2 miRNA seq; Danio rerio; miRNA Seq	GSM3427246		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:GSM3427246	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			1344896988.0	17696013.0	GSM3427246 r1	0:76 1:0	A:281151040;C:362525663;G:337235896;T:363973330;N:11059	76	0	281151040	362525663	337235896	363973330	11059	SRX4870979	SRS3925959	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00513	0.00084	0.99748	0.572	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49797	49797	SRR8040466	SRX4870978	SRS3925998	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	t28ct1 miRNA seq	GSM3427245	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28ct1 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	GSM3427245	GSM3427245: t28ct1 miRNA seq; Danio rerio; miRNA Seq	GSM3427245		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:GSM3427245	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			1092530324.0	14375399.0	GSM3427245 r1	0:76 1:0	A:223117238;C:311189912;G:305409606;T:252804765;N:8803	76	0	223117238	311189912	305409606	252804765	8803	SRX4870978	SRS3925998	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00305	0.00045	0.99722	0.55111	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49798	49798	SRR8040465	SRX4870977	SRS3925958	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	t24lps8 miRNA seq	GSM3427244	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24lps8 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	GSM3427244	GSM3427244: t24lps8 miRNA seq; Danio rerio; miRNA Seq	GSM3427244		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:GSM3427244	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			883122736.0	11620036.0	GSM3427244 r1	0:76 1:0	A:173839280;C:249832164;G:243138214;T:216305485;N:7593	76	0	173839280	249832164	243138214	216305485	7593	SRX4870977	SRS3925958	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00807	0.00098	0.99466	0.58038	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49799	49799	SRR8040464	SRX4870976	SRS3925957	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	t24lps6 miRNA seq	GSM3427243	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24lps6 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	GSM3427243	GSM3427243: t24lps6 miRNA seq; Danio rerio; miRNA Seq	GSM3427243		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:GSM3427243	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			940200788.0	12371063.0	GSM3427243 r1	0:76 1:0	A:202186441;C:257211490;G:262526872;T:218268364;N:7621	76	0	202186441	257211490	262526872	218268364	7621	SRX4870976	SRS3925957	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01545	0.00138	0.99573	0.63229	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49800	49800	SRR8040463	SRX4870975	SRS3925956	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	t24lps3 miRNA seq	GSM3427242	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24lps3 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	GSM3427242	GSM3427242: t24lps3 miRNA seq; Danio rerio; miRNA Seq	GSM3427242		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:GSM3427242	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			563241168.0	7411068.0	GSM3427242 r1	0:76 1:0	A:122781441;C:156393075;G:148935008;T:135126829;N:4815	76	0	122781441	156393075	148935008	135126829	4815	SRX4870975	SRS3925956	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.04539	0.00261	0.99245	0.45999	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49801	49801	SRR8040462	SRX4870974	SRS3925955	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	t24lps2 miRNA seq	GSM3427241	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24lps2 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	GSM3427241	GSM3427241: t24lps2 miRNA seq; Danio rerio; miRNA Seq	GSM3427241		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:GSM3427241	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			847700960.0	11153960.0	GSM3427241 r1	0:76 1:0	A:188114093;C:239338523;G:228371307;T:191870154;N:6883	76	0	188114093	239338523	228371307	191870154	6883	SRX4870974	SRS3925955	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.03556	0.00381	0.98959	0.60491	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49802	49802	SRR8040461	SRX4870973	SRS3925954	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	t24lps1 miRNA seq	GSM3427240	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24lps1 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	GSM3427240	GSM3427240: t24lps1 miRNA seq; Danio rerio; miRNA Seq	GSM3427240		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:GSM3427240	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			808775888.0	10641788.0	GSM3427240 r1	0:76 1:0	A:180792047;C:227912694;G:210745152;T:189319125;N:6870	76	0	180792047	227912694	210745152	189319125	6870	SRX4870973	SRS3925954	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.03455	0.00417	0.99265	0.6371	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49803	49803	SRR8040460	SRX4870972	SRS3925953	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	t24ct9 miRNA seq	GSM3427239	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24ct9 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	GSM3427239	GSM3427239: t24ct9 miRNA seq; Danio rerio; miRNA Seq	GSM3427239		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:GSM3427239	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			936832772.0	12326747.0	GSM3427239 r1	0:76 1:0	A:202919759;C:263054372;G:261102127;T:209748730;N:7784	76	0	202919759	263054372	261102127	209748730	7784	SRX4870972	SRS3925953	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00595	0.00103	0.99226	0.61297	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49804	49804	SRR8040459	SRX4870971	SRS3925952	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	t24ct8 miRNA seq	GSM3427238	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24ct8 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	GSM3427238	GSM3427238: t24ct8 miRNA seq; Danio rerio; miRNA Seq	GSM3427238		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:GSM3427238	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			877533848.0	11546498.0	GSM3427238 r1	0:76 1:0	A:179921346;C:248450344;G:244557540;T:204597462;N:7156	76	0	179921346	248450344	244557540	204597462	7156	SRX4870971	SRS3925952	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01508	0.00287	0.99231	0.54727	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49805	49805	SRR8040458	SRX4870969	SRS3925949	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	t24ct5 miRNA seq	GSM3427237	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24ct5 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	GSM3427237	GSM3427237: t24ct5 miRNA seq; Danio rerio; miRNA Seq	GSM3427237		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:GSM3427237	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			1051495872.0	13835472.0	GSM3427237 r1	0:76 1:0	A:206784217;C:298766167;G:302274285;T:243663140;N:8063	76	0	206784217	298766167	302274285	243663140	8063	SRX4870969	SRS3925949	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00753	0.00117	0.99415	0.59469	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49806	49806	SRR8040457	SRX4870968	SRS3925948	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	t24ct3 miRNA seq	GSM3427236	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24ct3 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	GSM3427236	GSM3427236: t24ct3 miRNA seq; Danio rerio; miRNA Seq	GSM3427236		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:GSM3427236	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			841297124.0	11069699.0	GSM3427236 r1	0:76 1:0	A:176905513;C:231337061;G:229078215;T:203969523;N:6812	76	0	176905513	231337061	229078215	203969523	6812	SRX4870968	SRS3925948	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.02085	0.00327	0.99586	0.60981	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49807	49807	SRR8040456	SRX4870967	SRS3926072	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	t24ct1 miRNA seq	GSM3427235	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24ct1 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	GSM3427235	GSM3427235: t24ct1 miRNA seq; Danio rerio; miRNA Seq	GSM3427235		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:GSM3427235	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP165278			821053840.0	10803340.0	GSM3427235 r1	0:76 1:0	A:176231478;C:227671335;G:218622493;T:198521972;N:6562	76	0	176231478	227671335	218622493	198521972	6562	SRX4870967	SRS3926072	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.02976	0.00433	0.99338	0.59559	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
55539	55539	SRR10532695	SRX7216660	SRS5719128	SRP233258	PRJNA591815	Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis	PRJNA591815	Other	MicroRNAs are sequentially processed by two RNAse III enzymes Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation where it becomes the most abundant miRNA. However the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.			miR 144 mutant	isolate:Lab reared\|age:2 days\|sex:not applicable\|tissue:peripheral blood\|genotype:miR 144 / \|phenotype:wild type\|treatment:n1\|BioSampleModel:Model organism or animal									Small RNA from peripheral blood from 2 dpf zebrafish embryos miR 451 mutant	sRNA Mut miR 144	sRNA Mut miR 144	Small RNA libraries were prepared from total RNA 0.5 g isolated from peripheral blood of wild type WT and miR 144 / embryos at 48 hpf Small RNAs were size selected in 10% denaturing polyacrylamide gel in 1X TBE in range from 18 to 75 bp. RNA extraction from the gel was achieved by incubation in 0.3 M NaCl overnight at 4C with following precipitation with isopropanol. Pre adenylated 3 custom adaptor WT: /5PHOS/NNCACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/; miR 144 / :/5PHOS/NNAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/ were ligated to small RNAs by T4 RNA ligase for 2 h at 22 C. post ligated products were size selected by gel from non ligated adaptor. Reverse transcription was performed by SuperScript III Reverse Transcription kit Thermo Fisher using custom RT Cloning Primer /5PHOS/NNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC SPC18 GGATCC SPC18 GTGACTGGAGTTCAGACGTGTGCTC. Then cDNA products were isolated by gel selection and then circularized by CircLigase ssDNA Ligase Epicentre. cDNA libraries were amplified in reactions containing forward and reverse Illumina index primers.			miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP233258	sRNA-miR-144.fastq.gz	fastq	284208421.0	7813754.0	sRNA miR 144.fastq.gz	0:36.37	A:63063755;C:66933795;G:92235682;T:61966771;N:8418	36		63063755	66933795	92235682	61966771	8418	SRX7216660	SRS5719128	SRA1002853	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.02041	0.00444	0.98512	0.44771	28	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	United Kingdom	2019-11-26	Hatching	Embryo	Blood	Hematopoietic System
55540	55540	SRR10532696	SRX7216659	SRS5719127	SRP233258	PRJNA591815	Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis	PRJNA591815	Other	MicroRNAs are sequentially processed by two RNAse III enzymes Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation where it becomes the most abundant miRNA. However the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.			wild type	isolate:Lab reared\|age:2 days\|sex:not applicable\|tissue:peripheral blood\|genotype:wild type\|phenotype:wild type\|treatment:n1\|BioSampleModel:Model organism or animal									Small RNA from peripheral blood from 2 dpf zebrafish embryos wild type	sRNA WT	sRNA WT	Small RNA libraries were prepared from total RNA 0.5 g isolated from peripheral blood of wild type WT and miR 144 / embryos at 48 hpf Small RNAs were size selected in 10% denaturing polyacrylamide gel in 1X TBE in range from 18 to 75 bp. RNA extraction from the gel was achieved by incubation in 0.3 M NaCl overnight at 4C with following precipitation with isopropanol. Pre adenylated 3 custom adaptor WT: /5PHOS/NNCACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/; miR 144 / :/5PHOS/NNAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/ were ligated to small RNAs by T4 RNA ligase for 2 h at 22 C. post ligated products were size selected by gel from non ligated adaptor. Reverse transcription was performed by SuperScript III Reverse Transcription kit Thermo Fisher using custom RT Cloning Primer /5PHOS/NNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC SPC18 GGATCC SPC18 GTGACTGGAGTTCAGACGTGTGCTC. Then cDNA products were isolated by gel selection and then circularized by CircLigase ssDNA Ligase Epicentre. cDNA libraries were amplified in reactions containing forward and reverse Illumina index primers.			miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP233258	sRNA-WT.fastq.gz	fastq	294275059.0	8550051.0	sRNA WT.fastq.gz	0:34.42	A:65237071;C:85092331;G:80441993;T:63494506;N:9158	34		65237071	85092331	80441993	63494506	9158	SRX7216659	SRS5719127	SRA1002853	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.00854	0.00213	0.99184	0.55467	31	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	United Kingdom	2019-11-26	Hatching	Embryo	Blood	Hematopoietic System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;