{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_source = \"TRANSCRIPTOMIC\" and tissue_curation = \"Spleen\"", "rows": [[38293, "SRR1647684", "SRX756919", "SRS742121", "SRP049663", "PRJNA266803", "Spring Varaemia of Carp Virus SVCV infection of adult zebrafish", "GSE63133", "Transcriptome Analysis", "During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 \u00b5L SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.", null, "pubmed:25535281", null, "24S", "GSM1541908", null, "source name:spleen|tissue:spleen|disease state:24h post SVCV infection", "24S", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "spleen", null, "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:spleen|disease state:24h post SVCV infection", "GSM1541908", "GSM1541908: 24S; Danio rerio; RNA Seq", "GSM1541908", null, "1", "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1541908", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049663", null, null, "24S_ATGTCA_L003_R1.fastq", "fastq", 1207014756.0, 23666956.0, "GSM1541908 r1", "0:51", "A:316359100;C:290453604;G:283305513;T:316815698;N:80841", 51, null, null, null, 316359100, 290453604, 283305513, 316815698, 80841, "SRX756919", "SRS742121", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.91158, null, 0.09021, null, 0.70867, null, 0.46907, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Spleen", "Hematopoietic System"], [38294, "SRR1647683", "SRX756918", "SRS742119", "SRP049663", "PRJNA266803", "Spring Varaemia of Carp Virus SVCV infection of adult zebrafish", "GSE63133", "Transcriptome Analysis", "During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 \u00b5L SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.", null, "pubmed:25535281", null, "6S", "GSM1541907", null, "source name:spleen|tissue:spleen|disease state:6h post SVCV infection", "6S", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "spleen", null, "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:spleen|disease state:6h post SVCV infection", "GSM1541907", "GSM1541907: 6S; Danio rerio; RNA Seq", "GSM1541907", null, "1", "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1541907", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049663", null, null, "6S_AGTTCC_L003_R1.fastq", "fastq", 1251006540.0, 24529540.0, "GSM1541907 r1", "0:51", "A:323805792;C:303846999;G:297418642;T:325862442;N:72665", 51, null, null, null, 323805792, 303846999, 297418642, 325862442, 72665, "SRX756918", "SRS742119", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.92105, null, 0.09005, null, 0.71273, null, 0.46937, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Spleen", "Hematopoietic System"], [38295, "SRR1647682", "SRX756917", "SRS742118", "SRP049663", "PRJNA266803", "Spring Varaemia of Carp Virus SVCV infection of adult zebrafish", "GSE63133", "Transcriptome Analysis", "During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 \u00b5L SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.", null, "pubmed:25535281", null, "0S", "GSM1541906", null, "source name:spleen|tissue:spleen|disease state:un infected", "0S", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "spleen", null, "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:spleen|disease state:un infected", "GSM1541906", "GSM1541906: 0S; Danio rerio; RNA Seq", "GSM1541906", null, "1", "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1541906", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049663", null, null, "0S_AGTCAA_L003_R1.fastq", "fastq", 1155087372.0, 22648772.0, "GSM1541906 r1", "0:51", "A:301183546;C:279328135;G:272663981;T:301834798;N:76912", 51, null, null, null, 301183546, 279328135, 272663981, 301834798, 76912, "SRX756917", "SRS742118", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.91841, null, 0.09679, null, 0.70546, null, 0.47624, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Spleen", "Hematopoietic System"], [39974, "SRR2726604", "SRX1354695", "SRS1121101", "SRP064895", "PRJNA298967", "Danio rerio Raw sequence reads", "PRJNA298967", "Whole Genome Sequencing", "Alternative polyadenylation in the anti bacterial immune response of zebrafish", null, null, null, null, "UC.fq.gz", null, "breed:missing|cultivar:missing|ecotype:missing|isolate:missing|strain:missing|age:6 month|dev stage:adult|sex:male|tissue:spleen|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Alternative polyadenylation in the anti bacterial immune response of zebrafish", "UC", "298967", "SAPAS three prime cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>55</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP064895", null, null, "UC.fq.gz", "fastq", 908330752.0, 16220192.0, "UC", "0:56", "A:268296300;C:164753303;G:152582935;T:321764605;N:933609", 56, null, null, null, 268296300, 164753303, 152582935, 321764605, 933609, "SRX1354695", "SRS1121101", "SRA305678", "Sun Yat-Sen University|Department of Biochemistry, College of Life Scienc", "Sun Yat-Sen University", 1, 0.76113, null, 0.14836, null, 0.86764, null, 0.49191, null, 56, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-10-19", "Adult", "Adult", "Spleen", "Hematopoietic System"], [39975, "SRR2726605", "SRX1343023", "SRS1117908", "SRP064895", "PRJNA298967", "Danio rerio Raw sequence reads", "PRJNA298967", "Whole Genome Sequencing", "Alternative polyadenylation in the anti bacterial immune response of zebrafish", null, null, null, null, "BC.fq.gz", null, "breed:missing|cultivar:missing|ecotype:missing|isolate:missing|strain:missing|age:6 month|dev stage:adult|sex:male|tissue:spleen|health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Alternative polyadenylation in the anti bacterial immune response of zebrafish", "298967", "298967", "SAPAS three prime cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>55</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP064895", null, null, "BC.fq.gz", "fastq", 613456536.0, 10954581.0, "BC", "0:56", "A:184952368;C:111595938;G:99647506;T:216155456;N:1105268", 56, null, null, null, 184952368, 111595938, 99647506, 216155456, 1105268, "SRX1343023", "SRS1117908", "SRA305678", "Sun Yat-Sen University|Department of Biochemistry, College of Life Scienc", "Sun Yat-Sen University", 1, 0.74636, null, 0.11848, null, 0.84678, null, 0.47133, null, 56, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-10-24", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47583, "SRR6661157", "SRX3638253", "SRS2904504", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplWTPHZ 3", "GSM2975201", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "SplWTPHZ 3", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975201", "GSM2975201: SplWTPHZ 3; Danio rerio; RNA Seq", "GSM2975201", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975201", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplWTPHZ_3.fastq.gz", "fastq", 863137362.0, 16924262.0, "GSM2975201 r1", "0:51", "A:243029420;C:186621398;G:190769119;T:242704294;N:13131", 51, null, null, null, 243029420, 186621398, 190769119, 242704294, 13131, "SRX3638253", "SRS2904504", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.94871, null, 0.18797, null, 0.7289, null, 0.48689, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47584, "SRR6661156", "SRX3638252", "SRS2904503", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplWTPHZ 2", "GSM2975200", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "SplWTPHZ 2", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975200", "GSM2975200: SplWTPHZ 2; Danio rerio; RNA Seq", "GSM2975200", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975200", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplWTPHZ_2.fastq.gz", "fastq", 748057494.0, 14667794.0, "GSM2975200 r1", "0:51", "A:212731080;C:159238564;G:163993235;T:212082953;N:11662", 51, null, null, null, 212731080, 159238564, 163993235, 212082953, 11662, "SRX3638252", "SRS2904503", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.94641, null, 0.22364, null, 0.7264, null, 0.48998, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47585, "SRR6661155", "SRX3638251", "SRS2904502", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplWTPHZ 1", "GSM2975199", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "SplWTPHZ 1", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975199", "GSM2975199: SplWTPHZ 1; Danio rerio; RNA Seq", "GSM2975199", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975199", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplWTPHZ_1.fastq.gz", "fastq", 771862917.0, 15134567.0, "GSM2975199 r1", "0:51", "A:220317243;C:164032479;G:167543123;T:219958265;N:11807", 51, null, null, null, 220317243, 164032479, 167543123, 219958265, 11807, "SRX3638251", "SRS2904502", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.94835, null, 0.1926, null, 0.71453, null, 0.48677, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47586, "SRR6661154", "SRX3638250", "SRS2904501", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplWT 3", "GSM2975198", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "SplWT 3", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975198", "GSM2975198: SplWT 3; Danio rerio; RNA Seq", "GSM2975198", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975198", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplWT_3.fastq.gz", "fastq", 815973888.0, 15999488.0, "GSM2975198 r1", "0:51", "A:236186435;C:169473350;G:175246943;T:235055142;N:12018", 51, null, null, null, 236186435, 169473350, 175246943, 235055142, 12018, "SRX3638250", "SRS2904501", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.94554, null, 0.25855, null, 0.71873, null, 0.54675, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47587, "SRR6661153", "SRX3638249", "SRS2904499", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplWT 2", "GSM2975197", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "SplWT 2", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975197", "GSM2975197: SplWT 2; Danio rerio; RNA Seq", "GSM2975197", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975197", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplWT_2.fastq.gz", "fastq", 909644262.0, 17836162.0, "GSM2975197 r1", "0:51", "A:259661486;C:192636111;G:198048163;T:259284494;N:14008", 51, null, null, null, 259661486, 192636111, 198048163, 259284494, 14008, "SRX3638249", "SRS2904499", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.94781, null, 0.22979, null, 0.69962, null, 0.49839, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47588, "SRR6661152", "SRX3638248", "SRS2904500", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplWT 1", "GSM2975196", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "SplWT 1", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975196", "GSM2975196: SplWT 1; Danio rerio; RNA Seq", "GSM2975196", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975196", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplWT_1.fastq.gz", "fastq", 888755274.0, 17426574.0, "GSM2975196 r1", "0:51", "A:241072815;C:200347978;G:205733626;T:241587449;N:13406", 51, null, null, null, 241072815, 200347978, 205733626, 241587449, 13406, "SRX3638248", "SRS2904500", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.95759, null, 0.1342, null, 0.72918, null, 0.52233, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47589, "SRR6661151", "SRX3638247", "SRS2904498", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplDKOPHZ 3", "GSM2975195", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "SplDKOPHZ 3", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975195", "GSM2975195: SplDKOPHZ 3; Danio rerio; RNA Seq", "GSM2975195", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975195", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplDKOPHZ_3.fastq.gz", "fastq", 881441160.0, 17283160.0, "GSM2975195 r1", "0:51", "A:243254581;C:194198200;G:199055092;T:244919975;N:13312", 51, null, null, null, 243254581, 194198200, 199055092, 244919975, 13312, "SRX3638247", "SRS2904498", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.90441, null, 0.14881, null, 0.71447, null, 0.51129, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47590, "SRR6661150", "SRX3638246", "SRS2904497", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplDKOPHZ 2", "GSM2975194", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "SplDKOPHZ 2", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975194", "GSM2975194: SplDKOPHZ 2; Danio rerio; RNA Seq", "GSM2975194", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975194", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplDKOPHZ_2.fastq.gz", "fastq", 795840414.0, 15604714.0, "GSM2975194 r1", "0:51", "A:229921467;C:166126021;G:170186584;T:229594266;N:12076", 51, null, null, null, 229921467, 166126021, 170186584, 229594266, 12076, "SRX3638246", "SRS2904497", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.88657, null, 0.23556, null, 0.7194, null, 0.51207, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47591, "SRR6661149", "SRX3638245", "SRS2904495", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplDKOPHZ 1", "GSM2975193", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "SplDKOPHZ 1", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975193", "GSM2975193: SplDKOPHZ 1; Danio rerio; RNA Seq", "GSM2975193", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975193", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplDKOPHZ_1.fastq.gz", "fastq", 788951436.0, 15469636.0, "GSM2975193 r1", "0:51", "A:217408862;C:175236911;G:178930271;T:217363444;N:11948", 51, null, null, null, 217408862, 175236911, 178930271, 217363444, 11948, "SRX3638245", "SRS2904495", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.90945, null, 0.10065, null, 0.72468, null, 0.48596, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47592, "SRR6661148", "SRX3638244", "SRS2904496", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplDKO 3", "GSM2975192", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "SplDKO 3", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975192", "GSM2975192: SplDKO 3; Danio rerio; RNA Seq", "GSM2975192", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975192", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplDKO_3.fastq.gz", "fastq", 732609543.0, 14364893.0, "GSM2975192 r1", "0:51", "A:209020386;C:154988652;G:160405898;T:208183578;N:11029", 51, null, null, null, 209020386, 154988652, 160405898, 208183578, 11029, "SRX3638244", "SRS2904496", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.88228, null, 0.23609, null, 0.72529, null, 0.50392, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47593, "SRR6661147", "SRX3638243", "SRS2904493", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplDKO 2", "GSM2975191", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "SplDKO 2", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975191", "GSM2975191: SplDKO 2; Danio rerio; RNA Seq", "GSM2975191", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975191", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplDKO_2.fastq.gz", "fastq", 747985635.0, 14666385.0, "GSM2975191 r1", "0:51", "A:209892939;C:160527969;G:165683955;T:211869190;N:11582", 51, null, null, null, 209892939, 160527969, 165683955, 211869190, 11582, "SRX3638243", "SRS2904493", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.90267, null, 0.20054, null, 0.7249, null, 0.53668, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47594, "SRR6661146", "SRX3638242", "SRS2904494", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplDKO 1", "GSM2975190", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "SplDKO 1", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975190", "GSM2975190: SplDKO 1; Danio rerio; RNA Seq", "GSM2975190", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975190", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplDKO_1.fastq.gz", "fastq", 724574391.0, 14207341.0, "GSM2975190 r1", "0:51", "A:207549130;C:151913145;G:156789401;T:208311727;N:10988", 51, null, null, null, 207549130, 151913145, 156789401, 208311727, 10988, "SRX3638242", "SRS2904494", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.89742, null, 0.2275, null, 0.71547, null, 0.5072, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49748, "SRR8040452", "SRX4870965", "SRS3925946", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps5 RNA seq", "GSM3427234", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32lps5 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427234", "GSM3427234: t32lps5 RNA seq; Danio rerio; RNA Seq", "GSM3427234", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427234", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2525095950.0, 33667946.0, "GSM3427234 r1", "0:75 1:0", "A:654325529;C:574214700;G:560979222;T:735543925;N:32574", 75, 0, null, null, 654325529, 574214700, 560979222, 735543925, 32574, "SRX4870965", "SRS3925946", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.94279, null, 0.11158, null, 0.7739, null, 0.56131, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49749, "SRR8040451", "SRX4870964", "SRS3925945", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps4 RNA seq", "GSM3427233", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32lps4 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427233", "GSM3427233: t32lps4 RNA seq; Danio rerio; RNA Seq", "GSM3427233", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427233", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2324475900.0, 30993012.0, "GSM3427233 r1", "0:75 1:0", "A:593299460;C:533734154;G:526980483;T:670430972;N:30831", 75, 0, null, null, 593299460, 533734154, 526980483, 670430972, 30831, "SRX4870964", "SRS3925945", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.9455, null, 0.10812, null, 0.78046, null, 0.55958, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49750, "SRR8040450", "SRX4870962", "SRS3925943", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps3 RNA seq", "GSM3427232", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32lps3 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427232", "GSM3427232: t32lps3 RNA seq; Danio rerio; RNA Seq", "GSM3427232", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427232", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2390945250.0, 31879270.0, "GSM3427232 r1", "0:75 1:0", "A:620617289;C:546536575;G:538087155;T:685671110;N:33121", 75, 0, null, null, 620617289, 546536575, 538087155, 685671110, 33121, "SRX4870962", "SRS3925943", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.94216, null, 0.12594, null, 0.74925, null, 0.54113, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49751, "SRR8040449", "SRX4870961", "SRS3925942", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps2 RNA seq", "GSM3427231", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32lps2 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427231", "GSM3427231: t32lps2 RNA seq; Danio rerio; RNA Seq", "GSM3427231", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427231", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2372211900.0, 31629492.0, "GSM3427231 r1", "0:75 1:0", "A:609244327;C:553579722;G:546387461;T:662968297;N:32093", 75, 0, null, null, 609244327, 553579722, 546387461, 662968297, 32093, "SRX4870961", "SRS3925942", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.91064, null, 0.09975, null, 0.7318, null, 0.52325, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49752, "SRR8040448", "SRX4870960", "SRS3925941", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps1 RNA seq", "GSM3427230", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32lps1 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427230", "GSM3427230: t32lps1 RNA seq; Danio rerio; RNA Seq", "GSM3427230", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427230", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2601300000.0, 34684000.0, "GSM3427230 r1", "0:75 1:0", "A:696279292;C:582818011;G:571718581;T:750447755;N:36361", 75, 0, null, null, 696279292, 582818011, 571718581, 750447755, 36361, "SRX4870960", "SRS3925941", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.93957, null, 0.13624, null, 0.74641, null, 0.53521, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49753, "SRR8040447", "SRX4870959", "SRS3925940", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct10 RNA seq", "GSM3427229", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32ct10 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427229", "GSM3427229: t32ct10 RNA seq; Danio rerio; RNA Seq", "GSM3427229", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427229", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2206367925.0, 29418239.0, "GSM3427229 r1", "0:75 1:0", "A:564695219;C:513292663;G:507293808;T:621057423;N:28812", 75, 0, null, null, 564695219, 513292663, 507293808, 621057423, 28812, "SRX4870959", "SRS3925940", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.94594, null, 0.10744, null, 0.75511, null, 0.39959, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49754, "SRR8040446", "SRX4870958", "SRS3925939", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct8 RNA seq", "GSM3427228", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32ct8 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427228", "GSM3427228: t32ct8 RNA seq; Danio rerio; RNA Seq", "GSM3427228", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427228", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2160654900.0, 28808732.0, "GSM3427228 r1", "0:75 1:0", "A:560268124;C:491395956;G:494788088;T:614174312;N:28420", 75, 0, null, null, 560268124, 491395956, 494788088, 614174312, 28420, "SRX4870958", "SRS3925939", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.91437, null, 0.1131, null, 0.74661, null, 0.54441, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49755, "SRR8040445", "SRX4870957", "SRS3925938", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct6 RNA seq", "GSM3427227", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32ct6 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427227", "GSM3427227: t32ct6 RNA seq; Danio rerio; RNA Seq", "GSM3427227", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427227", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2175448725.0, 29005983.0, "GSM3427227 r1", "0:75 1:0", "A:588911336;C:487829921;G:471925092;T:626753522;N:28854", 75, 0, null, null, 588911336, 487829921, 471925092, 626753522, 28854, "SRX4870957", "SRS3925938", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.93789, null, 0.14514, null, 0.73839, null, 0.51589, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49756, "SRR8040444", "SRX4870956", "SRS3925937", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct3 RNA seq", "GSM3427226", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32ct3 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427226", "GSM3427226: t32ct3 RNA seq; Danio rerio; RNA Seq", "GSM3427226", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427226", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2350450425.0, 31339339.0, "GSM3427226 r1", "0:75 1:0", "A:612558543;C:533417342;G:511898107;T:692543546;N:32887", 75, 0, null, null, 612558543, 533417342, 511898107, 692543546, 32887, "SRX4870956", "SRS3925937", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.88939, null, 0.13696, null, 0.74649, null, 0.5071, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49757, "SRR8040443", "SRX4870955", "SRS3925936", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct2 RNA seq", "GSM3427225", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32ct2 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427225", "GSM3427225: t32ct2 RNA seq; Danio rerio; RNA Seq", "GSM3427225", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427225", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2500728150.0, 33343042.0, "GSM3427225 r1", "0:75 1:0", "A:663109698;C:565815864;G:564300306;T:707468578;N:33704", 75, 0, null, null, 663109698, 565815864, 564300306, 707468578, 33704, "SRX4870955", "SRS3925936", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.92821, null, 0.27272, null, 0.71969, null, 0.48781, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49758, "SRR8040442", "SRX4870954", "SRS3925988", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps8 RNA seq", "GSM3427224", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28lps8 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427224", "GSM3427224: t28lps8 RNA seq; Danio rerio; RNA Seq", "GSM3427224", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427224", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2342903700.0, 31238716.0, "GSM3427224 r1", "0:75 1:0", "A:613986696;C:535703169;G:527411229;T:665771221;N:31385", 75, 0, null, null, 613986696, 535703169, 527411229, 665771221, 31385, "SRX4870954", "SRS3925988", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.92238, null, 0.11108, null, 0.75223, null, 0.54609, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49759, "SRR8040441", "SRX4870953", "SRS3925935", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps4 RNA seq", "GSM3427223", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28lps4 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427223", "GSM3427223: t28lps4 RNA seq; Danio rerio; RNA Seq", "GSM3427223", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427223", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2009201550.0, 26789354.0, "GSM3427223 r1", "0:75 1:0", "A:503118595;C:466998217;G:461838042;T:577221133;N:25563", 75, 0, null, null, 503118595, 466998217, 461838042, 577221133, 25563, "SRX4870953", "SRS3925935", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.85044, null, 0.10362, null, 0.78149, null, 0.59209, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49760, "SRR8040440", "SRX4870952", "SRS3925934", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps3 RNA seq", "GSM3427222", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28lps3 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427222", "GSM3427222: t28lps3 RNA seq; Danio rerio; RNA Seq", "GSM3427222", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427222", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2262918375.0, 30172245.0, "GSM3427222 r1", "0:75 1:0", "A:557712391;C:559312209;G:525961809;T:619902191;N:29775", 75, 0, null, null, 557712391, 559312209, 525961809, 619902191, 29775, "SRX4870952", "SRS3925934", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.75792, null, 0.0861, null, 0.77977, null, 0.47016, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49761, "SRR8040439", "SRX4870951", "SRS3925933", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps2 RNA seq", "GSM3427221", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28lps2 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427221", "GSM3427221: t28lps2 RNA seq; Danio rerio; RNA Seq", "GSM3427221", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427221", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2362744425.0, 31503259.0, "GSM3427221 r1", "0:75 1:0", "A:605359081;C:550864600;G:543725417;T:662762619;N:32708", 75, 0, null, null, 605359081, 550864600, 543725417, 662762619, 32708, "SRX4870951", "SRS3925933", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.92027, null, 0.10164, null, 0.7403, null, 0.52342, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49762, "SRR8040438", "SRX4870950", "SRS3925932", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps1 RNA seq", "GSM3427220", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28lps1 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427220", "GSM3427220: t28lps1 RNA seq; Danio rerio; RNA Seq", "GSM3427220", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427220", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2219433000.0, 29592440.0, "GSM3427220 r1", "0:75 1:0", "A:559427934;C:519857518;G:513429485;T:626687457;N:30606", 75, 0, null, null, 559427934, 519857518, 513429485, 626687457, 30606, "SRX4870950", "SRS3925932", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.89861, null, 0.09731, null, 0.76889, null, 0.4978, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49763, "SRR8040437", "SRX4870949", "SRS3925931", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct7 RNA seq", "GSM3427219", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28ct7 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427219", "GSM3427219: t28ct7 RNA seq; Danio rerio; RNA Seq", "GSM3427219", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427219", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2329584075.0, 31061121.0, "GSM3427219 r1", "0:75 1:0", "A:624440550;C:517755267;G:499439713;T:687917841;N:30704", 75, 0, null, null, 624440550, 517755267, 499439713, 687917841, 30704, "SRX4870949", "SRS3925931", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.88755, null, 0.13982, null, 0.75739, null, 0.56552, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49764, "SRR8040436", "SRX4870948", "SRS3925930", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct5 RNA seq", "GSM3427218", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28ct5 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427218", "GSM3427218: t28ct5 RNA seq; Danio rerio; RNA Seq", "GSM3427218", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427218", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2116347225.0, 28217963.0, "GSM3427218 r1", "0:75 1:0", "A:549735276;C:488049942;G:477129323;T:601405177;N:27507", 75, 0, null, null, 549735276, 488049942, 477129323, 601405177, 27507, "SRX4870948", "SRS3925930", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.94198, null, 0.11445, null, 0.75487, null, 0.53068, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49765, "SRR8040435", "SRX4870947", "SRS3925929", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct3 RNA seq", "GSM3427217", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28ct3 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427217", "GSM3427217: t28ct3 RNA seq; Danio rerio; RNA Seq", "GSM3427217", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427217", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2689388775.0, 35858517.0, "GSM3427217 r1", "0:75 1:0", "A:723021338;C:600600385;G:595495733;T:770233672;N:37647", 75, 0, null, null, 723021338, 600600385, 595495733, 770233672, 37647, "SRX4870947", "SRS3925929", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.9433, null, 0.12005, null, 0.75175, null, 0.52805, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49766, "SRR8040434", "SRX4870946", "SRS3925927", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct2 RNA seq", "GSM3427216", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28ct2 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427216", "GSM3427216: t28ct2 RNA seq; Danio rerio; RNA Seq", "GSM3427216", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427216", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2358123450.0, 31441646.0, "GSM3427216 r1", "0:75 1:0", "A:608599109;C:548957677;G:537939593;T:662594226;N:32845", 75, 0, null, null, 608599109, 548957677, 537939593, 662594226, 32845, "SRX4870946", "SRS3925927", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.93343, null, 0.09904, null, 0.73701, null, 0.50221, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49767, "SRR8040433", "SRX4870945", "SRS3925928", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct1 RNA seq", "GSM3427215", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28ct1 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427215", "GSM3427215: t28ct1 RNA seq; Danio rerio; RNA Seq", "GSM3427215", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427215", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2340413625.0, 31205515.0, "GSM3427215 r1", "0:75 1:0", "A:601455783;C:547481954;G:534319560;T:657124045;N:32283", 75, 0, null, null, 601455783, 547481954, 534319560, 657124045, 32283, "SRX4870945", "SRS3925928", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.91963, null, 0.11224, null, 0.7363, null, 0.52602, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49768, "SRR8040432", "SRX4870944", "SRS3925926", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps8 RNA seq", "GSM3427214", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24lps8 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427214", "GSM3427214: t24lps8 RNA seq; Danio rerio; RNA Seq", "GSM3427214", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427214", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 1914339900.0, 25524532.0, "GSM3427214 r1", "0:75 1:0", "A:512209644;C:432894621;G:420067370;T:549142945;N:25320", 75, 0, null, null, 512209644, 432894621, 420067370, 549142945, 25320, "SRX4870944", "SRS3925926", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.92034, null, 0.12782, null, 0.73777, null, 0.53097, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49769, "SRR8040431", "SRX4870943", "SRS3925925", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps4 RNA seq", "GSM3427213", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24lps4 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427213", "GSM3427213: t24lps4 RNA seq; Danio rerio; RNA Seq", "GSM3427213", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427213", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2137202850.0, 28496038.0, "GSM3427213 r1", "0:75 1:0", "A:542475947;C:498947754;G:490366774;T:605383850;N:28525", 75, 0, null, null, 542475947, 498947754, 490366774, 605383850, 28525, "SRX4870943", "SRS3925925", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.91347, null, 0.09882, null, 0.75763, null, 0.46833, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49770, "SRR8040430", "SRX4870942", "SRS3925924", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps3 RNA seq", "GSM3427212", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24lps3 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427212", "GSM3427212: t24lps3 RNA seq; Danio rerio; RNA Seq", "GSM3427212", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427212", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2514206700.0, 33522756.0, "GSM3427212 r1", "0:75 1:0", "A:663829025;C:573707517;G:558298485;T:718336661;N:35012", 75, 0, null, null, 663829025, 573707517, 558298485, 718336661, 35012, "SRX4870942", "SRS3925924", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.93997, null, 0.11968, null, 0.74241, null, 0.53459, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49771, "SRR8040429", "SRX4870941", "SRS3925923", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps2 RNA seq", "GSM3427211", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24lps2 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427211", "GSM3427211: t24lps2 RNA seq; Danio rerio; RNA Seq", "GSM3427211", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427211", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2502607650.0, 33368102.0, "GSM3427211 r1", "0:75 1:0", "A:659207653;C:572452612;G:556598074;T:714314698;N:34613", 75, 0, null, null, 659207653, 572452612, 556598074, 714314698, 34613, "SRX4870941", "SRS3925923", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.92032, null, 0.12899, null, 0.7441, null, 0.52707, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49772, "SRR8040428", "SRX4870940", "SRS3925921", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps1 RNA seq", "GSM3427210", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24lps1 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427210", "GSM3427210: t24lps1 RNA seq; Danio rerio; RNA Seq", "GSM3427210", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427210", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2301013650.0, 30680182.0, "GSM3427210 r1", "0:75 1:0", "A:600014931;C:531214958;G:529006695;T:640746698;N:30368", 75, 0, null, null, 600014931, 531214958, 529006695, 640746698, 30368, "SRX4870940", "SRS3925921", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.94819, null, 0.10959, null, 0.74706, null, 0.44871, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49773, "SRR8040427", "SRX4870939", "SRS3925922", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct8 RNA seq", "GSM3427209", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24ct8 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427209", "GSM3427209: t24ct8 RNA seq; Danio rerio; RNA Seq", "GSM3427209", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427209", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2196418725.0, 29285583.0, "GSM3427209 r1", "0:75 1:0", "A:573278624;C:504375268;G:494497295;T:624238861;N:28677", 75, 0, null, null, 573278624, 504375268, 494497295, 624238861, 28677, "SRX4870939", "SRS3925922", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.94225, null, 0.11903, null, 0.75051, null, 0.55244, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49774, "SRR8040426", "SRX4870938", "SRS3925919", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct5 RNA seq", "GSM3427208", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24ct5 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427208", "GSM3427208: t24ct5 RNA seq; Danio rerio; RNA Seq", "GSM3427208", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427208", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2267199975.0, 30229333.0, "GSM3427208 r1", "0:75 1:0", "A:584789099;C:523482900;G:517770578;T:641127463;N:29935", 75, 0, null, null, 584789099, 523482900, 517770578, 641127463, 29935, "SRX4870938", "SRS3925919", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.88505, null, 0.11534, null, 0.74566, null, 0.55279, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49775, "SRR8040425", "SRX4870937", "SRS3925920", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct4 RNA seq", "GSM3427207", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24ct4 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427207", "GSM3427207: t24ct4 RNA seq; Danio rerio; RNA Seq", "GSM3427207", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427207", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2127502425.0, 28366699.0, "GSM3427207 r1", "0:75 1:0", "A:543019165;C:503067510;G:498801425;T:582586507;N:27818", 75, 0, null, null, 543019165, 503067510, 498801425, 582586507, 27818, "SRX4870937", "SRS3925920", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.9223, null, 0.07915, null, 0.72401, null, 0.51588, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49776, "SRR8040424", "SRX4870936", "SRS3925917", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct3 RNA seq", "GSM3427206", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24ct3 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427206", "GSM3427206: t24ct3 RNA seq; Danio rerio; RNA Seq", "GSM3427206", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427206", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2708072025.0, 36107627.0, "GSM3427206 r1", "0:75 1:0", "A:672991238;C:642923577;G:634295347;T:757824608;N:37255", 75, 0, null, null, 672991238, 642923577, 634295347, 757824608, 37255, "SRX4870936", "SRS3925917", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.95238, null, 0.09, null, 0.75513, null, 0.52869, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49777, "SRR8040423", "SRX4870935", "SRS3925918", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 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 extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct2 RNA seq", "GSM3427205", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24ct2 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \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 modifications. 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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \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", "GSM3427205", "GSM3427205: t24ct2 RNA seq; Danio rerio; RNA Seq", "GSM3427205", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \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 mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427205", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2495119875.0, 33268265.0, "GSM3427205 r1", "0:75 1:0", "A:627918584;C:589525055;G:590001770;T:687639074;N:35392", 75, 0, null, null, 627918584, 589525055, 590001770, 687639074, 35392, "SRX4870935", "SRS3925918", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.95519, null, 0.08888, null, 0.74746, null, 0.44744, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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"], [63895, "SRR14213371", "SRX10579916", "SRS8684384", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Spleen3", "GSM5237140", null, "source name:zebrafish spleen|genotype:wild type|tissue:spleen|strain:TLAB", "Spleen3", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish spleen", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:spleen|strain:TLAB", "GSM5237140", "GSM5237140: Spleen3; Danio rerio; RNA Seq", "GSM5237140", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237140", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Spleen3.fastq", "fastq", 2469245600.0, 24692456.0, "GSM5237140 r1", "0:100", "A:595265067;C:649103304;G:625399353;T:599383209;N:94667", 100, null, null, null, 595265067, 649103304, 625399353, 599383209, 94667, "SRX10579916", "SRS8684384", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.9388, null, 0.16508, null, 0.75205, null, 0.59719, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [63896, "SRR14213370", "SRX10579915", "SRS8684383", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Spleen2", "GSM5237139", null, "source name:zebrafish spleen|genotype:wild type|tissue:spleen|strain:TLAB", "Spleen2", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish spleen", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:spleen|strain:TLAB", "GSM5237139", "GSM5237139: Spleen2; Danio rerio; RNA Seq", "GSM5237139", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237139", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Spleen2.fastq", "fastq", 1372663100.0, 13726631.0, "GSM5237139 r1", "0:100", "A:303080845;C:392345861;G:369765807;T:307418421;N:52166", 100, null, null, null, 303080845, 392345861, 369765807, 307418421, 52166, "SRX10579915", "SRS8684383", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96541, null, 0.18478, null, 0.78565, null, 0.60522, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"], [63897, "SRR14213369", "SRX10579914", "SRS8684382", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Spleen1", "GSM5237138", null, "source name:zebrafish spleen|genotype:wild type|tissue:spleen|strain:TLAB", "Spleen1", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish spleen", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:spleen|strain:TLAB", "GSM5237138", "GSM5237138: Spleen1; Danio rerio; RNA Seq", "GSM5237138", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237138", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Spleen1.fastq", "fastq", 2268815600.0, 22688156.0, "GSM5237138 r1", "0:100", "A:570901318;C:562128594;G:552921437;T:582778510;N:85741", 100, null, null, null, 570901318, 562128594, 552921437, 582778510, 85741, "SRX10579914", "SRS8684382", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.93633, null, 0.14981, null, 0.72825, null, 0.52073, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Spleen", "Hematopoietic System"]], "truncated": false, "filtered_table_rows_count": 80, "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], [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 from run_metadata where \"experiment.library_layout\" = :p0 and \"experiment.library_source\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "TRANSCRIPTOMIC", "p2": "Spleen"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 50, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen&experiment.library_strategy=miRNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 80, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Spleen", "selected": true}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen", "results": [{"value": "cDNA", "label": "cDNA", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen&experiment.library_selection=cDNA", "selected": false}, {"value": "size fractionation", "label": "size fractionation", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen&experiment.library_selection=size+fractionation", "selected": false}, {"value": "PCR", "label": "PCR", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen&experiment.library_selection=PCR", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 80, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 80, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen", "results": [{"value": "Adult", "label": "Adult", "count": 77, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen&devstage_curation_coarse=Adult", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 3, "toggle_url": 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"http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen&devstage_curation=Undetermined", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen", "results": [{"value": "Hematopoietic System", "label": "Hematopoietic System", "count": 80, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen&tissue_curation_coarse=Hematopoietic+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen", "results": [{"value": "Spleen", "label": "Spleen", "count": 80, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen", "results": [{"value": "unknown", "label": "unknown", "count": 80, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Spleen&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, 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