metadata: run_metadata: 80 rows where experiment.library_layout = "SINGLE" and tissue

80 rows where experiment.library_layout = "SINGLE" and tissue_curation = "Spleen"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
38293	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 µL 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.		pubmed:25535281	24S	GSM1541908	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		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		tissue:spleen\|disease state:24h post SVCV infection	GSM1541908	GSM1541908: 24S; Danio rerio; RNA Seq	GSM1541908		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		SRP049663	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		316359100	290453604	283305513	316815698	80841	SRX756919	SRS742121	SRA200717	GEO	Institute of Hydrobiology, Chinese Academy of Sciences	1	0.91158	0.09021	0.70867	0.46907	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	China	2014-11-10	Undetermined	Adult	Spleen	Hematopoietic System
38294	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 µL 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.		pubmed:25535281	6S	GSM1541907	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		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		tissue:spleen\|disease state:6h post SVCV infection	GSM1541907	GSM1541907: 6S; Danio rerio; RNA Seq	GSM1541907		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		SRP049663	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		323805792	303846999	297418642	325862442	72665	SRX756918	SRS742119	SRA200717	GEO	Institute of Hydrobiology, Chinese Academy of Sciences	1	0.92105	0.09005	0.71273	0.46937	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	China	2014-11-10	Undetermined	Adult	Spleen	Hematopoietic System
38295	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 µL 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.		pubmed:25535281	0S	GSM1541906	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		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		tissue:spleen\|disease state:un infected	GSM1541906	GSM1541906: 0S; Danio rerio; RNA Seq	GSM1541906		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		SRP049663	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		301183546	279328135	272663981	301834798	76912	SRX756917	SRS742118	SRA200717	GEO	Institute of Hydrobiology, Chinese Academy of Sciences	1	0.91841	0.09679	0.70546	0.47624	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	China	2014-11-10	Undetermined	Adult	Spleen	Hematopoietic System
39974	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				UC.fq.gz	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									Alternative polyadenylation in the anti bacterial immune response of zebrafish	UC	298967	SAPAS three prime cDNA library			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	UC.fq.gz	fastq	908330752.0	16220192.0	UC	0:56	A:268296300;C:164753303;G:152582935;T:321764605;N:933609	56		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	0.14836	0.86764	0.49191	56	B	usable mapping rate	illumina	early_illumina	unknown	random_priming	unknown	bulk	unknown	unknown	China	2015-10-19	Adult	Adult	Spleen	Hematopoietic System
39975	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				BC.fq.gz	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									Alternative polyadenylation in the anti bacterial immune response of zebrafish	298967	298967	SAPAS three prime cDNA library			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	BC.fq.gz	fastq	613456536.0	10954581.0	BC	0:56	A:184952368;C:111595938;G:99647506;T:216155456;N:1105268	56		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	0.11848	0.84678	0.47133	56	B	usable mapping rate	illumina	early_illumina	unknown	random_priming	unknown	bulk	unknown	unknown	China	2015-10-24	Adult	Adult	Spleen	Hematopoietic System
47583	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 Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü 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.		pubmed:30248094	SplWTPHZ 3	GSM2975201	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 µg/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		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		SRP131956	SplWTPHZ_3.fastq.gz	fastq	863137362.0	16924262.0	GSM2975201 r1	0:51	A:243029420;C:186621398;G:190769119;T:242704294;N:13131	51		243029420	186621398	190769119	242704294	13131	SRX3638253	SRS2904504	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.94871	0.18797	0.7289	0.48689	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47584	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 Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü 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.		pubmed:30248094	SplWTPHZ 2	GSM2975200	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 µg/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		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		SRP131956	SplWTPHZ_2.fastq.gz	fastq	748057494.0	14667794.0	GSM2975200 r1	0:51	A:212731080;C:159238564;G:163993235;T:212082953;N:11662	51		212731080	159238564	163993235	212082953	11662	SRX3638252	SRS2904503	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.94641	0.22364	0.7264	0.48998	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47585	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 Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü 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.		pubmed:30248094	SplWTPHZ 1	GSM2975199	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 µg/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		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		SRP131956	SplWTPHZ_1.fastq.gz	fastq	771862917.0	15134567.0	GSM2975199 r1	0:51	A:220317243;C:164032479;G:167543123;T:219958265;N:11807	51		220317243	164032479	167543123	219958265	11807	SRX3638251	SRS2904502	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.94835	0.1926	0.71453	0.48677	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47586	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 Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü 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.		pubmed:30248094	SplWT 3	GSM2975198	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 µg/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		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		SRP131956	SplWT_3.fastq.gz	fastq	815973888.0	15999488.0	GSM2975198 r1	0:51	A:236186435;C:169473350;G:175246943;T:235055142;N:12018	51		236186435	169473350	175246943	235055142	12018	SRX3638250	SRS2904501	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.94554	0.25855	0.71873	0.54675	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47587	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 Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü 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.		pubmed:30248094	SplWT 2	GSM2975197	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 µg/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		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		SRP131956	SplWT_2.fastq.gz	fastq	909644262.0	17836162.0	GSM2975197 r1	0:51	A:259661486;C:192636111;G:198048163;T:259284494;N:14008	51		259661486	192636111	198048163	259284494	14008	SRX3638249	SRS2904499	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.94781	0.22979	0.69962	0.49839	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47588	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 Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü 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.		pubmed:30248094	SplWT 1	GSM2975196	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 µg/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		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		SRP131956	SplWT_1.fastq.gz	fastq	888755274.0	17426574.0	GSM2975196 r1	0:51	A:241072815;C:200347978;G:205733626;T:241587449;N:13406	51		241072815	200347978	205733626	241587449	13406	SRX3638248	SRS2904500	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.95759	0.1342	0.72918	0.52233	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47589	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 Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü 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.		pubmed:30248094	SplDKOPHZ 3	GSM2975195	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 µg/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		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		SRP131956	SplDKOPHZ_3.fastq.gz	fastq	881441160.0	17283160.0	GSM2975195 r1	0:51	A:243254581;C:194198200;G:199055092;T:244919975;N:13312	51		243254581	194198200	199055092	244919975	13312	SRX3638247	SRS2904498	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.90441	0.14881	0.71447	0.51129	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47590	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 Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü 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.		pubmed:30248094	SplDKOPHZ 2	GSM2975194	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 µg/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		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		SRP131956	SplDKOPHZ_2.fastq.gz	fastq	795840414.0	15604714.0	GSM2975194 r1	0:51	A:229921467;C:166126021;G:170186584;T:229594266;N:12076	51		229921467	166126021	170186584	229594266	12076	SRX3638246	SRS2904497	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.88657	0.23556	0.7194	0.51207	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47591	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 Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü 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.		pubmed:30248094	SplDKOPHZ 1	GSM2975193	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 µg/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		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		SRP131956	SplDKOPHZ_1.fastq.gz	fastq	788951436.0	15469636.0	GSM2975193 r1	0:51	A:217408862;C:175236911;G:178930271;T:217363444;N:11948	51		217408862	175236911	178930271	217363444	11948	SRX3638245	SRS2904495	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.90945	0.10065	0.72468	0.48596	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47592	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 Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü 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.		pubmed:30248094	SplDKO 3	GSM2975192	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 µg/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		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		SRP131956	SplDKO_3.fastq.gz	fastq	732609543.0	14364893.0	GSM2975192 r1	0:51	A:209020386;C:154988652;G:160405898;T:208183578;N:11029	51		209020386	154988652	160405898	208183578	11029	SRX3638244	SRS2904496	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.88228	0.23609	0.72529	0.50392	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47593	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 Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü 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.		pubmed:30248094	SplDKO 2	GSM2975191	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 µg/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		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		SRP131956	SplDKO_2.fastq.gz	fastq	747985635.0	14666385.0	GSM2975191 r1	0:51	A:209892939;C:160527969;G:165683955;T:211869190;N:11582	51		209892939	160527969	165683955	211869190	11582	SRX3638243	SRS2904493	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.90267	0.20054	0.7249	0.53668	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47594	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 Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü 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.		pubmed:30248094	SplDKO 1	GSM2975190	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 µg/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		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		SRP131956	SplDKO_1.fastq.gz	fastq	724574391.0	14207341.0	GSM2975190 r1	0:51	A:207549130;C:151913145;G:156789401;T:208311727;N:10988	51		207549130	151913145	156789401	208311727	10988	SRX3638242	SRS2904494	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.89742	0.2275	0.71547	0.5072	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
49748	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32lps5 RNA seq	GSM3427234	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427234	GSM3427234: t32lps5 RNA seq; Danio rerio; RNA Seq	GSM3427234		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427234	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2525095950.0	33667946.0	GSM3427234 r1	0:75 1:0	A:654325529;C:574214700;G:560979222;T:735543925;N:32574	75	0	654325529	574214700	560979222	735543925	32574	SRX4870965	SRS3925946	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.94279	0.11158	0.7739	0.56131	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49749	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32lps4 RNA seq	GSM3427233	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427233	GSM3427233: t32lps4 RNA seq; Danio rerio; RNA Seq	GSM3427233		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427233	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2324475900.0	30993012.0	GSM3427233 r1	0:75 1:0	A:593299460;C:533734154;G:526980483;T:670430972;N:30831	75	0	593299460	533734154	526980483	670430972	30831	SRX4870964	SRS3925945	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.9455	0.10812	0.78046	0.55958	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49750	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32lps3 RNA seq	GSM3427232	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427232	GSM3427232: t32lps3 RNA seq; Danio rerio; RNA Seq	GSM3427232		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427232	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2390945250.0	31879270.0	GSM3427232 r1	0:75 1:0	A:620617289;C:546536575;G:538087155;T:685671110;N:33121	75	0	620617289	546536575	538087155	685671110	33121	SRX4870962	SRS3925943	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.94216	0.12594	0.74925	0.54113	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49751	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32lps2 RNA seq	GSM3427231	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427231	GSM3427231: t32lps2 RNA seq; Danio rerio; RNA Seq	GSM3427231		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427231	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2372211900.0	31629492.0	GSM3427231 r1	0:75 1:0	A:609244327;C:553579722;G:546387461;T:662968297;N:32093	75	0	609244327	553579722	546387461	662968297	32093	SRX4870961	SRS3925942	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.91064	0.09975	0.7318	0.52325	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49752	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32lps1 RNA seq	GSM3427230	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427230	GSM3427230: t32lps1 RNA seq; Danio rerio; RNA Seq	GSM3427230		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427230	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2601300000.0	34684000.0	GSM3427230 r1	0:75 1:0	A:696279292;C:582818011;G:571718581;T:750447755;N:36361	75	0	696279292	582818011	571718581	750447755	36361	SRX4870960	SRS3925941	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.93957	0.13624	0.74641	0.53521	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49753	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32ct10 RNA seq	GSM3427229	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427229	GSM3427229: t32ct10 RNA seq; Danio rerio; RNA Seq	GSM3427229		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427229	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2206367925.0	29418239.0	GSM3427229 r1	0:75 1:0	A:564695219;C:513292663;G:507293808;T:621057423;N:28812	75	0	564695219	513292663	507293808	621057423	28812	SRX4870959	SRS3925940	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.94594	0.10744	0.75511	0.39959	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49754	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32ct8 RNA seq	GSM3427228	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427228	GSM3427228: t32ct8 RNA seq; Danio rerio; RNA Seq	GSM3427228		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427228	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2160654900.0	28808732.0	GSM3427228 r1	0:75 1:0	A:560268124;C:491395956;G:494788088;T:614174312;N:28420	75	0	560268124	491395956	494788088	614174312	28420	SRX4870958	SRS3925939	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.91437	0.1131	0.74661	0.54441	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49755	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32ct6 RNA seq	GSM3427227	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427227	GSM3427227: t32ct6 RNA seq; Danio rerio; RNA Seq	GSM3427227		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427227	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2175448725.0	29005983.0	GSM3427227 r1	0:75 1:0	A:588911336;C:487829921;G:471925092;T:626753522;N:28854	75	0	588911336	487829921	471925092	626753522	28854	SRX4870957	SRS3925938	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.93789	0.14514	0.73839	0.51589	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49756	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32ct3 RNA seq	GSM3427226	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427226	GSM3427226: t32ct3 RNA seq; Danio rerio; RNA Seq	GSM3427226		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427226	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2350450425.0	31339339.0	GSM3427226 r1	0:75 1:0	A:612558543;C:533417342;G:511898107;T:692543546;N:32887	75	0	612558543	533417342	511898107	692543546	32887	SRX4870956	SRS3925937	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.88939	0.13696	0.74649	0.5071	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49757	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32ct2 RNA seq	GSM3427225	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427225	GSM3427225: t32ct2 RNA seq; Danio rerio; RNA Seq	GSM3427225		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427225	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2500728150.0	33343042.0	GSM3427225 r1	0:75 1:0	A:663109698;C:565815864;G:564300306;T:707468578;N:33704	75	0	663109698	565815864	564300306	707468578	33704	SRX4870955	SRS3925936	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.92821	0.27272	0.71969	0.48781	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49758	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28lps8 RNA seq	GSM3427224	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427224	GSM3427224: t28lps8 RNA seq; Danio rerio; RNA Seq	GSM3427224		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427224	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2342903700.0	31238716.0	GSM3427224 r1	0:75 1:0	A:613986696;C:535703169;G:527411229;T:665771221;N:31385	75	0	613986696	535703169	527411229	665771221	31385	SRX4870954	SRS3925988	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.92238	0.11108	0.75223	0.54609	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49759	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28lps4 RNA seq	GSM3427223	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427223	GSM3427223: t28lps4 RNA seq; Danio rerio; RNA Seq	GSM3427223		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427223	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2009201550.0	26789354.0	GSM3427223 r1	0:75 1:0	A:503118595;C:466998217;G:461838042;T:577221133;N:25563	75	0	503118595	466998217	461838042	577221133	25563	SRX4870953	SRS3925935	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.85044	0.10362	0.78149	0.59209	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49760	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28lps3 RNA seq	GSM3427222	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427222	GSM3427222: t28lps3 RNA seq; Danio rerio; RNA Seq	GSM3427222		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427222	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2262918375.0	30172245.0	GSM3427222 r1	0:75 1:0	A:557712391;C:559312209;G:525961809;T:619902191;N:29775	75	0	557712391	559312209	525961809	619902191	29775	SRX4870952	SRS3925934	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.75792	0.0861	0.77977	0.47016	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49761	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28lps2 RNA seq	GSM3427221	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427221	GSM3427221: t28lps2 RNA seq; Danio rerio; RNA Seq	GSM3427221		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427221	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2362744425.0	31503259.0	GSM3427221 r1	0:75 1:0	A:605359081;C:550864600;G:543725417;T:662762619;N:32708	75	0	605359081	550864600	543725417	662762619	32708	SRX4870951	SRS3925933	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.92027	0.10164	0.7403	0.52342	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49762	49762	SRR8040438	SRX4870950	SRS3925932	SRP165277	PRJNA495917	Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish	GSE121163	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28lps1 RNA seq	GSM3427220	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28lps1 RNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427220	GSM3427220: t28lps1 RNA seq; Danio rerio; RNA Seq	GSM3427220		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427220	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2219433000.0	29592440.0	GSM3427220 r1	0:75 1:0	A:559427934;C:519857518;G:513429485;T:626687457;N:30606	75	0	559427934	519857518	513429485	626687457	30606	SRX4870950	SRS3925932	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.89861	0.09731	0.76889	0.4978	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49763	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28ct7 RNA seq	GSM3427219	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427219	GSM3427219: t28ct7 RNA seq; Danio rerio; RNA Seq	GSM3427219		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427219	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2329584075.0	31061121.0	GSM3427219 r1	0:75 1:0	A:624440550;C:517755267;G:499439713;T:687917841;N:30704	75	0	624440550	517755267	499439713	687917841	30704	SRX4870949	SRS3925931	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.88755	0.13982	0.75739	0.56552	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49764	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28ct5 RNA seq	GSM3427218	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427218	GSM3427218: t28ct5 RNA seq; Danio rerio; RNA Seq	GSM3427218		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427218	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2116347225.0	28217963.0	GSM3427218 r1	0:75 1:0	A:549735276;C:488049942;G:477129323;T:601405177;N:27507	75	0	549735276	488049942	477129323	601405177	27507	SRX4870948	SRS3925930	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.94198	0.11445	0.75487	0.53068	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49765	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28ct3 RNA seq	GSM3427217	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427217	GSM3427217: t28ct3 RNA seq; Danio rerio; RNA Seq	GSM3427217		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427217	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2689388775.0	35858517.0	GSM3427217 r1	0:75 1:0	A:723021338;C:600600385;G:595495733;T:770233672;N:37647	75	0	723021338	600600385	595495733	770233672	37647	SRX4870947	SRS3925929	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.9433	0.12005	0.75175	0.52805	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49766	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28ct2 RNA seq	GSM3427216	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427216	GSM3427216: t28ct2 RNA seq; Danio rerio; RNA Seq	GSM3427216		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427216	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2358123450.0	31441646.0	GSM3427216 r1	0:75 1:0	A:608599109;C:548957677;G:537939593;T:662594226;N:32845	75	0	608599109	548957677	537939593	662594226	32845	SRX4870946	SRS3925927	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.93343	0.09904	0.73701	0.50221	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49767	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28ct1 RNA seq	GSM3427215	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427215	GSM3427215: t28ct1 RNA seq; Danio rerio; RNA Seq	GSM3427215		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427215	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2340413625.0	31205515.0	GSM3427215 r1	0:75 1:0	A:601455783;C:547481954;G:534319560;T:657124045;N:32283	75	0	601455783	547481954	534319560	657124045	32283	SRX4870945	SRS3925928	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.91963	0.11224	0.7363	0.52602	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49768	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24lps8 RNA seq	GSM3427214	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427214	GSM3427214: t24lps8 RNA seq; Danio rerio; RNA Seq	GSM3427214		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427214	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			1914339900.0	25524532.0	GSM3427214 r1	0:75 1:0	A:512209644;C:432894621;G:420067370;T:549142945;N:25320	75	0	512209644	432894621	420067370	549142945	25320	SRX4870944	SRS3925926	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.92034	0.12782	0.73777	0.53097	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49769	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24lps4 RNA seq	GSM3427213	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427213	GSM3427213: t24lps4 RNA seq; Danio rerio; RNA Seq	GSM3427213		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427213	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2137202850.0	28496038.0	GSM3427213 r1	0:75 1:0	A:542475947;C:498947754;G:490366774;T:605383850;N:28525	75	0	542475947	498947754	490366774	605383850	28525	SRX4870943	SRS3925925	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.91347	0.09882	0.75763	0.46833	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49770	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24lps3 RNA seq	GSM3427212	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427212	GSM3427212: t24lps3 RNA seq; Danio rerio; RNA Seq	GSM3427212		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427212	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2514206700.0	33522756.0	GSM3427212 r1	0:75 1:0	A:663829025;C:573707517;G:558298485;T:718336661;N:35012	75	0	663829025	573707517	558298485	718336661	35012	SRX4870942	SRS3925924	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.93997	0.11968	0.74241	0.53459	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49771	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24lps2 RNA seq	GSM3427211	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427211	GSM3427211: t24lps2 RNA seq; Danio rerio; RNA Seq	GSM3427211		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427211	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2502607650.0	33368102.0	GSM3427211 r1	0:75 1:0	A:659207653;C:572452612;G:556598074;T:714314698;N:34613	75	0	659207653	572452612	556598074	714314698	34613	SRX4870941	SRS3925923	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.92032	0.12899	0.7441	0.52707	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49772	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24lps1 RNA seq	GSM3427210	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427210	GSM3427210: t24lps1 RNA seq; Danio rerio; RNA Seq	GSM3427210		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427210	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2301013650.0	30680182.0	GSM3427210 r1	0:75 1:0	A:600014931;C:531214958;G:529006695;T:640746698;N:30368	75	0	600014931	531214958	529006695	640746698	30368	SRX4870940	SRS3925921	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.94819	0.10959	0.74706	0.44871	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49773	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24ct8 RNA seq	GSM3427209	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427209	GSM3427209: t24ct8 RNA seq; Danio rerio; RNA Seq	GSM3427209		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427209	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2196418725.0	29285583.0	GSM3427209 r1	0:75 1:0	A:573278624;C:504375268;G:494497295;T:624238861;N:28677	75	0	573278624	504375268	494497295	624238861	28677	SRX4870939	SRS3925922	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.94225	0.11903	0.75051	0.55244	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49774	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24ct5 RNA seq	GSM3427208	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427208	GSM3427208: t24ct5 RNA seq; Danio rerio; RNA Seq	GSM3427208		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427208	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2267199975.0	30229333.0	GSM3427208 r1	0:75 1:0	A:584789099;C:523482900;G:517770578;T:641127463;N:29935	75	0	584789099	523482900	517770578	641127463	29935	SRX4870938	SRS3925919	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.88505	0.11534	0.74566	0.55279	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49775	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24ct4 RNA seq	GSM3427207	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427207	GSM3427207: t24ct4 RNA seq; Danio rerio; RNA Seq	GSM3427207		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427207	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2127502425.0	28366699.0	GSM3427207 r1	0:75 1:0	A:543019165;C:503067510;G:498801425;T:582586507;N:27818	75	0	543019165	503067510	498801425	582586507	27818	SRX4870937	SRS3925920	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.9223	0.07915	0.72401	0.51588	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49776	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24ct3 RNA seq	GSM3427206	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427206	GSM3427206: t24ct3 RNA seq; Danio rerio; RNA Seq	GSM3427206		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427206	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2708072025.0	36107627.0	GSM3427206 r1	0:75 1:0	A:672991238;C:642923577;G:634295347;T:757824608;N:37255	75	0	672991238	642923577	634295347	757824608	37255	SRX4870936	SRS3925917	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.95238	0.09	0.75513	0.52869	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49777	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 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 \|fold change\| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24ct2 RNA seq	GSM3427205	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 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427205	GSM3427205: t24ct2 RNA seq; Danio rerio; RNA Seq	GSM3427205		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427205	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP165277			2495119875.0	33268265.0	GSM3427205 r1	0:75 1:0	A:627918584;C:589525055;G:590001770;T:687639074;N:35392	75	0	627918584	589525055	590001770	687639074	35392	SRX4870935	SRS3925918	SRA793499	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.95519	0.08888	0.74746	0.44744	75	B	usable mapping rate	illumina	nextseq	5prime	poly_a	nebnext	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49778	49778	SRR8040485	SRX4870997	SRS3925977	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32lps7 miRNA seq	GSM3427264	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps7 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427264	GSM3427264: t32lps7 miRNA seq; Danio rerio; miRNA Seq	GSM3427264		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427264	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			2979410976.0	39202776.0	GSM3427264 r1	0:76 1:0	A:680890914;C:823795284;G:813206458;T:661494032;N:24288	76	0	680890914	823795284	813206458	661494032	24288	SRX4870997	SRS3925977	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00172	0.00036	0.99659	0.5774	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49779	49779	SRR8040484	SRX4870996	SRS3925976	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32lps5 miRNA seq	GSM3427263	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps5 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427263	GSM3427263: t32lps5 miRNA seq; Danio rerio; miRNA Seq	GSM3427263		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427263	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			3748512888.0	49322538.0	GSM3427263 r1	0:76 1:0	A:827904249;C:957754082;G:980630416;T:982193588;N:30553	76	0	827904249	957754082	980630416	982193588	30553	SRX4870996	SRS3925976	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00336	0.00087	0.99657	0.58597	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49780	49780	SRR8040483	SRX4870995	SRS3925975	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32lps3 miRNA seq	GSM3427262	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps3 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427262	GSM3427262: t32lps3 miRNA seq; Danio rerio; miRNA Seq	GSM3427262		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427262	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			738838712.0	9721562.0	GSM3427262 r1	0:76 1:0	A:153616530;C:205779426;G:206416216;T:173020629;N:5911	76	0	153616530	205779426	206416216	173020629	5911	SRX4870995	SRS3925975	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01547	0.00084	0.99614	0.65654	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49781	49781	SRR8040482	SRX4870994	SRS3925974	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32lps2 miRNA seq	GSM3427261	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps2 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427261	GSM3427261: t32lps2 miRNA seq; Danio rerio; miRNA Seq	GSM3427261		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427261	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			826032068.0	10868843.0	GSM3427261 r1	0:76 1:0	A:173874245;C:231864336;G:237091534;T:183195515;N:6438	76	0	173874245	231864336	237091534	183195515	6438	SRX4870994	SRS3925974	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00642	0.00032	0.99799	0.64507	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49782	49782	SRR8040481	SRX4870993	SRS3925973	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32lps1 miRNA seq	GSM3427260	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32lps1 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427260	GSM3427260: t32lps1 miRNA seq; Danio rerio; miRNA Seq	GSM3427260		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427260	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			939595752.0	12363102.0	GSM3427260 r1	0:76 1:0	A:208106865;C:264360671;G:242572550;T:224548001;N:7665	76	0	208106865	264360671	242572550	224548001	7665	SRX4870993	SRS3925973	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00675	0.00042	0.99776	0.6162	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49783	49783	SRR8040480	SRX4870992	SRS3925972	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32ct9 miRNA seq	GSM3427259	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32ct9 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427259	GSM3427259: t32ct9 miRNA seq; Danio rerio; miRNA Seq	GSM3427259		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427259	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			2182814316.0	28721241.0	GSM3427259 r1	0:76 1:0	A:538572480;C:545202669;G:589186456;T:509834541;N:18170	76	0	538572480	545202669	589186456	509834541	18170	SRX4870992	SRS3925972	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00546	0.00069	0.99466	0.54142	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49784	49784	SRR8040479	SRX4870991	SRS3925971	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32ct8 miRNA seq	GSM3427258	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32ct8 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427258	GSM3427258: t32ct8 miRNA seq; Danio rerio; miRNA Seq	GSM3427258		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427258	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			1782092536.0	23448586.0	GSM3427258 r1	0:76 1:0	A:374737718;C:453267098;G:524775360;T:429298160;N:14200	76	0	374737718	453267098	524775360	429298160	14200	SRX4870991	SRS3925971	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01211	0.00262	0.99322	0.61785	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49785	49785	SRR8040478	SRX4870990	SRS3925970	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32ct7 miRNA seq	GSM3427257	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32ct7 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427257	GSM3427257: t32ct7 miRNA seq; Danio rerio; miRNA Seq	GSM3427257		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427257	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			1276775908.0	16799683.0	GSM3427257 r1	0:76 1:0	A:293029271;C:327721470;G:322223336;T:333791186;N:10645	76	0	293029271	327721470	322223336	333791186	10645	SRX4870990	SRS3925970	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00721	0.00121	0.99691	0.60335	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49786	49786	SRR8040477	SRX4870989	SRS3925969	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32ct6 miRNA seq	GSM3427256	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32ct6 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427256	GSM3427256: t32ct6 miRNA seq; Danio rerio; miRNA Seq	GSM3427256		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427256	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			865696012.0	11390737.0	GSM3427256 r1	0:76 1:0	A:176770645;C:244509184;G:239312533;T:205096390;N:7260	76	0	176770645	244509184	239312533	205096390	7260	SRX4870989	SRS3925969	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01202	0.00047	0.99685	0.63568	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49787	49787	SRR8040476	SRX4870988	SRS3925968	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t32ct3 miRNA seq	GSM3427255	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t32ct3 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427255	GSM3427255: t32ct3 miRNA seq; Danio rerio; miRNA Seq	GSM3427255		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427255	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			682433716.0	8979391.0	GSM3427255 r1	0:76 1:0	A:124505314;C:191879438;G:199861760;T:166181598;N:5606	76	0	124505314	191879438	199861760	166181598	5606	SRX4870988	SRS3925968	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00115	0.00016	0.99766	0.63905	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49788	49788	SRR8040475	SRX4870987	SRS3925966	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28lps8 miRNA seq	GSM3427254	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28lps8 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427254	GSM3427254: t28lps8 miRNA seq; Danio rerio; miRNA Seq	GSM3427254		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427254	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			1616866180.0	21274555.0	GSM3427254 r1	0:76 1:0	A:318698931;C:431888920;G:467466474;T:398799027;N:12828	76	0	318698931	431888920	467466474	398799027	12828	SRX4870987	SRS3925966	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00516	0.00033	0.99805	0.60541	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49789	49789	SRR8040474	SRX4870986	SRS3926099	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28lps5 miRNA seq	GSM3427253	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28lps5 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427253	GSM3427253: t28lps5 miRNA seq; Danio rerio; miRNA Seq	GSM3427253		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427253	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			685130044.0	9014869.0	GSM3427253 r1	0:76 1:0	A:157108408;C:176642434;G:187178331;T:164195292;N:5579	76	0	157108408	176642434	187178331	164195292	5579	SRX4870986	SRS3926099	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01486	0.00126	0.99547	0.61029	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49790	49790	SRR8040473	SRX4870985	SRS3925965	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28lps4 miRNA seq	GSM3427252	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28lps4 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427252	GSM3427252: t28lps4 miRNA seq; Danio rerio; miRNA Seq	GSM3427252		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427252	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			1939474552.0	25519402.0	GSM3427252 r1	0:76 1:0	A:360469874;C:575927354;G:555750389;T:447311541;N:15394	76	0	360469874	575927354	555750389	447311541	15394	SRX4870985	SRS3925965	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00727	0.00123	0.9948	0.57604	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49791	49791	SRR8040472	SRX4870984	SRS3925964	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28lps2 miRNA seq	GSM3427251	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28lps2 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427251	GSM3427251: t28lps2 miRNA seq; Danio rerio; miRNA Seq	GSM3427251		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427251	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			1099817964.0	14471289.0	GSM3427251 r1	0:76 1:0	A:243156900;C:278653612;G:304671994;T:273326443;N:9015	76	0	243156900	278653612	304671994	273326443	9015	SRX4870984	SRS3925964	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01845	0.0012	0.99671	0.58128	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49792	49792	SRR8040471	SRX4870983	SRS3925963	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28lps1 miRNA seq	GSM3427250	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28lps1 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427250	GSM3427250: t28lps1 miRNA seq; Danio rerio; miRNA Seq	GSM3427250		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427250	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			448779772.0	5904997.0	GSM3427250 r1	0:76 1:0	A:90816279;C:135297788;G:114875760;T:107786041;N:3904	76	0	90816279	135297788	114875760	107786041	3904	SRX4870983	SRS3925963	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.03409	0.00322	0.99371	0.59951	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49793	49793	SRR8040470	SRX4870982	SRS3925961	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28ct7 miRNA seq	GSM3427249	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28ct7 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427249	GSM3427249: t28ct7 miRNA seq; Danio rerio; miRNA Seq	GSM3427249		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427249	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			385887644.0	5077469.0	GSM3427249 r1	0:76 1:0	A:87709108;C:102972334;G:97802557;T:97400488;N:3157	76	0	87709108	102972334	97802557	97400488	3157	SRX4870982	SRS3925961	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.03137	0.00448	0.99354	0.64505	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49794	49794	SRR8040469	SRX4870981	SRS3925960	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28ct5 miRNA seq	GSM3427248	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28ct5 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427248	GSM3427248: t28ct5 miRNA seq; Danio rerio; miRNA Seq	GSM3427248		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427248	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			530506600.0	6980350.0	GSM3427248 r1	0:76 1:0	A:116331973;C:147098854;G:132744863;T:134326464;N:4446	76	0	116331973	147098854	132744863	134326464	4446	SRX4870981	SRS3925960	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.0176	0.0022	0.99586	0.65278	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49795	49795	SRR8040468	SRX4870980	SRS3926000	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28ct3 miRNA seq	GSM3427247	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28ct3 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427247	GSM3427247: t28ct3 miRNA seq; Danio rerio; miRNA Seq	GSM3427247		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427247	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			854083592.0	11237942.0	GSM3427247 r1	0:76 1:0	A:207803970;C:226907346;G:210770016;T:208595483;N:6777	76	0	207803970	226907346	210770016	208595483	6777	SRX4870980	SRS3926000	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00898	0.00088	0.99685	0.55397	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49796	49796	SRR8040467	SRX4870979	SRS3925959	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28ct2 miRNA seq	GSM3427246	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28ct2 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427246	GSM3427246: t28ct2 miRNA seq; Danio rerio; miRNA Seq	GSM3427246		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427246	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			1344896988.0	17696013.0	GSM3427246 r1	0:76 1:0	A:281151040;C:362525663;G:337235896;T:363973330;N:11059	76	0	281151040	362525663	337235896	363973330	11059	SRX4870979	SRS3925959	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00513	0.00084	0.99748	0.572	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49797	49797	SRR8040466	SRX4870978	SRS3925998	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t28ct1 miRNA seq	GSM3427245	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t28ct1 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427245	GSM3427245: t28ct1 miRNA seq; Danio rerio; miRNA Seq	GSM3427245		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427245	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			1092530324.0	14375399.0	GSM3427245 r1	0:76 1:0	A:223117238;C:311189912;G:305409606;T:252804765;N:8803	76	0	223117238	311189912	305409606	252804765	8803	SRX4870978	SRS3925998	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00305	0.00045	0.99722	0.55111	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49798	49798	SRR8040465	SRX4870977	SRS3925958	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24lps8 miRNA seq	GSM3427244	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24lps8 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427244	GSM3427244: t24lps8 miRNA seq; Danio rerio; miRNA Seq	GSM3427244		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427244	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			883122736.0	11620036.0	GSM3427244 r1	0:76 1:0	A:173839280;C:249832164;G:243138214;T:216305485;N:7593	76	0	173839280	249832164	243138214	216305485	7593	SRX4870977	SRS3925958	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00807	0.00098	0.99466	0.58038	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49799	49799	SRR8040464	SRX4870976	SRS3925957	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24lps6 miRNA seq	GSM3427243	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24lps6 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427243	GSM3427243: t24lps6 miRNA seq; Danio rerio; miRNA Seq	GSM3427243		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427243	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			940200788.0	12371063.0	GSM3427243 r1	0:76 1:0	A:202186441;C:257211490;G:262526872;T:218268364;N:7621	76	0	202186441	257211490	262526872	218268364	7621	SRX4870976	SRS3925957	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01545	0.00138	0.99573	0.63229	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49800	49800	SRR8040463	SRX4870975	SRS3925956	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24lps3 miRNA seq	GSM3427242	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24lps3 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427242	GSM3427242: t24lps3 miRNA seq; Danio rerio; miRNA Seq	GSM3427242		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427242	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			563241168.0	7411068.0	GSM3427242 r1	0:76 1:0	A:122781441;C:156393075;G:148935008;T:135126829;N:4815	76	0	122781441	156393075	148935008	135126829	4815	SRX4870975	SRS3925956	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.04539	0.00261	0.99245	0.45999	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49801	49801	SRR8040462	SRX4870974	SRS3925955	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24lps2 miRNA seq	GSM3427241	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24lps2 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427241	GSM3427241: t24lps2 miRNA seq; Danio rerio; miRNA Seq	GSM3427241		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427241	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			847700960.0	11153960.0	GSM3427241 r1	0:76 1:0	A:188114093;C:239338523;G:228371307;T:191870154;N:6883	76	0	188114093	239338523	228371307	191870154	6883	SRX4870974	SRS3925955	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.03556	0.00381	0.98959	0.60491	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49802	49802	SRR8040461	SRX4870973	SRS3925954	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24lps1 miRNA seq	GSM3427240	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24lps1 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427240	GSM3427240: t24lps1 miRNA seq; Danio rerio; miRNA Seq	GSM3427240		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427240	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			808775888.0	10641788.0	GSM3427240 r1	0:76 1:0	A:180792047;C:227912694;G:210745152;T:189319125;N:6870	76	0	180792047	227912694	210745152	189319125	6870	SRX4870973	SRS3925954	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.03455	0.00417	0.99265	0.6371	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49803	49803	SRR8040460	SRX4870972	SRS3925953	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24ct9 miRNA seq	GSM3427239	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24ct9 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427239	GSM3427239: t24ct9 miRNA seq; Danio rerio; miRNA Seq	GSM3427239		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427239	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			936832772.0	12326747.0	GSM3427239 r1	0:76 1:0	A:202919759;C:263054372;G:261102127;T:209748730;N:7784	76	0	202919759	263054372	261102127	209748730	7784	SRX4870972	SRS3925953	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00595	0.00103	0.99226	0.61297	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49804	49804	SRR8040459	SRX4870971	SRS3925952	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24ct8 miRNA seq	GSM3427238	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24ct8 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427238	GSM3427238: t24ct8 miRNA seq; Danio rerio; miRNA Seq	GSM3427238		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427238	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			877533848.0	11546498.0	GSM3427238 r1	0:76 1:0	A:179921346;C:248450344;G:244557540;T:204597462;N:7156	76	0	179921346	248450344	244557540	204597462	7156	SRX4870971	SRS3925952	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.01508	0.00287	0.99231	0.54727	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49805	49805	SRR8040458	SRX4870969	SRS3925949	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24ct5 miRNA seq	GSM3427237	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24ct5 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427237	GSM3427237: t24ct5 miRNA seq; Danio rerio; miRNA Seq	GSM3427237		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427237	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			1051495872.0	13835472.0	GSM3427237 r1	0:76 1:0	A:206784217;C:298766167;G:302274285;T:243663140;N:8063	76	0	206784217	298766167	302274285	243663140	8063	SRX4870969	SRS3925949	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.00753	0.00117	0.99415	0.59469	76	T	under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49806	49806	SRR8040457	SRX4870968	SRS3925948	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24ct3 miRNA seq	GSM3427236	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24ct3 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427236	GSM3427236: t24ct3 miRNA seq; Danio rerio; miRNA Seq	GSM3427236		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427236	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			841297124.0	11069699.0	GSM3427236 r1	0:76 1:0	A:176905513;C:231337061;G:229078215;T:203969523;N:6812	76	0	176905513	231337061	229078215	203969523	6812	SRX4870968	SRS3925948	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.02085	0.00327	0.99586	0.60981	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
49807	49807	SRR8040456	SRX4870967	SRS3926072	SRP165278	PRJNA495918	Embryonic incubation temperature has a long term effect on the microRNA transcriptome of adult zebrafish	GSE121164	Transcriptome Analysis	Zebrafish eggs were collected at 28 °C and split into three temperature groups 24 °C 28 °C 32 °C for incubation. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gadually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf seven replicates from each group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another seven replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was isolated. Five LPS treated replicates and five controls were used for building small RNA libraries and sequencing. A total of 112 novel miRNAs were identified using miRDeep2. By comparing fish from different embryonic incubation tmeperatures 32 miRNAs 29 up /3 down regulated were identified differentially expressed DEmiRs adjusted p value < 0.05 \|fold change\| > 2.0 DESeq2 in fish from embryonic incubation temperature of 32 °C compared to fish kept at constant 28 °C 3 DEmiRs 2 up /1 down regulated were identified in response to LPS in fish kept at 28 °C. A total of 9 116 target genes were predicted using miRanda v3.3a including 8 224 genes targeted by 32 DE miRNAs and 892 genes targeted by 3 DE miRNAs. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C.	parent bioproject:PRJNA495914		t24ct1 miRNA seq	GSM3427235	tissue:spleen\|strain:AB\|developmental stage:adult\|age:100 dpf	t24ct1 miRNA seq	Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were sequentially mapped to the mature miRNA of zebrafish another 15 teleost species Astatotilapia burtoni Cyprinus carpio Electrophorus electricus Fugu rubripes Gadus morhua Hippoglossus hippoglossus Ictalurus punctatus Metrizclima zebra Neolamprologus brichardi Oryzias latipes Oreochromis niloticus Pundamilia nyererei Paralichthys olivaceus Salmo salar Tetraodon nigroviridis and three model species Drosophila melanogaster Mus musculus Homo sapiens in miRBase Release 22. Other non coding RNAs tRNA rRNA snRNA snoRNA were filterred out and remaining reads were used for identifying novel miRNAs by miRDeep2. All mapped reads were combined and subjected to DESeq2 v1.11.1 for differential miRNA expression analysis Target genes of DEmiRs were predicted by miRanda v3.3a Genome build: miRBase release 22 Supplementary files format and content: tab delimited matrix containing read counts of each library	spleen	Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C.	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.	strain:AB\|developmental stage:adult\|age:100 dpf	GSM3427235	GSM3427235: t24ct1 miRNA seq; Danio rerio; miRNA Seq	GSM3427235		1	Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some changes. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the manual of NEXTflex Small RNA Seq Kit v3 Bioo Scientific USA. Fifty ng of total RNAs from each replicate were ligated with three prime 4N and five prime 4N adenylated adapters sequentially and reverse transcribed into first strand complement DNAs cDNAs. Using universal and barcoded primers the cNDAs were amplified on a thermal cycler with the program of: 95 °C for 2 min 1 cycle; 95 °C for 20 s 60 °C for 30 s 72 °C for 15 s 22 cycles; 72 °C for 2 min 1 cycle. The size selection 150 bp was based on a 10% TBE PAGE gel. The quality and concentration of miRNA libraries were determined using the High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA.	GEO Accession:GSM3427235	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500		SRP165278			821053840.0	10803340.0	GSM3427235 r1	0:76 1:0	A:176231478;C:227671335;G:218622493;T:198521972;N:6562	76	0	176231478	227671335	218622493	198521972	6562	SRX4870967	SRS3926072	SRA793500	GEO	Faculty of Biosciences and Aquaculture, Nord University	1	0.02976	0.00433	0.99338	0.59559	76	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Norway	2018-10-12	Adult	Adult	Spleen	Hematopoietic System
63895	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.		pubmed:34556579	Spleen3	GSM5237140	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		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°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|tissue:spleen\|strain:TLAB	GSM5237140	GSM5237140: Spleen3; Danio rerio; RNA Seq	GSM5237140		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		SRP314470	Spleen3.fastq	fastq	2469245600.0	24692456.0	GSM5237140 r1	0:100	A:595265067;C:649103304;G:625399353;T:599383209;N:94667	100		595265067	649103304	625399353	599383209	94667	SRX10579916	SRS8684384	SRA1217576	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.9388	0.16508	0.75205	0.59719	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2021-04-12	Undetermined	Undetermined	Spleen	Hematopoietic System
63896	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.		pubmed:34556579	Spleen2	GSM5237139	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		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°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|tissue:spleen\|strain:TLAB	GSM5237139	GSM5237139: Spleen2; Danio rerio; RNA Seq	GSM5237139		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		SRP314470	Spleen2.fastq	fastq	1372663100.0	13726631.0	GSM5237139 r1	0:100	A:303080845;C:392345861;G:369765807;T:307418421;N:52166	100		303080845	392345861	369765807	307418421	52166	SRX10579915	SRS8684383	SRA1217576	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.96541	0.18478	0.78565	0.60522	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2021-04-12	Undetermined	Undetermined	Spleen	Hematopoietic System
63897	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.		pubmed:34556579	Spleen1	GSM5237138	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		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°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|tissue:spleen\|strain:TLAB	GSM5237138	GSM5237138: Spleen1; Danio rerio; RNA Seq	GSM5237138		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		SRP314470	Spleen1.fastq	fastq	2268815600.0	22688156.0	GSM5237138 r1	0:100	A:570901318;C:562128594;G:552921437;T:582778510;N:85741	100		570901318	562128594	552921437	582778510	85741	SRX10579914	SRS8684382	SRA1217576	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.93633	0.14981	0.72825	0.52073	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2021-04-12	Undetermined	Undetermined	Spleen	Hematopoietic System

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