{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_strategy = \"miRNA-Seq\" and tissue_curation_coarse = \"Hematopoietic System\"", "rows": [[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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps7 miRNA seq", "GSM3427264", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 2979410976.0, 39202776.0, "GSM3427264 r1", "0:76 1:0", "A:680890914;C:823795284;G:813206458;T:661494032;N:24288", 76, 0, null, null, 680890914, 823795284, 813206458, 661494032, 24288, "SRX4870997", "SRS3925977", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00172, null, 0.00036, null, 0.99659, null, 0.5774, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps5 miRNA seq", "GSM3427263", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 3748512888.0, 49322538.0, "GSM3427263 r1", "0:76 1:0", "A:827904249;C:957754082;G:980630416;T:982193588;N:30553", 76, 0, null, null, 827904249, 957754082, 980630416, 982193588, 30553, "SRX4870996", "SRS3925976", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00336, null, 0.00087, null, 0.99657, null, 0.58597, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps3 miRNA seq", "GSM3427262", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 738838712.0, 9721562.0, "GSM3427262 r1", "0:76 1:0", "A:153616530;C:205779426;G:206416216;T:173020629;N:5911", 76, 0, null, null, 153616530, 205779426, 206416216, 173020629, 5911, "SRX4870995", "SRS3925975", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.01547, null, 0.00084, null, 0.99614, null, 0.65654, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps2 miRNA seq", "GSM3427261", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 826032068.0, 10868843.0, "GSM3427261 r1", "0:76 1:0", "A:173874245;C:231864336;G:237091534;T:183195515;N:6438", 76, 0, null, null, 173874245, 231864336, 237091534, 183195515, 6438, "SRX4870994", "SRS3925974", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00642, null, 0.00032, null, 0.99799, null, 0.64507, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps1 miRNA seq", "GSM3427260", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 939595752.0, 12363102.0, "GSM3427260 r1", "0:76 1:0", "A:208106865;C:264360671;G:242572550;T:224548001;N:7665", 76, 0, null, null, 208106865, 264360671, 242572550, 224548001, 7665, "SRX4870993", "SRS3925973", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00675, null, 0.00042, null, 0.99776, null, 0.6162, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct9 miRNA seq", "GSM3427259", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 2182814316.0, 28721241.0, "GSM3427259 r1", "0:76 1:0", "A:538572480;C:545202669;G:589186456;T:509834541;N:18170", 76, 0, null, null, 538572480, 545202669, 589186456, 509834541, 18170, "SRX4870992", "SRS3925972", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00546, null, 0.00069, null, 0.99466, null, 0.54142, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct8 miRNA seq", "GSM3427258", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 1782092536.0, 23448586.0, "GSM3427258 r1", "0:76 1:0", "A:374737718;C:453267098;G:524775360;T:429298160;N:14200", 76, 0, null, null, 374737718, 453267098, 524775360, 429298160, 14200, "SRX4870991", "SRS3925971", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.01211, null, 0.00262, null, 0.99322, null, 0.61785, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct7 miRNA seq", "GSM3427257", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 1276775908.0, 16799683.0, "GSM3427257 r1", "0:76 1:0", "A:293029271;C:327721470;G:322223336;T:333791186;N:10645", 76, 0, null, null, 293029271, 327721470, 322223336, 333791186, 10645, "SRX4870990", "SRS3925970", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00721, null, 0.00121, null, 0.99691, null, 0.60335, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct6 miRNA seq", "GSM3427256", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 865696012.0, 11390737.0, "GSM3427256 r1", "0:76 1:0", "A:176770645;C:244509184;G:239312533;T:205096390;N:7260", 76, 0, null, null, 176770645, 244509184, 239312533, 205096390, 7260, "SRX4870989", "SRS3925969", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.01202, null, 0.00047, null, 0.99685, null, 0.63568, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct3 miRNA seq", "GSM3427255", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 682433716.0, 8979391.0, "GSM3427255 r1", "0:76 1:0", "A:124505314;C:191879438;G:199861760;T:166181598;N:5606", 76, 0, null, null, 124505314, 191879438, 199861760, 166181598, 5606, "SRX4870988", "SRS3925968", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00115, null, 0.00016, null, 0.99766, null, 0.63905, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps8 miRNA seq", "GSM3427254", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 1616866180.0, 21274555.0, "GSM3427254 r1", "0:76 1:0", "A:318698931;C:431888920;G:467466474;T:398799027;N:12828", 76, 0, null, null, 318698931, 431888920, 467466474, 398799027, 12828, "SRX4870987", "SRS3925966", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00516, null, 0.00033, null, 0.99805, null, 0.60541, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps5 miRNA seq", "GSM3427253", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 685130044.0, 9014869.0, "GSM3427253 r1", "0:76 1:0", "A:157108408;C:176642434;G:187178331;T:164195292;N:5579", 76, 0, null, null, 157108408, 176642434, 187178331, 164195292, 5579, "SRX4870986", "SRS3926099", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.01486, null, 0.00126, null, 0.99547, null, 0.61029, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps4 miRNA seq", "GSM3427252", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 1939474552.0, 25519402.0, "GSM3427252 r1", "0:76 1:0", "A:360469874;C:575927354;G:555750389;T:447311541;N:15394", 76, 0, null, null, 360469874, 575927354, 555750389, 447311541, 15394, "SRX4870985", "SRS3925965", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00727, null, 0.00123, null, 0.9948, null, 0.57604, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps2 miRNA seq", "GSM3427251", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 1099817964.0, 14471289.0, "GSM3427251 r1", "0:76 1:0", "A:243156900;C:278653612;G:304671994;T:273326443;N:9015", 76, 0, null, null, 243156900, 278653612, 304671994, 273326443, 9015, "SRX4870984", "SRS3925964", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.01845, null, 0.0012, null, 0.99671, null, 0.58128, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps1 miRNA seq", "GSM3427250", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 448779772.0, 5904997.0, "GSM3427250 r1", "0:76 1:0", "A:90816279;C:135297788;G:114875760;T:107786041;N:3904", 76, 0, null, null, 90816279, 135297788, 114875760, 107786041, 3904, "SRX4870983", "SRS3925963", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.03409, null, 0.00322, null, 0.99371, null, 0.59951, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct7 miRNA seq", "GSM3427249", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 385887644.0, 5077469.0, "GSM3427249 r1", "0:76 1:0", "A:87709108;C:102972334;G:97802557;T:97400488;N:3157", 76, 0, null, null, 87709108, 102972334, 97802557, 97400488, 3157, "SRX4870982", "SRS3925961", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.03137, null, 0.00448, null, 0.99354, null, 0.64505, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct5 miRNA seq", "GSM3427248", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 530506600.0, 6980350.0, "GSM3427248 r1", "0:76 1:0", "A:116331973;C:147098854;G:132744863;T:134326464;N:4446", 76, 0, null, null, 116331973, 147098854, 132744863, 134326464, 4446, "SRX4870981", "SRS3925960", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.0176, null, 0.0022, null, 0.99586, null, 0.65278, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct3 miRNA seq", "GSM3427247", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 854083592.0, 11237942.0, "GSM3427247 r1", "0:76 1:0", "A:207803970;C:226907346;G:210770016;T:208595483;N:6777", 76, 0, null, null, 207803970, 226907346, 210770016, 208595483, 6777, "SRX4870980", "SRS3926000", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00898, null, 0.00088, null, 0.99685, null, 0.55397, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct2 miRNA seq", "GSM3427246", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 1344896988.0, 17696013.0, "GSM3427246 r1", "0:76 1:0", "A:281151040;C:362525663;G:337235896;T:363973330;N:11059", 76, 0, null, null, 281151040, 362525663, 337235896, 363973330, 11059, "SRX4870979", "SRS3925959", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00513, null, 0.00084, null, 0.99748, null, 0.572, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct1 miRNA seq", "GSM3427245", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 1092530324.0, 14375399.0, "GSM3427245 r1", "0:76 1:0", "A:223117238;C:311189912;G:305409606;T:252804765;N:8803", 76, 0, null, null, 223117238, 311189912, 305409606, 252804765, 8803, "SRX4870978", "SRS3925998", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00305, null, 0.00045, null, 0.99722, null, 0.55111, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps8 miRNA seq", "GSM3427244", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 883122736.0, 11620036.0, "GSM3427244 r1", "0:76 1:0", "A:173839280;C:249832164;G:243138214;T:216305485;N:7593", 76, 0, null, null, 173839280, 249832164, 243138214, 216305485, 7593, "SRX4870977", "SRS3925958", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00807, null, 0.00098, null, 0.99466, null, 0.58038, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps6 miRNA seq", "GSM3427243", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 940200788.0, 12371063.0, "GSM3427243 r1", "0:76 1:0", "A:202186441;C:257211490;G:262526872;T:218268364;N:7621", 76, 0, null, null, 202186441, 257211490, 262526872, 218268364, 7621, "SRX4870976", "SRS3925957", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.01545, null, 0.00138, null, 0.99573, null, 0.63229, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps3 miRNA seq", "GSM3427242", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 563241168.0, 7411068.0, "GSM3427242 r1", "0:76 1:0", "A:122781441;C:156393075;G:148935008;T:135126829;N:4815", 76, 0, null, null, 122781441, 156393075, 148935008, 135126829, 4815, "SRX4870975", "SRS3925956", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.04539, null, 0.00261, null, 0.99245, null, 0.45999, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps2 miRNA seq", "GSM3427241", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 847700960.0, 11153960.0, "GSM3427241 r1", "0:76 1:0", "A:188114093;C:239338523;G:228371307;T:191870154;N:6883", 76, 0, null, null, 188114093, 239338523, 228371307, 191870154, 6883, "SRX4870974", "SRS3925955", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.03556, null, 0.00381, null, 0.98959, null, 0.60491, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps1 miRNA seq", "GSM3427240", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 808775888.0, 10641788.0, "GSM3427240 r1", "0:76 1:0", "A:180792047;C:227912694;G:210745152;T:189319125;N:6870", 76, 0, null, null, 180792047, 227912694, 210745152, 189319125, 6870, "SRX4870973", "SRS3925954", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.03455, null, 0.00417, null, 0.99265, null, 0.6371, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct9 miRNA seq", "GSM3427239", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 936832772.0, 12326747.0, "GSM3427239 r1", "0:76 1:0", "A:202919759;C:263054372;G:261102127;T:209748730;N:7784", 76, 0, null, null, 202919759, 263054372, 261102127, 209748730, 7784, "SRX4870972", "SRS3925953", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00595, null, 0.00103, null, 0.99226, null, 0.61297, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct8 miRNA seq", "GSM3427238", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 877533848.0, 11546498.0, "GSM3427238 r1", "0:76 1:0", "A:179921346;C:248450344;G:244557540;T:204597462;N:7156", 76, 0, null, null, 179921346, 248450344, 244557540, 204597462, 7156, "SRX4870971", "SRS3925952", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.01508, null, 0.00287, null, 0.99231, null, 0.54727, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct5 miRNA seq", "GSM3427237", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 1051495872.0, 13835472.0, "GSM3427237 r1", "0:76 1:0", "A:206784217;C:298766167;G:302274285;T:243663140;N:8063", 76, 0, null, null, 206784217, 298766167, 302274285, 243663140, 8063, "SRX4870969", "SRS3925949", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.00753, null, 0.00117, null, 0.99415, null, 0.59469, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct3 miRNA seq", "GSM3427236", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 841297124.0, 11069699.0, "GSM3427236 r1", "0:76 1:0", "A:176905513;C:231337061;G:229078215;T:203969523;N:6812", 76, 0, null, null, 176905513, 231337061, 229078215, 203969523, 6812, "SRX4870968", "SRS3925948", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.02085, null, 0.00327, null, 0.99586, null, 0.60981, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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 \u00b0C and split into three temperature groups 24 \u00b0C 28 \u00b0C 32 \u00b0C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gadually changed to 28 \u00b0C and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 \u00b5l 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 \u00b0C compared to fish kept at constant 28 \u00b0C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 \u00b0C. 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 \u00b0C 28 \u00b0C 32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct1 miRNA seq", "GSM3427235", null, "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 \u03bcl 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 \u00b0C.", "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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 \u00b1 0.5 \u00b0C. 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 \u00b1 0.5 \u00b0C 28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. 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", null, "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 \u03bcl 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 \u00b0C for 30 min centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 \u03bcl 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 \u03bcl 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 \u00b0C for 2 min 1 cycle; 95 \u00b0C for 20 s 60 \u00b0C for 30 s 72 \u00b0C for 15 s 22 cycles; 72 \u00b0C 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", null, "SRP165278", null, null, null, null, 821053840.0, 10803340.0, "GSM3427235 r1", "0:76 1:0", "A:176231478;C:227671335;G:218622493;T:198521972;N:6562", 76, 0, null, null, 176231478, 227671335, 218622493, 198521972, 6562, "SRX4870967", "SRS3926072", "SRA793500", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.02976, null, 0.00433, null, 0.99338, null, 0.59559, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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.", null, null, null, null, "miR 144 mutant", null, "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", null, null, null, null, null, null, null, null, "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/N*NCACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/; miR 144 / :/5PHOS/N*NAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/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.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233258", null, null, "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, null, null, null, 63063755, 66933795, 92235682, 61966771, 8418, "SRX7216660", "SRS5719128", "SRA1002853", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.02041, null, 0.00444, null, 0.98512, null, 0.44771, null, 28, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-11-26", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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.", null, null, null, null, "wild type", null, "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", null, null, null, null, null, null, null, null, "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/N*NCACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/; miR 144 / :/5PHOS/N*NAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/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.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233258", null, null, "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, null, null, null, 65237071, 85092331, 80441993, 63494506, 9158, "SRX7216659", "SRS5719127", "SRA1002853", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.00854, null, 0.00213, null, 0.99184, null, 0.55467, null, 31, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-11-26", "Hatching", "Embryo", "Blood", "Hematopoietic System"]], "truncated": false, "filtered_table_rows_count": 32, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], 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