metadata: run_metadata: 188 rows where experiment.library_selection = "cDNA", technology = "unknown" and tissue_curation

188 rows where experiment.library_selection = "cDNA", technology = "unknown" and tissue_curation_coarse = "Hematopoietic System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	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.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
24784	24784	SRR25502048	SRX21232930	SRS18488024	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.		pubmed:28382966	Sample 15 05316 MCK mut3	GSM7678168	tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05316 MCK mut3	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf	GSM7678168	GSM7678168: Sample 15 05316 MCK mut3; Danio rerio; RNA Seq	GSM7678168 r1	GSM7678168	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114		15-05316_MCK_mut3_GTGCTT_L002_R1_001.fastq.gz 15-05316_MCK_mut3_GTGCTT_L002_R2_001.fastq.gz	fastq fastq	4329868620.0	20618422.0	GSM7678168 r1	0:105 1:105	A:1075032412;C:1077085067;G:1119735718;T:1057797736;N:217687	105	105	1075032412	1077085067	1119735718	1057797736	217687	SRX21232930	SRS18488024	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.78961	0.91048	0.20166	0.23232	0.81556	0.81115	0.59478	0.59379	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24785	24785	SRR25502049	SRX21232929	SRS18488023	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.		pubmed:28382966	Sample 15 05316 MCK mut2	GSM7678167	tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05316 MCK mut2	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf	GSM7678167	GSM7678167: Sample 15 05316 MCK mut2; Danio rerio; RNA Seq	GSM7678167 r1	GSM7678167	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114		15-05316_MCK_mut2_ACCTCA_L002_R1_001.fastq.gz 15-05316_MCK_mut2_ACCTCA_L002_R2_001.fastq.gz	fastq fastq	4444374270.0	21163687.0	GSM7678167 r1	0:105 1:105	A:1114919906;C:1098541058;G:1145427151;T:1085262902;N:223253	105	105	1114919906	1098541058	1145427151	1085262902	223253	SRX21232929	SRS18488023	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.74961	0.90068	0.18596	0.22057	0.81115	0.80754	0.5829	0.58615	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24786	24786	SRR25502050	SRX21232928	SRS18488022	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.		pubmed:28382966	Sample 15 05316 MCK mut1	GSM7678166	tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05316 MCK mut1	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf	GSM7678166	GSM7678166: Sample 15 05316 MCK mut1; Danio rerio; RNA Seq	GSM7678166 r1	GSM7678166	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114		15-05316_MCK_mut1_GCACTA_L002_R1_001.fastq.gz 15-05316_MCK_mut1_GCACTA_L002_R2_001.fastq.gz	fastq fastq	4459467180.0	21235558.0	GSM7678166 r1	0:105 1:105	A:1206908747;C:1012207561;G:1060393698;T:1179731376;N:225798	105	105	1206908747	1012207561	1060393698	1179731376	225798	SRX21232928	SRS18488022	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.75719	0.88462	0.20719	0.24095	0.78559	0.77914	0.50538	0.55691	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24787	24787	SRR25502051	SRX21232927	SRS18488021	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.		pubmed:28382966	Sample 15 05315 MCK WT3	GSM7678165	tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05315 MCK WT3	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf	GSM7678165	GSM7678165: Sample 15 05315 MCK WT3; Danio rerio; RNA Seq	GSM7678165 r1	GSM7678165	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114		15-05315_MCK_WT3_AGTGAG_L002_R1_001.fastq.gz 15-05315_MCK_WT3_AGTGAG_L002_R2_001.fastq.gz	fastq fastq	3925329240.0	18692044.0	GSM7678165 r1	0:105 1:105	A:1022654212;C:930239389;G:973328942;T:998905803;N:200894	105	105	1022654212	930239389	973328942	998905803	200894	SRX21232927	SRS18488021	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.75647	0.89377	0.19165	0.22718	0.81057	0.80501	0.51173	0.54819	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24788	24788	SRR25502052	SRX21232926	SRS18488020	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.		pubmed:28382966	Sample 15 05314 MCK WT2	GSM7678164	tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05314 MCK WT2	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf	GSM7678164	GSM7678164: Sample 15 05314 MCK WT2; Danio rerio; RNA Seq	GSM7678164 r1	GSM7678164	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114		15-05314_MCK_WT2_TGGTGA_L002_R2_001.fastq.gz 15-05314_MCK_WT2_TGGTGA_L002_R1_001.fastq.gz	fastq fastq	4100489820.0	19526142.0	GSM7678164 r1	0:105 1:105	A:1022482319;C:1016090490;G:1063619365;T:998086417;N:211229	105	105	1022482319	1016090490	1063619365	998086417	211229	SRX21232926	SRS18488020	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.76378	0.90522	0.20093	0.23619	0.82467	0.82049	0.57261	0.562	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24789	24789	SRR25502053	SRX21232925	SRS18488019	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.		pubmed:28382966	Sample 15 05313 MCK WT1	GSM7678163	tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05313 MCK WT1	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf	GSM7678163	GSM7678163: Sample 15 05313 MCK WT1; Danio rerio; RNA Seq	GSM7678163 r1	GSM7678163	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114		15-05313_MCK_WT1_AACCAG_L002_R1_001.fastq.gz 15-05313_MCK_WT1_AACCAG_L002_R2_001.fastq.gz	fastq fastq	4135721100.0	19693910.0	GSM7678163 r1	0:105 1:105	A:1048700719;C:1014162128;G:1070155053;T:1002495763;N:207437	105	105	1048700719	1014162128	1070155053	1002495763	207437	SRX21232925	SRS18488019	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.70974	0.9073	0.1771	0.22534	0.82483	0.81625	0.56311	0.55183	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
31522	31522	SRR28418937	SRX24023264	SRS20817617	SRP497230	PRJNA1090848	Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq]	GSE262188	Transcriptome Analysis	Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision its dynamic and role in HSPC development is poorly investigated. Here we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors such as PU.1 .		pubmed:38886858	HPSC rep3 RNA seq 3month	GSM8159257	source name:hematopoietic stem cell\|tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry\|geo loc name:missing\|collection date:missing	HPSC rep3 RNA seq 3month	The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	hematopoietic stem cell		Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina		tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry	GSM8159257	GSM8159257: HPSC rep3 RNA seq 3month; Danio rerio; RNA Seq	GSM8159257 r1	GSM8159257	1	Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP497230	loader:fastq load.py	RNA-seq_Adult_HPSC_rep3_R1.fq.gz RNA-seq_Adult_HPSC_rep3_R2.fq.gz	fastq fastq	11621758500.0	38739195.0	GSM8159257 r1	0:150 1:150	A:3144084931;C:2632272493;G:2693165513;T:3151802925;N:432638	150	150	3144084931	2632272493	2693165513	3151802925	432638	SRX24023264	SRS20817617	SRA1831889	South China University of Technology	South China University of Technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-21	Adult	Adult	Blood	Hematopoietic System
31523	31523	SRR28418938	SRX24023263	SRS20817616	SRP497230	PRJNA1090848	Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq]	GSE262188	Transcriptome Analysis	Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision its dynamic and role in HSPC development is poorly investigated. Here we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors such as PU.1 .		pubmed:38886858	HPSC rep2 RNA seq 3month	GSM8159256	source name:hematopoietic stem cell\|tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry\|geo loc name:missing\|collection date:missing	HPSC rep2 RNA seq 3month	The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	hematopoietic stem cell		Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina		tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry	GSM8159256	GSM8159256: HPSC rep2 RNA seq 3month; Danio rerio; RNA Seq	GSM8159256 r1	GSM8159256	1	Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP497230	loader:fastq load.py	RNA-seq_Adult_HPSC_rep2_R1.fq.gz RNA-seq_Adult_HPSC_rep2_R2.fq.gz	fastq fastq	9951217200.0	33170724.0	GSM8159256 r1	0:150 1:150	A:2755384814;C:2209586340;G:2237522365;T:2748523249;N:200432	150	150	2755384814	2209586340	2237522365	2748523249	200432	SRX24023263	SRS20817616	SRA1831889	South China University of Technology	South China University of Technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-21	Adult	Adult	Blood	Hematopoietic System
31524	31524	SRR28418939	SRX24023262	SRS20817615	SRP497230	PRJNA1090848	Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq]	GSE262188	Transcriptome Analysis	Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision its dynamic and role in HSPC development is poorly investigated. Here we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors such as PU.1 .		pubmed:38886858	HPSC rep1 RNA seq 3month	GSM8159255	source name:hematopoietic stem cell\|tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry\|geo loc name:missing\|collection date:missing	HPSC rep1 RNA seq 3month	The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	hematopoietic stem cell		Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina		tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry	GSM8159255	GSM8159255: HPSC rep1 RNA seq 3month; Danio rerio; RNA Seq	GSM8159255 r1	GSM8159255	1	Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP497230	loader:fastq load.py	RNA-seq_Adult_HPSC_rep1_R1.fq.gz RNA-seq_Adult_HPSC_rep1_R2.fq.gz	fastq fastq	11096617200.0	36988724.0	GSM8159255 r1	0:150 1:150	A:3071303610;C:2460399138;G:2510824334;T:3053621175;N:468943	150	150	3071303610	2460399138	2510824334	3053621175	468943	SRX24023262	SRS20817615	SRA1831889	South China University of Technology	South China University of Technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-21	Adult	Adult	Blood	Hematopoietic System
38257	38257	SRR1609758	SRX730411	SRS719632	SRP048807	PRJNA263496	Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish	GSE62221	Transcriptome Analysis	The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures		pubmed:26227973	spleen10	GSM1523053	source name:spleen\|tissue:spleen\|temperature:10°C\|strain:Tubingen\|age:6 mpf	spleen10	Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. 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: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	spleen	fish were maintained 12h to adapt low temperatures and then killed by pithing	Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:spleen\|temperature:10°C\|strain:Tubingen\|age:6 mpf	GSM1523053	GSM1523053: spleen10; Danio rerio; RNA Seq	GSM1523053		1	Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1523053	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP048807		spleen10_2.fq.gz spleen10_1.fq.gz	fastq fastq	5089614600.0	25448073.0	GSM1523053 r1	0:100 1:100	A:1315179584;C:1230198758;G:1227165313;T:1316987828;N:83117	100	100	1315179584	1230198758	1227165313	1316987828	83117	SRX730411	SRS719632	SRA189240	GEO	Shanghai Ocean University	2	0.9612	0.9561	0.04114	0.04116	0.77518	0.77926	0.42558	0.42199	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	China	2014-10-09	Adult	Adult	Spleen	Hematopoietic System
38258	38258	SRR1609757	SRX730410	SRS719631	SRP048807	PRJNA263496	Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish	GSE62221	Transcriptome Analysis	The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures		pubmed:26227973	spleen18	GSM1523052	source name:spleen\|tissue:spleen\|temperature:18°C\|strain:Tubingen\|age:6 mpf	spleen18	Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. 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: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	spleen	fish were maintained 12h to adapt low temperatures and then killed by pithing	Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:spleen\|temperature:18°C\|strain:Tubingen\|age:6 mpf	GSM1523052	GSM1523052: spleen18; Danio rerio; RNA Seq	GSM1523052		1	Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1523052	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP048807		spleen18_1.fq.gz spleen18_2.fq.gz	fastq fastq	4494055400.0	22470277.0	GSM1523052 r1	0:100 1:100	A:1167396911;C:1079923943;G:1078183614;T:1168479101;N:71831	100	100	1167396911	1079923943	1078183614	1168479101	71831	SRX730410	SRS719631	SRA189240	GEO	Shanghai Ocean University	2	0.96809	0.96224	0.02675	0.02626	0.80012	0.80369	0.28419	0.28966	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	China	2014-10-09	Adult	Adult	Spleen	Hematopoietic System
38259	38259	SRR1609756	SRX730409	SRS719630	SRP048807	PRJNA263496	Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish	GSE62221	Transcriptome Analysis	The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures		pubmed:26227973	spleen28	GSM1523051	source name:spleen\|tissue:spleen\|temperature:28°C\|strain:Tubingen\|age:6 mpf	spleen28	Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. 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: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	spleen	fish were maintained 12h to adapt low temperatures and then killed by pithing	Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:spleen\|temperature:28°C\|strain:Tubingen\|age:6 mpf	GSM1523051	GSM1523051: spleen28; Danio rerio; RNA Seq	GSM1523051		1	Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1523051	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP048807		spleen28_2.fq.gz spleen28_1.fq.gz	fastq fastq	3499734800.0	17498674.0	GSM1523051 r1	0:100 1:100	A:912324481;C:841616616;G:837795621;T:907938558;N:59524	100	100	912324481	841616616	837795621	907938558	59524	SRX730409	SRS719630	SRA189240	GEO	Shanghai Ocean University	2	0.95732	0.95047	0.04767	0.04837	0.75507	0.7613	0.5152	0.51185	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	China	2014-10-09	Adult	Adult	Spleen	Hematopoietic System
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
39665	39665	SRR2027911	SRX1029315	SRS937775	SRP058376	PRJNA284108	RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures	GSE68920	Transcriptome Analysis	We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.		pubmed:31832066	6dpf mpeg1:mCherryPosMmarinumGFPPos rep3	GSM1686459	source name:zebra fish larvae\|tissue:20 mpeg1 positive macrophages\|cell population:GFP positive\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	6dpf mpeg1:mCherryPosMmarinumGFPPos rep3	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample	zebra fish larvae	Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich	tissue:20 mpeg1 positive macrophages\|cell population:GFP positive\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	GSM1686459	GSM1686459: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep3; Danio rerio; RNA Seq	GSM1686459		1	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	GEO Accession:GSM1686459	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058376		ZFG-14-09_06_ATTCCT_L003_R1_001.fastq.gz	fastq	988427889.0	19380939.0	GSM1686459 r1	0:51	A:322268594;C:166925867;G:171531103;T:327506982;N:195343	51		322268594	166925867	171531103	327506982	195343	SRX1029315	SRS937775	SRA268539	GEO	Institute of Biology, Leiden University	1	0.6999		0.24019		0.85358		0.56832		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Netherlands	2015-05-15	Larval	Larval	Blood	Hematopoietic System
39666	39666	SRR2027910	SRX1029314	SRS937773	SRP058376	PRJNA284108	RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures	GSE68920	Transcriptome Analysis	We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.		pubmed:31832066	6dpf mpeg1:mCherryPosMmarinumGFPPos rep2	GSM1686458	source name:zebra fish larvae\|tissue:20 mpeg1 positive macrophages\|cell population:GFP positive\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	6dpf mpeg1:mCherryPosMmarinumGFPPos rep2	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample	zebra fish larvae	Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich	tissue:20 mpeg1 positive macrophages\|cell population:GFP positive\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	GSM1686458	GSM1686458: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep2; Danio rerio; RNA Seq	GSM1686458		1	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	GEO Accession:GSM1686458	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058376		ZFG-14-09_05_ACTGAT_L003_R1_001.fastq.gz	fastq	846771207.0	16603357.0	GSM1686458 r1	0:51	A:268435928;C:150903620;G:153931870;T:273331733;N:168056	51		268435928	150903620	153931870	273331733	168056	SRX1029314	SRS937773	SRA268539	GEO	Institute of Biology, Leiden University	1	0.72025		0.17943		0.87937		0.5683		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Netherlands	2015-05-15	Larval	Larval	Blood	Hematopoietic System
39667	39667	SRR2027909	SRX1029313	SRS937774	SRP058376	PRJNA284108	RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures	GSE68920	Transcriptome Analysis	We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.		pubmed:31832066	6dpf mpeg1:mCherryPosMmarinumGFPPos rep1	GSM1686457	source name:zebra fish larvae\|tissue:20 mpeg1 positive macrophages\|cell population:GFP positive\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	6dpf mpeg1:mCherryPosMmarinumGFPPos rep1	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample	zebra fish larvae	Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich	tissue:20 mpeg1 positive macrophages\|cell population:GFP positive\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	GSM1686457	GSM1686457: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep1; Danio rerio; RNA Seq	GSM1686457		1	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	GEO Accession:GSM1686457	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058376		ZFG-14-09_04_GAGTGG_L003_R1_001.fastq.gz	fastq	807459642.0	15832542.0	GSM1686457 r1	0:51	A:260516660;C:140425216;G:145411663;T:260942267;N:163836	51		260516660	140425216	145411663	260942267	163836	SRX1029313	SRS937774	SRA268539	GEO	Institute of Biology, Leiden University	1	0.7097		0.17187		0.93304		0.64092		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Netherlands	2015-05-15	Larval	Larval	Blood	Hematopoietic System
39668	39668	SRR2027908	SRX1029312	SRS937776	SRP058376	PRJNA284108	RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures	GSE68920	Transcriptome Analysis	We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.		pubmed:31832066	6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3	GSM1686456	source name:zebra fish larvae\|tissue:20 mpeg1 positive macrophages\|cell population:GFP negative\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample	zebra fish larvae	Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich	tissue:20 mpeg1 positive macrophages\|cell population:GFP negative\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	GSM1686456	GSM1686456: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3; Danio rerio; RNA Seq	GSM1686456		1	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	GEO Accession:GSM1686456	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058376		ZFG-14-09_03_CGTACG_L003_R1_001.fastq.gz	fastq	1523483526.0	29872226.0	GSM1686456 r1	0:51	A:499019794;C:267493952;G:277264815;T:479405699;N:299266	51		499019794	267493952	277264815	479405699	299266	SRX1029312	SRS937776	SRA268539	GEO	Institute of Biology, Leiden University	1	0.67328		0.15117		0.91179		0.54858		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Netherlands	2015-05-15	Larval	Larval	Blood	Hematopoietic System
39669	39669	SRR2027907	SRX1029311	SRS937777	SRP058376	PRJNA284108	RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures	GSE68920	Transcriptome Analysis	We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.		pubmed:31832066	6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2	GSM1686455	source name:zebra fish larvae\|tissue:20 mpeg1 positive macrophages\|cell population:GFP negative\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample	zebra fish larvae	Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich	tissue:20 mpeg1 positive macrophages\|cell population:GFP negative\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	GSM1686455	GSM1686455: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2; Danio rerio; RNA Seq	GSM1686455		1	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	GEO Accession:GSM1686455	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058376		ZFG-14-09_02_GTTTCG_L003_R1_001.fastq.gz	fastq	938675094.0	18405394.0	GSM1686455 r1	0:51	A:284384359;C:173449465;G:178039777;T:302612825;N:188668	51		284384359	173449465	178039777	302612825	188668	SRX1029311	SRS937777	SRA268539	GEO	Institute of Biology, Leiden University	1	0.72884		0.14723		0.90767		0.57414		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Netherlands	2015-05-15	Larval	Larval	Blood	Hematopoietic System
39670	39670	SRR2027906	SRX1029310	SRS937778	SRP058376	PRJNA284108	RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures	GSE68920	Transcriptome Analysis	We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.		pubmed:31832066	6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1	GSM1686454	source name:zebra fish larvae\|tissue:20 mpeg1 positive macrophages\|cell population:GFP negative\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample	zebra fish larvae	Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich	tissue:20 mpeg1 positive macrophages\|cell population:GFP negative\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	GSM1686454	GSM1686454: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1; Danio rerio; RNA Seq	GSM1686454		1	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	GEO Accession:GSM1686454	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058376		ZFG-14-09_01_GTGGCC_L003_R1_001.fastq.gz	fastq	1248324348.0	24476948.0	GSM1686454 r1	0:51	A:391067882;C:223380294;G:229132022;T:404526410;N:217740	51		391067882	223380294	229132022	404526410	217740	SRX1029310	SRS937778	SRA268539	GEO	Institute of Biology, Leiden University	1	0.70232		0.14257		0.92894		0.59305		51		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Netherlands	2015-05-15	Larval	Larval	Blood	Hematopoietic System
40807	40807	SRR3381847	SRX1704280	SRS1396343	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Treated 3 blood	GSM2122871	source name:whole blood cortisol\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	Treated 3 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood cortisol	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	GSM2122871	GSM2122871: Treated 3 blood; Danio rerio; RNA Seq	GSM2122871		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122871	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DY1ANXX_s6_1_GSLv3-7_38_SL139795.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_38_SL139795.fastq.gz	fastq fastq	1349428600.0	13494286.0	GSM2122871 r1	0:50 1:50	A:391483366;C:283353944;G:288253777;T:386190051;N:147462	50	50	391483366	283353944	288253777	386190051	147462	SRX1704280	SRS1396343	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.88853	0.89204	0.22815	0.23941	0.73917	0.73979	0.53637	0.53893	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40808	40808	SRR3381848	SRX1704280	SRS1396343	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Treated 3 blood	GSM2122871	source name:whole blood cortisol\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	Treated 3 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood cortisol	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	GSM2122871	GSM2122871: Treated 3 blood; Danio rerio; RNA Seq	GSM2122871		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122871	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8BH2ANXX_s5_1_GSLv3-7_38_SL139795.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_38_SL139795.fastq.gz	fastq fastq	1020366100.0	10203661.0	GSM2122871 r2	0:50 1:50	A:296023946;C:213173706;G:215342808;T:295806226;N:19414	50	50	296023946	213173706	215342808	295806226	19414	SRX1704280	SRS1396343	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.88792	0.89203	0.21382	0.24279	0.7652	0.7444	0.53618	0.54254	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40809	40809	SRR3381849	SRX1704280	SRS1396343	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Treated 3 blood	GSM2122871	source name:whole blood cortisol\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	Treated 3 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood cortisol	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	GSM2122871	GSM2122871: Treated 3 blood; Danio rerio; RNA Seq	GSM2122871		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122871	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8BH2ANXX_s6_1_GSLv3-7_38_SL139795.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_38_SL139795.fastq.gz	fastq fastq	1008129000.0	10081290.0	GSM2122871 r3	0:50 1:50	A:292536545;C:210308039;G:212529262;T:292736486;N:18668	50	50	292536545	210308039	212529262	292736486	18668	SRX1704280	SRS1396343	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.88682	0.89249	0.21573	0.24321	0.7657	0.74456	0.53948	0.54456	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40810	40810	SRR3381850	SRX1704280	SRS1396343	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Treated 3 blood	GSM2122871	source name:whole blood cortisol\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	Treated 3 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood cortisol	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	GSM2122871	GSM2122871: Treated 3 blood; Danio rerio; RNA Seq	GSM2122871		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122871	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DY1ANXX_s5_1_GSLv3-7_38_SL139795.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_38_SL139795.fastq.gz	fastq fastq	1348814000.0	13488140.0	GSM2122871 r4	0:50 1:50	A:391186639;C:283404571;G:288274584;T:385756613;N:191593	50	50	391186639	283404571	288274584	385756613	191593	SRX1704280	SRS1396343	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.88673	0.89303	0.22875	0.24107	0.74276	0.74134	0.53585	0.54514	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40811	40811	SRR3381843	SRX1704279	SRS1396344	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Treated 2 blood	GSM2122870	source name:whole blood cortisol\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	Treated 2 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood cortisol	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	GSM2122870	GSM2122870: Treated 2 blood; Danio rerio; RNA Seq	GSM2122870		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122870	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DY1ANXX_s6_1_GSLv3-7_37_SL139794.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_37_SL139794.fastq.gz	fastq fastq	1251398700.0	12513987.0	GSM2122870 r1	0:50 1:50	A:383059535;C:243111832;G:248681985;T:376401618;N:143730	50	50	383059535	243111832	248681985	376401618	143730	SRX1704279	SRS1396344	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.86725	0.86597	0.35725	0.37228	0.74312	0.73961	0.53136	0.53663	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40812	40812	SRR3381844	SRX1704279	SRS1396344	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Treated 2 blood	GSM2122870	source name:whole blood cortisol\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	Treated 2 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood cortisol	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	GSM2122870	GSM2122870: Treated 2 blood; Danio rerio; RNA Seq	GSM2122870		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122870	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8BH2ANXX_s5_1_GSLv3-7_37_SL139794.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_37_SL139794.fastq.gz	fastq fastq	959597100.0	9595971.0	GSM2122870 r2	0:50 1:50	A:294644349;C:184893976;G:188222172;T:291818696;N:17907	50	50	294644349	184893976	188222172	291818696	17907	SRX1704279	SRS1396344	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.86953	0.86626	0.33903	0.3765	0.77264	0.74432	0.53426	0.53782	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40813	40813	SRR3381845	SRX1704279	SRS1396344	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Treated 2 blood	GSM2122870	source name:whole blood cortisol\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	Treated 2 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood cortisol	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	GSM2122870	GSM2122870: Treated 2 blood; Danio rerio; RNA Seq	GSM2122870		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122870	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DY1ANXX_s5_1_GSLv3-7_37_SL139794.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_37_SL139794.fastq.gz	fastq fastq	1245250000.0	12452500.0	GSM2122870 r3	0:50 1:50	A:381219052;C:241987476;G:247543915;T:374295403;N:204154	50	50	381219052	241987476	247543915	374295403	204154	SRX1704279	SRS1396344	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.86789	0.86686	0.35484	0.37206	0.74119	0.73679	0.50299	0.53759	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40814	40814	SRR3381846	SRX1704279	SRS1396344	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Treated 2 blood	GSM2122870	source name:whole blood cortisol\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	Treated 2 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood cortisol	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	GSM2122870	GSM2122870: Treated 2 blood; Danio rerio; RNA Seq	GSM2122870		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122870	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8BH2ANXX_s6_1_GSLv3-7_37_SL139794.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_37_SL139794.fastq.gz	fastq fastq	950337100.0	9503371.0	GSM2122870 r4	0:50 1:50	A:291821125;C:182753545;G:186179426;T:289565320;N:17684	50	50	291821125	182753545	186179426	289565320	17684	SRX1704279	SRS1396344	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.86635	0.86476	0.34245	0.3786	0.77309	0.74474	0.50694	0.53099	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40815	40815	SRR3381839	SRX1704278	SRS1396345	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Treated 1 blood	GSM2122869	source name:whole blood cortisol\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	Treated 1 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood cortisol	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	GSM2122869	GSM2122869: Treated 1 blood; Danio rerio; RNA Seq	GSM2122869		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122869	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DY1ANXX_s5_1_GSLv3-7_36_SL139793.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_36_SL139793.fastq.gz	fastq fastq	1067516000.0	10675160.0	GSM2122869 r1	0:50 1:50	A:289362409;C:244764167;G:247658920;T:285596522;N:133982	50	50	289362409	244764167	247658920	285596522	133982	SRX1704278	SRS1396345	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.90704	0.92219	0.1113	0.11316	0.73645	0.73746	0.52358	0.53128	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40816	40816	SRR3381840	SRX1704278	SRS1396345	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Treated 1 blood	GSM2122869	source name:whole blood cortisol\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	Treated 1 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood cortisol	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	GSM2122869	GSM2122869: Treated 1 blood; Danio rerio; RNA Seq	GSM2122869		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122869	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8BH2ANXX_s5_1_GSLv3-7_36_SL139793.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_36_SL139793.fastq.gz	fastq fastq	802301400.0	8023014.0	GSM2122869 r2	0:50 1:50	A:216222361;C:183743858;G:183958773;T:218361744;N:14664	50	50	216222361	183743858	183958773	218361744	14664	SRX1704278	SRS1396345	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.90734	0.92073	0.10828	0.11414	0.75816	0.74156	0.52518	0.53162	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40817	40817	SRR3381841	SRX1704278	SRS1396345	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Treated 1 blood	GSM2122869	source name:whole blood cortisol\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	Treated 1 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood cortisol	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	GSM2122869	GSM2122869: Treated 1 blood; Danio rerio; RNA Seq	GSM2122869		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122869	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DY1ANXX_s6_1_GSLv3-7_36_SL139793.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_36_SL139793.fastq.gz	fastq fastq	1068410400.0	10684104.0	GSM2122869 r3	0:50 1:50	A:289709397;C:244889156;G:247758297;T:285941886;N:111664	50	50	289709397	244889156	247758297	285941886	111664	SRX1704278	SRS1396345	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.90673	0.9217	0.11124	0.11262	0.73779	0.73819	0.52628	0.53419	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40818	40818	SRR3381842	SRX1704278	SRS1396345	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Treated 1 blood	GSM2122869	source name:whole blood cortisol\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	Treated 1 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood cortisol	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:cortisol	GSM2122869	GSM2122869: Treated 1 blood; Danio rerio; RNA Seq	GSM2122869		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122869	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8BH2ANXX_s6_1_GSLv3-7_36_SL139793.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_36_SL139793.fastq.gz	fastq fastq	792180400.0	7921804.0	GSM2122869 r4	0:50 1:50	A:213515752;C:181199374;G:181507201;T:215943851;N:14222	50	50	213515752	181199374	181507201	215943851	14222	SRX1704278	SRS1396345	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.90574	0.92099	0.11022	0.11558	0.75773	0.74158	0.52565	0.52697	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40819	40819	SRR3381835	SRX1704277	SRS1396346	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 3 blood	GSM2122868	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 3 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122868	GSM2122868: Control 3 blood; Danio rerio; RNA Seq	GSM2122868		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122868	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8BH2ANXX_s6_1_GSLv3-7_35_SL139792.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_35_SL139792.fastq.gz	fastq fastq	1006437300.0	10064373.0	GSM2122868 r1	0:50 1:50	A:270736589;C:231073543;G:230348781;T:274259695;N:18692	50	50	270736589	231073543	230348781	274259695	18692	SRX1704277	SRS1396346	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.89576	0.91552	0.11015	0.11108	0.77108	0.75708	0.52238	0.55295	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40820	40820	SRR3381836	SRX1704277	SRS1396346	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 3 blood	GSM2122868	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 3 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122868	GSM2122868: Control 3 blood; Danio rerio; RNA Seq	GSM2122868		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122868	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8BH2ANXX_s5_1_GSLv3-7_35_SL139792.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_35_SL139792.fastq.gz	fastq fastq	1019872300.0	10198723.0	GSM2122868 r2	0:50 1:50	A:274310405;C:234397316;G:233653220;T:277492635;N:18724	50	50	274310405	234397316	233653220	277492635	18724	SRX1704277	SRS1396346	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.89872	0.91671	0.10908	0.10998	0.76848	0.7559	0.55678	0.52913	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40821	40821	SRR3381837	SRX1704277	SRS1396346	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 3 blood	GSM2122868	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 3 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122868	GSM2122868: Control 3 blood; Danio rerio; RNA Seq	GSM2122868		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122868	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DY1ANXX_s6_1_GSLv3-7_35_SL139792.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_35_SL139792.fastq.gz	fastq fastq	1350419100.0	13504191.0	GSM2122868 r3	0:50 1:50	A:365416324;C:310498635;G:312632921;T:361739733;N:131487	50	50	365416324	310498635	312632921	361739733	131487	SRX1704277	SRS1396346	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.89828	0.91602	0.11147	0.11073	0.74941	0.75053	0.54012	0.53979	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40822	40822	SRR3381838	SRX1704277	SRS1396346	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 3 blood	GSM2122868	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 3 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122868	GSM2122868: Control 3 blood; Danio rerio; RNA Seq	GSM2122868		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122868	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DY1ANXX_s5_1_GSLv3-7_35_SL139792.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_35_SL139792.fastq.gz	fastq fastq	1352817900.0	13528179.0	GSM2122868 r4	0:50 1:50	A:366001448;C:311109301;G:313269573;T:362247619;N:189959	50	50	366001448	311109301	313269573	362247619	189959	SRX1704277	SRS1396346	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.89762	0.91702	0.11094	0.1109	0.74864	0.7498	0.53153	0.55731	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40823	40823	SRR3381831	SRX1704276	SRS1396347	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 2 blood	GSM2122867	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 2 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122867	GSM2122867: Control 2 blood; Danio rerio; RNA Seq	GSM2122867		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122867	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DY1ANXX_s5_1_GSLv3-7_34_SL139791.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_34_SL139791.fastq.gz	fastq fastq	1320276500.0	13202765.0	GSM2122867 r1	0:50 1:50	A:347340148;C:314346533;G:315984111;T:342435896;N:169812	50	50	347340148	314346533	315984111	342435896	169812	SRX1704276	SRS1396347	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.92673	0.93522	0.1474	0.1486	0.77695	0.77822	0.5491	0.55404	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40824	40824	SRR3381832	SRX1704276	SRS1396347	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 2 blood	GSM2122867	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 2 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122867	GSM2122867: Control 2 blood; Danio rerio; RNA Seq	GSM2122867		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122867	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8BH2ANXX_s6_1_GSLv3-7_34_SL139791.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_34_SL139791.fastq.gz	fastq fastq	980312400.0	9803124.0	GSM2122867 r2	0:50 1:50	A:256051139;C:233456025;G:232307447;T:258480444;N:17345	50	50	256051139	233456025	232307447	258480444	17345	SRX1704276	SRS1396347	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.92686	0.9359	0.1445	0.14733	0.79537	0.78244	0.55823	0.5607	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40825	40825	SRR3381833	SRX1704276	SRS1396347	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 2 blood	GSM2122867	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 2 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122867	GSM2122867: Control 2 blood; Danio rerio; RNA Seq	GSM2122867		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122867	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8BH2ANXX_s5_1_GSLv3-7_34_SL139791.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_34_SL139791.fastq.gz	fastq fastq	996477700.0	9964777.0	GSM2122867 r3	0:50 1:50	A:260257795;C:237526121;G:236299803;T:262375630;N:18351	50	50	260257795	237526121	236299803	262375630	18351	SRX1704276	SRS1396347	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.9292	0.93713	0.143	0.14889	0.79531	0.7834	0.55615	0.55279	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40826	40826	SRR3381834	SRX1704276	SRS1396347	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 2 blood	GSM2122867	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 2 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122867	GSM2122867: Control 2 blood; Danio rerio; RNA Seq	GSM2122867		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122867	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DY1ANXX_s6_1_GSLv3-7_34_SL139791.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_34_SL139791.fastq.gz	fastq fastq	1319184300.0	13191843.0	GSM2122867 r4	0:50 1:50	A:347098468;C:314043165;G:315610117;T:342302442;N:130108	50	50	347098468	314043165	315610117	342302442	130108	SRX1704276	SRS1396347	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.92671	0.93595	0.14826	0.14877	0.77792	0.77873	0.55524	0.5557	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40827	40827	SRR3381825	SRX1704275	SRS1396348	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 1 blood	GSM2122866	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 1 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122866	GSM2122866: Control 1 blood; Danio rerio; RNA Seq	GSM2122866		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122866	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8BH2ANXX_s6_1_GSLv3-7_33_SL139790.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_33_SL139790.fastq.gz	fastq fastq	692276000.0	6922760.0	GSM2122866 r1	0:50 1:50	A:191405813;C:153586292;G:152965257;T:194306049;N:12589	50	50	191405813	153586292	152965257	194306049	12589	SRX1704275	SRS1396348	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.9083	0.91142	0.16578	0.17743	0.75789	0.74221	0.55181	0.54476	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40828	40828	SRR3381826	SRX1704275	SRS1396348	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 1 blood	GSM2122866	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 1 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122866	GSM2122866: Control 1 blood; Danio rerio; RNA Seq	GSM2122866		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122866	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DY1ANXX_s5_1_GSLv3-7_33_SL139790.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_33_SL139790.fastq.gz	fastq fastq	911479300.0	9114793.0	GSM2122866 r2	0:50 1:50	A:253240601;C:202627238;G:203390297;T:252105631;N:115533	50	50	253240601	202627238	203390297	252105631	115533	SRX1704275	SRS1396348	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.90729	0.91334	0.17307	0.1777	0.73316	0.73419	0.55981	0.56826	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40829	40829	SRR3381827	SRX1704275	SRS1396348	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 1 blood	GSM2122866	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 1 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122866	GSM2122866: Control 1 blood; Danio rerio; RNA Seq	GSM2122866		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122866	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DY1ANXX_s6_1_GSLv3-7_33_SL139790.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_33_SL139790.fastq.gz	fastq fastq	910041600.0	9100416.0	GSM2122866 r3	0:50 1:50	A:252924440;C:202200821;G:202972517;T:251856107;N:87715	50	50	252924440	202200821	202972517	251856107	87715	SRX1704275	SRS1396348	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.90819	0.91345	0.17288	0.17678	0.73582	0.73448	0.55482	0.56579	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40830	40830	SRR3381828	SRX1704275	SRS1396348	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 1 blood	GSM2122866	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 1 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122866	GSM2122866: Control 1 blood; Danio rerio; RNA Seq	GSM2122866		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122866	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8BH2ANXX_s5_1_GSLv3-7_33_SL139790.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_33_SL139790.fastq.gz	fastq fastq	701940200.0	7019402.0	GSM2122866 r4	0:50 1:50	A:194036996;C:155992188;G:155284640;T:196613376;N:13000	50	50	194036996	155992188	155284640	196613376	13000	SRX1704275	SRS1396348	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.90959	0.91386	0.16429	0.17705	0.75544	0.7391	0.548	0.57224	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40831	40831	SRR3381829	SRX1704275	SRS1396348	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 1 blood	GSM2122866	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 1 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122866	GSM2122866: Control 1 blood; Danio rerio; RNA Seq	GSM2122866		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122866	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DKGANXX_s8_1_GSLv3-7_33_SL139790.fastq.gz C8DKGANXX_s8_2_GSLv3-7_33_SL139790.fastq.gz	fastq fastq	1596331500.0	15963315.0	GSM2122866 r5	0:50 1:50	A:444854958;C:353331559;G:354367449;T:442888766;N:888768	50	50	444854958	353331559	354367449	442888766	888768	SRX1704275	SRS1396348	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.90554	0.91175	0.17327	0.17968	0.73669	0.73728	0.55044	0.5651	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	Hematopoietic System
40832	40832	SRR3381830	SRX1704275	SRS1396348	SRP073272	PRJNA318414	Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]	GSE80260	Transcriptome Analysis	Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.	parent bioproject:PRJNA318502	pubmed:27444789	Control 1 blood	GSM2122866	source name:whole blood DMSO control\|strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	Control 1 blood	Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.	whole blood DMSO control	DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.	strain/background:AB\|tissue:whole blood\|age:adult\|embryonic treatment:DMSO	GSM2122866	GSM2122866: Control 1 blood; Danio rerio; RNA Seq	GSM2122866		1	RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.	GEO Accession:GSM2122866	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP073272		C8DKGANXX_s7_1_GSLv3-7_33_SL139790.fastq.gz C8DKGANXX_s7_2_GSLv3-7_33_SL139790.fastq.gz	fastq fastq	1600754600.0	16007546.0	GSM2122866 r6	0:50 1:50	A:446178544;C:354456079;G:355435947;T:443937350;N:746680	50	50	446178544	354456079	355435947	443937350	746680	SRX1704275	SRS1396348	SRA411416	GEO	Molecular and Biomedical Sciences, University of Maine	2	0.90709	0.91238	0.17011	0.17723	0.74054	0.73994	0.55938	0.55607	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2016-04-13	Adult	Adult	Blood	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
49188	49188	SRR7785379	SRX4640375	SRS3738589	SRP159583	PRJNA489308	Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis	PRJNA489308	Other	Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.				H67	breed:AB strain\|age:3 month\|sex:male\|tissue:Peripheral blood\|genotype:wild type\|replicate:replicate2\|BioSampleModel:Model organism or animal									H67	H67	H67	Wild type zebrafish control 2			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP159583		H67_S2_L001_R2_001.fastq.gz H67_S2_L001_R1_001.fastq.gz	fastq fastq	18477819300.0	61592731.0	H67 S2 L001 R2 001.fastq.gz	0:150 1:150	A:4887782016;C:4375793599;G:4438933003;T:4775205744;N:104938	150	150	4887782016	4375793599	4438933003	4775205744	104938	SRX4640375	SRS3738589	SRA766519	Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University\|Department: Department of Haematology	Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University	2	0.93322	0.93319	0.06946	0.06963	0.6747	0.68083	0.47183	0.47148	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	bulk	unknown	unknown	China	2019-09-20	Adult	Adult	Blood	Hematopoietic System
49189	49189	SRR7785380	SRX4640374	SRS3738594	SRP159583	PRJNA489308	Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis	PRJNA489308	Other	Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.				H66	breed:AB strain\|age:3 month\|sex:male\|tissue:Peripheral blood\|genotype:wild type\|replicate:replicate1\|BioSampleModel:Model organism or animal									H66	H66	H66	Wild type zebrafish control 1			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP159583		H66_S1_L001_R2_001.fastq.gz H66_S1_L001_R1_001.fastq.gz	fastq fastq	20487126300.0	68290421.0	H66 S1 L001 R2 001.fastq.gz	0:150 1:150	A:5445452582;C:4824876569;G:4904146081;T:5312533433;N:117635	150	150	5445452582	4824876569	4904146081	5312533433	117635	SRX4640374	SRS3738594	SRA766519	Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University\|Department: Department of Haematology	Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University	2	0.93306	0.9336	0.08694	0.08764	0.66687	0.6734	0.46489	0.47008	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	bulk	unknown	unknown	China	2019-09-20	Adult	Adult	Blood	Hematopoietic System
49190	49190	SRR7785381	SRX4640373	SRS3738593	SRP159583	PRJNA489308	Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis	PRJNA489308	Other	Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.				H124	breed:AB strain\|age:3 month\|sex:male\|tissue:Peripheral blood\|genotype:Tol2 EVI 1 EGFP transgenic\|replicate:replicate1\|BioSampleModel:Model organism or animal									H124	H124	H124	Tol2 EVI 1 EGFP transgenic zebrafish sample 1			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP159583		H124_S1_L001_R1_001.fastq.gz H124_S1_L001_R2_001.fastq.gz	fastq fastq	13178593800.0	43928646.0	H124 S1 L001 R1 001.fastq.gz	0:150 1:150	A:3507220604;C:3103991247;G:3164157369;T:3403051995;N:172585	150	150	3507220604	3103991247	3164157369	3403051995	172585	SRX4640373	SRS3738593	SRA766519	Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University\|Department: Department of Haematology	Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University	2	0.94147	0.94277	0.08109	0.08136	0.69483	0.70011	0.47542	0.47593	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	bulk	unknown	unknown	China	2019-09-20	Adult	Adult	Blood	Hematopoietic System
49191	49191	SRR7785382	SRX4640372	SRS3738592	SRP159583	PRJNA489308	Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis	PRJNA489308	Other	Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.				H93	breed:AB strain\|age:3 month\|sex:male\|tissue:Peripheral blood\|genotype:wild type\|replicate:replicate3\|BioSampleModel:Model organism or animal									H93	H93	H93	Wild type zebrafish control 3			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP159583		H93_S3_L001_R1_001.fastq.gz H93_S3_L001_R2_001.fastq.gz	fastq fastq	18197379600.0	60657932.0	H93 S3 L001 R1 001.fastq.gz	0:150 1:150	A:4814246240;C:4308418881;G:4375398316;T:4699211054;N:105109	150	150	4814246240	4308418881	4375398316	4699211054	105109	SRX4640372	SRS3738592	SRA766519	Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University\|Department: Department of Haematology	Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University	2	0.9312	0.93173	0.07454	0.07498	0.67065	0.6773	0.46807	0.47334	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	bulk	unknown	unknown	China	2019-09-20	Adult	Adult	Blood	Hematopoietic System
49192	49192	SRR7785383	SRX4640371	SRS3738590	SRP159583	PRJNA489308	Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis	PRJNA489308	Other	Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.				H126	breed:AB strain\|age:3 month\|sex:male\|tissue:Peripheral blood\|genotype:Tol2 EVI 1 EGFP transgenic\|replicate:replicate3\|BioSampleModel:Model organism or animal									H126	H126	H126	Tol2 EVI 1 EGFP transgenic zebrafish sample 3			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP159583		H126_S3_L001_R1_001.fastq.gz H126_S3_L001_R2_001.fastq.gz	fastq fastq	14979601800.0	49932006.0	H126 S3 L001 R2 001.fastq.gz	0:150 1:150	A:3961375940;C:3551410264;G:3640700651;T:3825918931;N:196014	150	150	3961375940	3551410264	3640700651	3825918931	196014	SRX4640371	SRS3738590	SRA766519	Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University\|Department: Department of Haematology	Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University	2	0.93717	0.93908	0.05823	0.05891	0.70552	0.71256	0.46146	0.45779	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	bulk	unknown	unknown	China	2019-09-20	Adult	Adult	Blood	Hematopoietic System
49193	49193	SRR7785384	SRX4640370	SRS3738588	SRP159583	PRJNA489308	Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis	PRJNA489308	Other	Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.				H125	breed:AB strain\|age:3 month\|sex:male\|tissue:Peripheral blood\|genotype:Tol2 EVI 1 EGFP transgenic\|replicate:replicate2\|BioSampleModel:Model organism or animal									H125	H125	H125	Tol2 EVI 1 EGFP transgenic zebrafish sample 2			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP159583		H125_S2_L001_R1_001.fastq.gz H125_S2_L001_R2_001.fastq.gz	fastq fastq	16012998000.0	53376660.0	H125 S2 L001 R1 001.fastq.gz	0:150 1:150	A:4365269809;C:3662731840;G:3768367416;T:4216409682;N:219253	150	150	4365269809	3662731840	3768367416	4216409682	219253	SRX4640370	SRS3738588	SRA766519	Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University\|Department: Department of Haematology	Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University	2	0.9402	0.94198	0.09449	0.09528	0.71999	0.72512	0.46106	0.47624	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	bulk	unknown	unknown	China	2018-09-04	Adult	Adult	Blood	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
51876	51876	SRR8922974	SRX5704273	SRS4643334	SRP192854	PRJNA533283	RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish	GSE129952	Transcriptome Analysis	The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.			erythroid cells: WT6	GSM3728533	tissue:erythroid cells\|age:24 hpf type:gata1 positive erythroid cells\|genotype/variation:wild type	erythroid cells: WT6	basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample	erythroid cells		Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.		age:24 hpf type:gata1 positive erythroid cells\|genotype/variation:wild type	GSM3728533	GSM3728533: erythroid cells: WT6; Danio rerio; RNA Seq	GSM3728533		1	Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.	GEO Accession:GSM3728533	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP192854		J633_AHFHNLBGX2_TAGCTT_LWT6.1_val_1.fq.gz J633_AHFHNLBGX2_TAGCTT_LWT6.2_val_2.fq.gz	fastq fastq	8611605345.0	32335443.0	GSM3728533 r1	0:133.59 1:132.74	A:1724489451;C:2542199793;G:2626828499;T:1716562999;N:1524603	133	132	1724489451	2542199793	2626828499	1716562999	1524603	SRX5704273	SRS4643334	SRA875634	GEO	Albert Einstein College of Medicine	2	0.91241	0.96131	0.10384	0.10826	0.77761	0.7767	0.69985	0.69519	128	128	B	B	biological fallback assumption	illumina	nextseq	full_length	rrna_depletion	smarter	bulk	unknown	unknown	United States	2019-04-17	Pharyngula	Embryo	Blood	Hematopoietic System
51877	51877	SRR8922973	SRX5704272	SRS4643333	SRP192854	PRJNA533283	RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish	GSE129952	Transcriptome Analysis	The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.			erythroid cells: WT5	GSM3728532	tissue:erythroid cells\|age:24 hpf type:gata1 positive erythroid cells\|genotype/variation:wild type	erythroid cells: WT5	basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample	erythroid cells		Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.		age:24 hpf type:gata1 positive erythroid cells\|genotype/variation:wild type	GSM3728532	GSM3728532: erythroid cells: WT5; Danio rerio; RNA Seq	GSM3728532		1	Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.	GEO Accession:GSM3728532	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP192854		J633_AHFHNLBGX2_TGACCA_LWT5.1_val_1.fq.gz J633_AHFHNLBGX2_TGACCA_LWT5.2_val_2.fq.gz	fastq fastq	8110446942.0	28906836.0	GSM3728532 r1	0:140.70 1:139.87	A:1479901358;C:2533764326;G:2613647627;T:1481710129;N:1423502	140	139	1479901358	2533764326	2613647627	1481710129	1423502	SRX5704272	SRS4643333	SRA875634	GEO	Albert Einstein College of Medicine	2	0.92578	0.97511	0.09182	0.09201	0.80503	0.80324	0.76985	0.7675	150	150	B	B	biological fallback assumption	illumina	nextseq	full_length	rrna_depletion	smarter	bulk	unknown	unknown	United States	2019-04-17	Pharyngula	Embryo	Blood	Hematopoietic System
51878	51878	SRR8922972	SRX5704271	SRS4643332	SRP192854	PRJNA533283	RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish	GSE129952	Transcriptome Analysis	The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.			erythroid cells: WT4	GSM3728531	tissue:erythroid cells\|age:24 hpf type:gata1 positive erythroid cells\|genotype/variation:wild type	erythroid cells: WT4	basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample	erythroid cells		Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.		age:24 hpf type:gata1 positive erythroid cells\|genotype/variation:wild type	GSM3728531	GSM3728531: erythroid cells: WT4; Danio rerio; RNA Seq	GSM3728531		1	Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.	GEO Accession:GSM3728531	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP192854		J633_AHFHNLBGX2_TTAGGC_LWT4.2_val_2.fq.gz J633_AHFHNLBGX2_TTAGGC_LWT4.1_val_1.fq.gz	fastq fastq	8627466135.0	32957109.0	GSM3728531 r1	0:131.12 1:130.66	A:1686521982;C:2592728511;G:2670950174;T:1675745501;N:1519967	131	130	1686521982	2592728511	2670950174	1675745501	1519967	SRX5704271	SRS4643332	SRA875634	GEO	Albert Einstein College of Medicine	2	0.91773	0.96731	0.11151	0.1134	0.78792	0.78597	0.73657	0.73692	104	104	B	B	biological fallback assumption	illumina	nextseq	full_length	rrna_depletion	smarter	bulk	unknown	unknown	United States	2019-04-17	Pharyngula	Embryo	Blood	Hematopoietic System
51879	51879	SRR8922971	SRX5704270	SRS4643331	SRP192854	PRJNA533283	RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish	GSE129952	Transcriptome Analysis	The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.			erythroid cells: WT3	GSM3728530	tissue:erythroid cells\|age:24 hpf type:gata1 positive erythroid cells\|genotype/variation:wild type	erythroid cells: WT3	basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample	erythroid cells		Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.		age:24 hpf type:gata1 positive erythroid cells\|genotype/variation:wild type	GSM3728530	GSM3728530: erythroid cells: WT3; Danio rerio; RNA Seq	GSM3728530		1	Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.	GEO Accession:GSM3728530	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP192854		J633_AHFHNLBGX2_CGATGT_LWT3.2_val_2.fq.gz J633_AHFHNLBGX2_CGATGT_LWT3.1_val_1.fq.gz	fastq fastq	7675701402.0	28099783.0	GSM3728530 r1	0:136.90 1:136.26	A:1496106079;C:2307580110;G:2386093773;T:1484556287;N:1365153	136	136	1496106079	2307580110	2386093773	1484556287	1365153	SRX5704270	SRS4643331	SRA875634	GEO	Albert Einstein College of Medicine	2	0.91833	0.96754	0.10771	0.10822	0.80135	0.80158	0.76757	0.7524	150	150	B	B	biological fallback assumption	illumina	nextseq	full_length	rrna_depletion	smarter	bulk	unknown	unknown	United States	2019-04-17	Pharyngula	Embryo	Blood	Hematopoietic System
51880	51880	SRR8922970	SRX5704269	SRS4643330	SRP192854	PRJNA533283	RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish	GSE129952	Transcriptome Analysis	The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.			erythroid cells: WT2	GSM3728529	tissue:erythroid cells\|age:24 hpf type:gata1 positive erythroid cells\|genotype/variation:sf3b1 mutant	erythroid cells: WT2	basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample	erythroid cells		Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.		age:24 hpf type:gata1 positive erythroid cells\|genotype/variation:sf3b1 mutant	GSM3728529	GSM3728529: erythroid cells: WT2; Danio rerio; RNA Seq	GSM3728529		1	Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.	GEO Accession:GSM3728529	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP192854		J633_AHFHNLBGX2_ATCACG_LWT2.2_val_2.fq.gz J633_AHFHNLBGX2_ATCACG_LWT2.1_val_1.fq.gz	fastq fastq	8749226933.0	32236600.0	GSM3728529 r1	0:135.97 1:135.43	A:1818348438;C:2523018672;G:2595068272;T:1811215171;N:1576380	135	135	1818348438	2523018672	2595068272	1811215171	1576380	SRX5704269	SRS4643330	SRA875634	GEO	Albert Einstein College of Medicine	2	0.91533	0.96543	0.12825	0.13005	0.77394	0.77344	0.70772	0.67993	143	143	B	B	biological fallback assumption	illumina	nextseq	full_length	rrna_depletion	smarter	bulk	unknown	unknown	United States	2019-04-17	Pharyngula	Embryo	Blood	Hematopoietic System

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