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62 rows where experiment.library_selection = "cDNA", technology = "unknown" and tissue_curation = "Spleen"

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devstage_curation_coarse 3

devstage_curation 3

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Spleen · 62 ✖

technology 1

  • unknown · 62 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 62 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
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
47583 47583 SRR6661157 SRX3638253 SRS2904504 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplWTPHZ 3 GSM2975201   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type SplWTPHZ 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type GSM2975201 GSM2975201: SplWTPHZ 3; Danio rerio; RNA Seq GSM2975201   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975201 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplWTPHZ_3.fastq.gz fastq 863137362.0 16924262.0 GSM2975201 r1 0:51 A:243029420;C:186621398;G:190769119;T:242704294;N:13131 51       243029420 186621398 190769119 242704294 13131 SRX3638253 SRS2904504 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.94871   0.18797   0.7289   0.48689   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47584 47584 SRR6661156 SRX3638252 SRS2904503 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplWTPHZ 2 GSM2975200   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type SplWTPHZ 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type GSM2975200 GSM2975200: SplWTPHZ 2; Danio rerio; RNA Seq GSM2975200   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975200 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplWTPHZ_2.fastq.gz fastq 748057494.0 14667794.0 GSM2975200 r1 0:51 A:212731080;C:159238564;G:163993235;T:212082953;N:11662 51       212731080 159238564 163993235 212082953 11662 SRX3638252 SRS2904503 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.94641   0.22364   0.7264   0.48998   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47585 47585 SRR6661155 SRX3638251 SRS2904502 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplWTPHZ 1 GSM2975199   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type SplWTPHZ 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type GSM2975199 GSM2975199: SplWTPHZ 1; Danio rerio; RNA Seq GSM2975199   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975199 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplWTPHZ_1.fastq.gz fastq 771862917.0 15134567.0 GSM2975199 r1 0:51 A:220317243;C:164032479;G:167543123;T:219958265;N:11807 51       220317243 164032479 167543123 219958265 11807 SRX3638251 SRS2904502 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.94835   0.1926   0.71453   0.48677   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47586 47586 SRR6661154 SRX3638250 SRS2904501 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplWT 3 GSM2975198   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type SplWT 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type GSM2975198 GSM2975198: SplWT 3; Danio rerio; RNA Seq GSM2975198   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975198 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplWT_3.fastq.gz fastq 815973888.0 15999488.0 GSM2975198 r1 0:51 A:236186435;C:169473350;G:175246943;T:235055142;N:12018 51       236186435 169473350 175246943 235055142 12018 SRX3638250 SRS2904501 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.94554   0.25855   0.71873   0.54675   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47587 47587 SRR6661153 SRX3638249 SRS2904499 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplWT 2 GSM2975197   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type SplWT 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type GSM2975197 GSM2975197: SplWT 2; Danio rerio; RNA Seq GSM2975197   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975197 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplWT_2.fastq.gz fastq 909644262.0 17836162.0 GSM2975197 r1 0:51 A:259661486;C:192636111;G:198048163;T:259284494;N:14008 51       259661486 192636111 198048163 259284494 14008 SRX3638249 SRS2904499 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.94781   0.22979   0.69962   0.49839   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47588 47588 SRR6661152 SRX3638248 SRS2904500 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplWT 1 GSM2975196   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type SplWT 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type GSM2975196 GSM2975196: SplWT 1; Danio rerio; RNA Seq GSM2975196   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975196 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplWT_1.fastq.gz fastq 888755274.0 17426574.0 GSM2975196 r1 0:51 A:241072815;C:200347978;G:205733626;T:241587449;N:13406 51       241072815 200347978 205733626 241587449 13406 SRX3638248 SRS2904500 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.95759   0.1342   0.72918   0.52233   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47589 47589 SRR6661151 SRX3638247 SRS2904498 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplDKOPHZ 3 GSM2975195   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO SplDKOPHZ 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975195 GSM2975195: SplDKOPHZ 3; Danio rerio; RNA Seq GSM2975195   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975195 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplDKOPHZ_3.fastq.gz fastq 881441160.0 17283160.0 GSM2975195 r1 0:51 A:243254581;C:194198200;G:199055092;T:244919975;N:13312 51       243254581 194198200 199055092 244919975 13312 SRX3638247 SRS2904498 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.90441   0.14881   0.71447   0.51129   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47590 47590 SRR6661150 SRX3638246 SRS2904497 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplDKOPHZ 2 GSM2975194   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO SplDKOPHZ 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975194 GSM2975194: SplDKOPHZ 2; Danio rerio; RNA Seq GSM2975194   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975194 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplDKOPHZ_2.fastq.gz fastq 795840414.0 15604714.0 GSM2975194 r1 0:51 A:229921467;C:166126021;G:170186584;T:229594266;N:12076 51       229921467 166126021 170186584 229594266 12076 SRX3638246 SRS2904497 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.88657   0.23556   0.7194   0.51207   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47591 47591 SRR6661149 SRX3638245 SRS2904495 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplDKOPHZ 1 GSM2975193   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO SplDKOPHZ 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975193 GSM2975193: SplDKOPHZ 1; Danio rerio; RNA Seq GSM2975193   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975193 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplDKOPHZ_1.fastq.gz fastq 788951436.0 15469636.0 GSM2975193 r1 0:51 A:217408862;C:175236911;G:178930271;T:217363444;N:11948 51       217408862 175236911 178930271 217363444 11948 SRX3638245 SRS2904495 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.90945   0.10065   0.72468   0.48596   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47592 47592 SRR6661148 SRX3638244 SRS2904496 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplDKO 3 GSM2975192   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO SplDKO 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975192 GSM2975192: SplDKO 3; Danio rerio; RNA Seq GSM2975192   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975192 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplDKO_3.fastq.gz fastq 732609543.0 14364893.0 GSM2975192 r1 0:51 A:209020386;C:154988652;G:160405898;T:208183578;N:11029 51       209020386 154988652 160405898 208183578 11029 SRX3638244 SRS2904496 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.88228   0.23609   0.72529   0.50392   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47593 47593 SRR6661147 SRX3638243 SRS2904493 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplDKO 2 GSM2975191   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO SplDKO 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975191 GSM2975191: SplDKO 2; Danio rerio; RNA Seq GSM2975191   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975191 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplDKO_2.fastq.gz fastq 747985635.0 14666385.0 GSM2975191 r1 0:51 A:209892939;C:160527969;G:165683955;T:211869190;N:11582 51       209892939 160527969 165683955 211869190 11582 SRX3638243 SRS2904493 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.90267   0.20054   0.7249   0.53668   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47594 47594 SRR6661146 SRX3638242 SRS2904494 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplDKO 1 GSM2975190   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO SplDKO 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975190 GSM2975190: SplDKO 1; Danio rerio; RNA Seq GSM2975190   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975190 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplDKO_1.fastq.gz fastq 724574391.0 14207341.0 GSM2975190 r1 0:51 A:207549130;C:151913145;G:156789401;T:208311727;N:10988 51       207549130 151913145 156789401 208311727 10988 SRX3638242 SRS2904494 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.89742   0.2275   0.71547   0.5072   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
49748 49748 SRR8040452 SRX4870965 SRS3925946 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t32lps5 RNA seq GSM3427234   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t32lps5 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427234 GSM3427234: t32lps5 RNA seq; Danio rerio; RNA Seq GSM3427234   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427234 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2525095950.0 33667946.0 GSM3427234 r1 0:75 1:0 A:654325529;C:574214700;G:560979222;T:735543925;N:32574 75 0     654325529 574214700 560979222 735543925 32574 SRX4870965 SRS3925946 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.94279   0.11158   0.7739   0.56131   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49749 49749 SRR8040451 SRX4870964 SRS3925945 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t32lps4 RNA seq GSM3427233   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t32lps4 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427233 GSM3427233: t32lps4 RNA seq; Danio rerio; RNA Seq GSM3427233   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427233 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2324475900.0 30993012.0 GSM3427233 r1 0:75 1:0 A:593299460;C:533734154;G:526980483;T:670430972;N:30831 75 0     593299460 533734154 526980483 670430972 30831 SRX4870964 SRS3925945 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.9455   0.10812   0.78046   0.55958   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49750 49750 SRR8040450 SRX4870962 SRS3925943 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t32lps3 RNA seq GSM3427232   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t32lps3 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427232 GSM3427232: t32lps3 RNA seq; Danio rerio; RNA Seq GSM3427232   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427232 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2390945250.0 31879270.0 GSM3427232 r1 0:75 1:0 A:620617289;C:546536575;G:538087155;T:685671110;N:33121 75 0     620617289 546536575 538087155 685671110 33121 SRX4870962 SRS3925943 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.94216   0.12594   0.74925   0.54113   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49751 49751 SRR8040449 SRX4870961 SRS3925942 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t32lps2 RNA seq GSM3427231   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t32lps2 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427231 GSM3427231: t32lps2 RNA seq; Danio rerio; RNA Seq GSM3427231   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427231 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2372211900.0 31629492.0 GSM3427231 r1 0:75 1:0 A:609244327;C:553579722;G:546387461;T:662968297;N:32093 75 0     609244327 553579722 546387461 662968297 32093 SRX4870961 SRS3925942 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.91064   0.09975   0.7318   0.52325   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49752 49752 SRR8040448 SRX4870960 SRS3925941 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t32lps1 RNA seq GSM3427230   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t32lps1 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427230 GSM3427230: t32lps1 RNA seq; Danio rerio; RNA Seq GSM3427230   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427230 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2601300000.0 34684000.0 GSM3427230 r1 0:75 1:0 A:696279292;C:582818011;G:571718581;T:750447755;N:36361 75 0     696279292 582818011 571718581 750447755 36361 SRX4870960 SRS3925941 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.93957   0.13624   0.74641   0.53521   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49753 49753 SRR8040447 SRX4870959 SRS3925940 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t32ct10 RNA seq GSM3427229   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t32ct10 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427229 GSM3427229: t32ct10 RNA seq; Danio rerio; RNA Seq GSM3427229   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427229 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2206367925.0 29418239.0 GSM3427229 r1 0:75 1:0 A:564695219;C:513292663;G:507293808;T:621057423;N:28812 75 0     564695219 513292663 507293808 621057423 28812 SRX4870959 SRS3925940 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.94594   0.10744   0.75511   0.39959   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49754 49754 SRR8040446 SRX4870958 SRS3925939 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t32ct8 RNA seq GSM3427228   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t32ct8 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427228 GSM3427228: t32ct8 RNA seq; Danio rerio; RNA Seq GSM3427228   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427228 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2160654900.0 28808732.0 GSM3427228 r1 0:75 1:0 A:560268124;C:491395956;G:494788088;T:614174312;N:28420 75 0     560268124 491395956 494788088 614174312 28420 SRX4870958 SRS3925939 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.91437   0.1131   0.74661   0.54441   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49755 49755 SRR8040445 SRX4870957 SRS3925938 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t32ct6 RNA seq GSM3427227   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t32ct6 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427227 GSM3427227: t32ct6 RNA seq; Danio rerio; RNA Seq GSM3427227   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427227 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2175448725.0 29005983.0 GSM3427227 r1 0:75 1:0 A:588911336;C:487829921;G:471925092;T:626753522;N:28854 75 0     588911336 487829921 471925092 626753522 28854 SRX4870957 SRS3925938 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.93789   0.14514   0.73839   0.51589   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49756 49756 SRR8040444 SRX4870956 SRS3925937 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t32ct3 RNA seq GSM3427226   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t32ct3 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427226 GSM3427226: t32ct3 RNA seq; Danio rerio; RNA Seq GSM3427226   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427226 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2350450425.0 31339339.0 GSM3427226 r1 0:75 1:0 A:612558543;C:533417342;G:511898107;T:692543546;N:32887 75 0     612558543 533417342 511898107 692543546 32887 SRX4870956 SRS3925937 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.88939   0.13696   0.74649   0.5071   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49757 49757 SRR8040443 SRX4870955 SRS3925936 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t32ct2 RNA seq GSM3427225   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t32ct2 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427225 GSM3427225: t32ct2 RNA seq; Danio rerio; RNA Seq GSM3427225   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427225 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2500728150.0 33343042.0 GSM3427225 r1 0:75 1:0 A:663109698;C:565815864;G:564300306;T:707468578;N:33704 75 0     663109698 565815864 564300306 707468578 33704 SRX4870955 SRS3925936 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.92821   0.27272   0.71969   0.48781   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49758 49758 SRR8040442 SRX4870954 SRS3925988 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t28lps8 RNA seq GSM3427224   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t28lps8 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427224 GSM3427224: t28lps8 RNA seq; Danio rerio; RNA Seq GSM3427224   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427224 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2342903700.0 31238716.0 GSM3427224 r1 0:75 1:0 A:613986696;C:535703169;G:527411229;T:665771221;N:31385 75 0     613986696 535703169 527411229 665771221 31385 SRX4870954 SRS3925988 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.92238   0.11108   0.75223   0.54609   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49759 49759 SRR8040441 SRX4870953 SRS3925935 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t28lps4 RNA seq GSM3427223   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t28lps4 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427223 GSM3427223: t28lps4 RNA seq; Danio rerio; RNA Seq GSM3427223   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427223 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2009201550.0 26789354.0 GSM3427223 r1 0:75 1:0 A:503118595;C:466998217;G:461838042;T:577221133;N:25563 75 0     503118595 466998217 461838042 577221133 25563 SRX4870953 SRS3925935 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.85044   0.10362   0.78149   0.59209   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49760 49760 SRR8040440 SRX4870952 SRS3925934 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t28lps3 RNA seq GSM3427222   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t28lps3 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427222 GSM3427222: t28lps3 RNA seq; Danio rerio; RNA Seq GSM3427222   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427222 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2262918375.0 30172245.0 GSM3427222 r1 0:75 1:0 A:557712391;C:559312209;G:525961809;T:619902191;N:29775 75 0     557712391 559312209 525961809 619902191 29775 SRX4870952 SRS3925934 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.75792   0.0861   0.77977   0.47016   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49761 49761 SRR8040439 SRX4870951 SRS3925933 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t28lps2 RNA seq GSM3427221   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t28lps2 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427221 GSM3427221: t28lps2 RNA seq; Danio rerio; RNA Seq GSM3427221   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427221 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2362744425.0 31503259.0 GSM3427221 r1 0:75 1:0 A:605359081;C:550864600;G:543725417;T:662762619;N:32708 75 0     605359081 550864600 543725417 662762619 32708 SRX4870951 SRS3925933 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.92027   0.10164   0.7403   0.52342   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49762 49762 SRR8040438 SRX4870950 SRS3925932 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t28lps1 RNA seq GSM3427220   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t28lps1 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427220 GSM3427220: t28lps1 RNA seq; Danio rerio; RNA Seq GSM3427220   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427220 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2219433000.0 29592440.0 GSM3427220 r1 0:75 1:0 A:559427934;C:519857518;G:513429485;T:626687457;N:30606 75 0     559427934 519857518 513429485 626687457 30606 SRX4870950 SRS3925932 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.89861   0.09731   0.76889   0.4978   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49763 49763 SRR8040437 SRX4870949 SRS3925931 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t28ct7 RNA seq GSM3427219   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t28ct7 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427219 GSM3427219: t28ct7 RNA seq; Danio rerio; RNA Seq GSM3427219   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427219 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2329584075.0 31061121.0 GSM3427219 r1 0:75 1:0 A:624440550;C:517755267;G:499439713;T:687917841;N:30704 75 0     624440550 517755267 499439713 687917841 30704 SRX4870949 SRS3925931 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.88755   0.13982   0.75739   0.56552   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49764 49764 SRR8040436 SRX4870948 SRS3925930 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t28ct5 RNA seq GSM3427218   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t28ct5 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427218 GSM3427218: t28ct5 RNA seq; Danio rerio; RNA Seq GSM3427218   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427218 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2116347225.0 28217963.0 GSM3427218 r1 0:75 1:0 A:549735276;C:488049942;G:477129323;T:601405177;N:27507 75 0     549735276 488049942 477129323 601405177 27507 SRX4870948 SRS3925930 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.94198   0.11445   0.75487   0.53068   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49765 49765 SRR8040435 SRX4870947 SRS3925929 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t28ct3 RNA seq GSM3427217   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t28ct3 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427217 GSM3427217: t28ct3 RNA seq; Danio rerio; RNA Seq GSM3427217   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427217 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2689388775.0 35858517.0 GSM3427217 r1 0:75 1:0 A:723021338;C:600600385;G:595495733;T:770233672;N:37647 75 0     723021338 600600385 595495733 770233672 37647 SRX4870947 SRS3925929 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.9433   0.12005   0.75175   0.52805   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49766 49766 SRR8040434 SRX4870946 SRS3925927 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t28ct2 RNA seq GSM3427216   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t28ct2 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427216 GSM3427216: t28ct2 RNA seq; Danio rerio; RNA Seq GSM3427216   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427216 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2358123450.0 31441646.0 GSM3427216 r1 0:75 1:0 A:608599109;C:548957677;G:537939593;T:662594226;N:32845 75 0     608599109 548957677 537939593 662594226 32845 SRX4870946 SRS3925927 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.93343   0.09904   0.73701   0.50221   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49767 49767 SRR8040433 SRX4870945 SRS3925928 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t28ct1 RNA seq GSM3427215   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t28ct1 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427215 GSM3427215: t28ct1 RNA seq; Danio rerio; RNA Seq GSM3427215   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427215 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2340413625.0 31205515.0 GSM3427215 r1 0:75 1:0 A:601455783;C:547481954;G:534319560;T:657124045;N:32283 75 0     601455783 547481954 534319560 657124045 32283 SRX4870945 SRS3925928 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.91963   0.11224   0.7363   0.52602   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49768 49768 SRR8040432 SRX4870944 SRS3925926 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t24lps8 RNA seq GSM3427214   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t24lps8 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427214 GSM3427214: t24lps8 RNA seq; Danio rerio; RNA Seq GSM3427214   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427214 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         1914339900.0 25524532.0 GSM3427214 r1 0:75 1:0 A:512209644;C:432894621;G:420067370;T:549142945;N:25320 75 0     512209644 432894621 420067370 549142945 25320 SRX4870944 SRS3925926 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.92034   0.12782   0.73777   0.53097   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49769 49769 SRR8040431 SRX4870943 SRS3925925 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t24lps4 RNA seq GSM3427213   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t24lps4 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427213 GSM3427213: t24lps4 RNA seq; Danio rerio; RNA Seq GSM3427213   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427213 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2137202850.0 28496038.0 GSM3427213 r1 0:75 1:0 A:542475947;C:498947754;G:490366774;T:605383850;N:28525 75 0     542475947 498947754 490366774 605383850 28525 SRX4870943 SRS3925925 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.91347   0.09882   0.75763   0.46833   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49770 49770 SRR8040430 SRX4870942 SRS3925924 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t24lps3 RNA seq GSM3427212   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t24lps3 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427212 GSM3427212: t24lps3 RNA seq; Danio rerio; RNA Seq GSM3427212   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427212 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2514206700.0 33522756.0 GSM3427212 r1 0:75 1:0 A:663829025;C:573707517;G:558298485;T:718336661;N:35012 75 0     663829025 573707517 558298485 718336661 35012 SRX4870942 SRS3925924 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.93997   0.11968   0.74241   0.53459   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49771 49771 SRR8040429 SRX4870941 SRS3925923 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t24lps2 RNA seq GSM3427211   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t24lps2 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427211 GSM3427211: t24lps2 RNA seq; Danio rerio; RNA Seq GSM3427211   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427211 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2502607650.0 33368102.0 GSM3427211 r1 0:75 1:0 A:659207653;C:572452612;G:556598074;T:714314698;N:34613 75 0     659207653 572452612 556598074 714314698 34613 SRX4870941 SRS3925923 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.92032   0.12899   0.7441   0.52707   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49772 49772 SRR8040428 SRX4870940 SRS3925921 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t24lps1 RNA seq GSM3427210   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t24lps1 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427210 GSM3427210: t24lps1 RNA seq; Danio rerio; RNA Seq GSM3427210   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427210 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2301013650.0 30680182.0 GSM3427210 r1 0:75 1:0 A:600014931;C:531214958;G:529006695;T:640746698;N:30368 75 0     600014931 531214958 529006695 640746698 30368 SRX4870940 SRS3925921 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.94819   0.10959   0.74706   0.44871   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49773 49773 SRR8040427 SRX4870939 SRS3925922 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t24ct8 RNA seq GSM3427209   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t24ct8 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427209 GSM3427209: t24ct8 RNA seq; Danio rerio; RNA Seq GSM3427209   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427209 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2196418725.0 29285583.0 GSM3427209 r1 0:75 1:0 A:573278624;C:504375268;G:494497295;T:624238861;N:28677 75 0     573278624 504375268 494497295 624238861 28677 SRX4870939 SRS3925922 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.94225   0.11903   0.75051   0.55244   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49774 49774 SRR8040426 SRX4870938 SRS3925919 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t24ct5 RNA seq GSM3427208   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t24ct5 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427208 GSM3427208: t24ct5 RNA seq; Danio rerio; RNA Seq GSM3427208   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427208 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2267199975.0 30229333.0 GSM3427208 r1 0:75 1:0 A:584789099;C:523482900;G:517770578;T:641127463;N:29935 75 0     584789099 523482900 517770578 641127463 29935 SRX4870938 SRS3925919 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.88505   0.11534   0.74566   0.55279   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49775 49775 SRR8040425 SRX4870937 SRS3925920 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t24ct4 RNA seq GSM3427207   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t24ct4 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427207 GSM3427207: t24ct4 RNA seq; Danio rerio; RNA Seq GSM3427207   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427207 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2127502425.0 28366699.0 GSM3427207 r1 0:75 1:0 A:543019165;C:503067510;G:498801425;T:582586507;N:27818 75 0     543019165 503067510 498801425 582586507 27818 SRX4870937 SRS3925920 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.9223   0.07915   0.72401   0.51588   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49776 49776 SRR8040424 SRX4870936 SRS3925917 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t24ct3 RNA seq GSM3427206   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t24ct3 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427206 GSM3427206: t24ct3 RNA seq; Danio rerio; RNA Seq GSM3427206   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427206 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2708072025.0 36107627.0 GSM3427206 r1 0:75 1:0 A:672991238;C:642923577;G:634295347;T:757824608;N:37255 75 0     672991238 642923577 634295347 757824608 37255 SRX4870936 SRS3925917 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.95238   0.09   0.75513   0.52869   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
49777 49777 SRR8040423 SRX4870935 SRS3925918 SRP165277 PRJNA495917 Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish GSE121163 Transcriptome Analysis Zebrafish eggs were collected at 28 °C and split into three embryonic incubation temperature groups 24 °C 28 °C 32 °C. When larvae reaching first feeding the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C and all fish were kept at 28 °C for later development until maturity. At 100 dpf 7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10 while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection the spleen was dissected and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally 251 differentially expressed genes DEGs 71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2 adjusted p value < 0.05 |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control 567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C 140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C 28 °C 32 °C. parent bioproject:PRJNA495914     t24ct2 RNA seq GSM3427205   tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf t24ct2 RNA seq Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library spleen Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich USA and kept for 12 h. Then fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately snap frozen in liquid nitrogen and stored at 80 °C. Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services SDS UK 100 200 300 and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark. strain:AB|developmental stage:adult|age:100 dpf GSM3427205 GSM3427205: t24ct2 RNA seq; Danio rerio; RNA Seq GSM3427205   1 Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific USA with some modifications. In brief spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube mixed thoroughly with 100 μl 70% Ethanol and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB USA. Fifty ng total RNAs from each replicate were purified with OligodT beads fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s 1 cycle; 98 °C for 10 s 65 °C for 75 s 14 cycles; 65 °C for 5 min 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies USA. GEO Accession:GSM3427205 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP165277         2495119875.0 33268265.0 GSM3427205 r1 0:75 1:0 A:627918584;C:589525055;G:590001770;T:687639074;N:35392 75 0     627918584 589525055 590001770 687639074 35392 SRX4870935 SRS3925918 SRA793499 GEO Faculty of Biosciences and Aquaculture, Nord University 1 0.95519   0.08888   0.74746   0.44744   75   B   usable mapping rate illumina nextseq 5prime poly_a nebnext bulk unknown unknown   Norway 2018-10-12 Adult Adult Spleen Hematopoietic System
53009 53009 SRR9662030 SRX6422906 SRS5079696 SRP213938 PRJNA553572 A map of cis regulatory elements and 3D genome structures in zebrafish GSE134055 Other The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.   pubmed:33239788;pubmed:35649578   YueLab RNA Seq Spleen rep2 GSM3934898   source name:Tissue|strain:Tuebingen|tissue:Spleen YueLab RNA Seq Spleen rep2 RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged Tissue   For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions strain:Tuebingen|tissue:Spleen GSM3934898 GSM3934898: YueLab RNA Seq Spleen rep2; Danio rerio; RNA Seq GSM3934898   1 For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. GEO Accession:GSM3934898 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer   SRP213938     YueLab-RNA-Seq-Spleen-rep2_1.fastq.gz YueLab-RNA-Seq-Spleen-rep2_2.fastq.gz fastq fastq 8309777463.0 41837414.0 GSM3934898 r1 0:98.87 1:99.75 A:2235106866;C:1723612712;G:1748992271;T:2601473305;N:592309 98 99     2235106866 1723612712 1748992271 2601473305 592309 SRX6422906 SRS5079696 SRA919194 GEO Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine 2 0.9718 0.97965 0.15676 0.11996 0.7347 0.73831 0.49813 0.50156 99 100 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2019-07-09 Pharyngula Embryo Spleen Hematopoietic System
53010 53010 SRR9662029 SRX6422905 SRS5079695 SRP213938 PRJNA553572 A map of cis regulatory elements and 3D genome structures in zebrafish GSE134055 Other The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.   pubmed:33239788;pubmed:35649578   YueLab RNA Seq Spleen rep1 GSM3934897   source name:Tissue|strain:Tuebingen|tissue:Spleen YueLab RNA Seq Spleen rep1 RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged Tissue   For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions strain:Tuebingen|tissue:Spleen GSM3934897 GSM3934897: YueLab RNA Seq Spleen rep1; Danio rerio; RNA Seq GSM3934897   1 For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. GEO Accession:GSM3934897 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer   SRP213938     YueLab-RNA-Seq-Spleen-rep1_1.fastq.gz YueLab-RNA-Seq-Spleen-rep1_2.fastq.gz fastq fastq 1940987484.0 9748717.0 GSM3934897 r1 0:99.62 1:99.48 A:522271746;C:424963046;G:430836475;T:562779653;N:136564 99 99     522271746 424963046 430836475 562779653 136564 SRX6422905 SRS5079695 SRA919194 GEO Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine 2 0.97325 0.97976 0.13741 0.12217 0.72129 0.73261 0.50119 0.4956 100 99 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2019-07-09 Pharyngula Embryo Spleen Hematopoietic System
62766 62766 SRR13374851 SRX9798198 SRS7982915 SRP300698 PRJNA690124 Investigation of Zebrafish Endogenous Retroviruses PRJNA690124 Other Shed Light on Zebrafish Endogenous Retrovirus like elements: Survey of the Composition Phylogeny and Expression         Spleen3   strain:AB|dev stage:adult|sex:male and female|tissue:spleen|health state:health|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: adult: spleen T21 T21 RNA extracted from tissue     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP300698     Spleen3.R1.fastq.gz Spleen3.R2.fastq.gz fastq fastq 6944249608.0 22994204.0 Spleen3.R1.fastq.gz 0:151 1:151 A:1791694656;C:1670042370;G:1729203945;T:1753264854;N:43783 151 151     1791694656 1670042370 1729203945 1753264854 43783 SRX9798198 SRS7982915 SRA1181129 Zhejiang University|College of life science Zhejiang University 2 0.94268 0.895 0.04275 0.0401 0.75716 0.76414 0.44872 0.45146 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2021-01-06 Adult Adult Spleen Hematopoietic System
62768 62768 SRR13374853 SRX9798196 SRS7982913 SRP300698 PRJNA690124 Investigation of Zebrafish Endogenous Retroviruses PRJNA690124 Other Shed Light on Zebrafish Endogenous Retrovirus like elements: Survey of the Composition Phylogeny and Expression         Spleen2   strain:AB|dev stage:adult|sex:male and female|tissue:spleen|health state:health|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: adult: spleen T20 T20 RNA extracted from tissue     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP300698     Spleen2.R1.fastq.gz Spleen2.R2.fastq.gz fastq fastq 6804474646.0 22531373.0 Spleen2.R1.fastq.gz 0:151 1:151 A:1776770612;C:1626287076;G:1682882382;T:1718492267;N:42309 151 151     1776770612 1626287076 1682882382 1718492267 42309 SRX9798196 SRS7982913 SRA1181129 Zhejiang University|College of life science Zhejiang University 2 0.93567 0.88963 0.04922 0.04623 0.74257 0.75041 0.50033 0.4547 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2021-01-06 Adult Adult Spleen Hematopoietic System
62769 62769 SRR13374854 SRX9798195 SRS7982912 SRP300698 PRJNA690124 Investigation of Zebrafish Endogenous Retroviruses PRJNA690124 Other Shed Light on Zebrafish Endogenous Retrovirus like elements: Survey of the Composition Phylogeny and Expression         Spleen1   strain:AB|dev stage:adult|sex:male and female|tissue:spleen|health state:health|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: adult: spleen T19 T19 RNA extracted from tissue     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP300698     Spleen1.R1.fastq.gz Spleen1.R2.fastq.gz fastq fastq 6574224108.0 21768954.0 Spleen1.R1.fastq.gz 0:151 1:151 A:1751438977;C:1525086872;G:1586987485;T:1710661856;N:48918 151 151     1751438977 1525086872 1586987485 1710661856 48918 SRX9798195 SRS7982912 SRA1181129 Zhejiang University|College of life science Zhejiang University 2 0.92679 0.88014 0.04944 0.04681 0.75199 0.75651 0.53852 0.53834 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2021-01-06 Adult Adult Spleen Hematopoietic System
62776 62776 SRR13376235 SRX9799599 SRS7984252 SRP300743 PRJNA690234 Expression of zebrafish endogenous retroviruses in response to SVCV infection PRJNA690234 Other Shed Light on Zebrafish Endogenous Retrovirus like elements: Survey of the Composition Phylogeny and Expression         Control Spleen 3   strain:AB|dev stage:adult|sex:male and female|tissue:spleen|treatment:injected with PBS|replicate:replicate = replicate 3|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: spleen: PBS T30 T30 adult zebrafish were injected with PBS RNA were extracted from spleen at xxxhpi     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP300743     Control_Spleen_3.R1.fastq.gz Control_Spleen_3.R2.fastq.gz fastq fastq 7550432766.0 25001433.0 Control Spleen 3.R1.fastq.gz 0:151 1:151 A:2018422580;C:1742507793;G:1796580720;T:1992799700;N:121973 151 151     2018422580 1742507793 1796580720 1992799700 121973 SRX9799599 SRS7984252 SRA1181241 Zhejiang University|College of life science Zhejiang University 2 0.92068 0.92127 0.06337 0.06399 0.68874 0.68822 0.47658 0.47523 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2021-01-07 Adult Adult Spleen Hematopoietic System
62777 62777 SRR13376236 SRX9799598 SRS7984251 SRP300743 PRJNA690234 Expression of zebrafish endogenous retroviruses in response to SVCV infection PRJNA690234 Other Shed Light on Zebrafish Endogenous Retrovirus like elements: Survey of the Composition Phylogeny and Expression         Control Spleen 2   strain:AB|dev stage:adult|sex:male and female|tissue:spleen|treatment:injected with PBS|replicate:replicate = replicate 2|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: spleen: PBS T29 T29 adult zebrafish were injected with PBS RNA were extracted from spleen at xxxhpi     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP300743     Control_Spleen_2.R1.fastq.gz Control_Spleen_2.R2.fastq.gz fastq fastq 10488973400.0 34731700.0 Control Spleen 2.R1.fastq.gz 0:151 1:151 A:2757134301;C:2413662609;G:2634278699;T:2683729731;N:168060 151 151     2757134301 2413662609 2634278699 2683729731 168060 SRX9799598 SRS7984251 SRA1181241 Zhejiang University|College of life science Zhejiang University 2 0.93334 0.93231 0.06005 0.05979 0.70532 0.70532 0.50937 0.50468 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2021-01-07 Adult Adult Spleen Hematopoietic System
62778 62778 SRR13376237 SRX9799597 SRS7984250 SRP300743 PRJNA690234 Expression of zebrafish endogenous retroviruses in response to SVCV infection PRJNA690234 Other Shed Light on Zebrafish Endogenous Retrovirus like elements: Survey of the Composition Phylogeny and Expression         Control Spleen 1   strain:AB|dev stage:adult|sex:male and female|tissue:spleen|treatment:injected with PBS|replicate:replicate = replicate 1|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: spleen: PBS T28 T28 adult zebrafish were injected with PBS RNA were extracted from spleen at xxxhpi     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP300743     Control_Spleen_1.R1.fastq.gz Control_Spleen_1.R2.fastq.gz fastq fastq 6933543406.0 22958753.0 Control Spleen 1.R1.fastq.gz 0:151 1:151 A:1839332870;C:1592223896;G:1685065238;T:1816810379;N:111023 151 151     1839332870 1592223896 1685065238 1816810379 111023 SRX9799597 SRS7984250 SRA1181241 Zhejiang University|College of life science Zhejiang University 2 0.9163 0.91686 0.04728 0.04769 0.69593 0.69615 0.46482 0.46496 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2021-01-07 Adult Adult Spleen Hematopoietic System
62783 62783 SRR13376242 SRX9799592 SRS7984245 SRP300743 PRJNA690234 Expression of zebrafish endogenous retroviruses in response to SVCV infection PRJNA690234 Other Shed Light on Zebrafish Endogenous Retrovirus like elements: Survey of the Composition Phylogeny and Expression         SVCV Spleen 3   strain:AB|dev stage:adult|sex:male and female|tissue:spleen|treatment:injected with SVCV|replicate:replicate = replicate 3|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: spleen: SVCV T39 T39 adult zebrafish were injected with SVCV RNA were extracted from spleen at xxxhpi     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP300743     SVCV_Spleen_3.R1.fastq.gz SVCV_Spleen_3.R2.fastq.gz fastq fastq 6444503028.0 21339414.0 SVCV Spleen 3.R1.fastq.gz 0:151 1:151 A:1714203208;C:1461493363;G:1592840158;T:1675864173;N:102126 151 151     1714203208 1461493363 1592840158 1675864173 102126 SRX9799592 SRS7984245 SRA1181241 Zhejiang University|College of life science Zhejiang University 2 0.91385 0.91498 0.06229 0.06243 0.70701 0.70832 0.49181 0.48908 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2021-01-07 Adult Adult Spleen Hematopoietic System
62784 62784 SRR13376243 SRX9799591 SRS7984244 SRP300743 PRJNA690234 Expression of zebrafish endogenous retroviruses in response to SVCV infection PRJNA690234 Other Shed Light on Zebrafish Endogenous Retrovirus like elements: Survey of the Composition Phylogeny and Expression         SVCV Spleen 2   strain:AB|dev stage:adult|sex:male and female|tissue:spleen|treatment:injected with SVCV|replicate:replicate = replicate 2|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: spleen: SVCV T38 T38 adult zebrafish were injected with SVCV RNA were extracted from spleen at xxxhpi     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP300743     SVCV_Spleen_2.R1.fastq.gz SVCV_Spleen_2.R2.fastq.gz fastq fastq 7381144250.0 24440875.0 SVCV Spleen 2.R1.fastq.gz 0:151 1:151 A:1990654513;C:1680305155;G:1777929120;T:1932136628;N:118834 151 151     1990654513 1680305155 1777929120 1932136628 118834 SRX9799591 SRS7984244 SRA1181241 Zhejiang University|College of life science Zhejiang University 2 0.91045 0.90637 0.06763 0.06729 0.69828 0.69867 0.48254 0.48277 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2021-01-07 Adult Adult Spleen Hematopoietic System
62785 62785 SRR13376244 SRX9799590 SRS7984243 SRP300743 PRJNA690234 Expression of zebrafish endogenous retroviruses in response to SVCV infection PRJNA690234 Other Shed Light on Zebrafish Endogenous Retrovirus like elements: Survey of the Composition Phylogeny and Expression         SVCV Spleen 1   strain:AB|dev stage:adult|sex:male and female|tissue:spleen|treatment:injected with SVCV|replicate:replicate = replicate 1|BioSampleModel:Model organism or animal                 RNA seq of zebrafish: spleen: SVCV T37 T37 adult zebrafish were injected with SVCV RNA were extracted from spleen at xxxhpi     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP300743     SVCV_Spleen_1.R1.fastq.gz SVCV_Spleen_1.R2.fastq.gz fastq fastq 6497966994.0 21516447.0 SVCV Spleen 1.R1.fastq.gz 0:151 1:151 A:1740978204;C:1501650940;G:1547916054;T:1707317926;N:103870 151 151     1740978204 1501650940 1547916054 1707317926 103870 SRX9799590 SRS7984243 SRA1181241 Zhejiang University|College of life science Zhejiang University 2 0.9219 0.92023 0.06415 0.06403 0.70303 0.70418 0.45339 0.45701 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2021-01-07 Adult Adult Spleen Hematopoietic System
63895 63895 SRR14213371 SRX10579916 SRS8684384 SRP314470 PRJNA721381 RNA Seq from zebrafish adult tissues GSE171906 Transcriptome Analysis The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.   pubmed:34556579   Spleen3 GSM5237140   source name:zebrafish spleen|genotype:wild type|tissue:spleen|strain:TLAB Spleen3 Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM zebrafish spleen   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|tissue:spleen|strain:TLAB GSM5237140 GSM5237140: Spleen3; Danio rerio; RNA Seq GSM5237140   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM5237140 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP314470     Spleen3.fastq fastq 2469245600.0 24692456.0 GSM5237140 r1 0:100 A:595265067;C:649103304;G:625399353;T:599383209;N:94667 100       595265067 649103304 625399353 599383209 94667 SRX10579916 SRS8684384 SRA1217576 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.9388   0.16508   0.75205   0.59719   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2021-04-12 Undetermined Undetermined Spleen Hematopoietic System
63896 63896 SRR14213370 SRX10579915 SRS8684383 SRP314470 PRJNA721381 RNA Seq from zebrafish adult tissues GSE171906 Transcriptome Analysis The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.   pubmed:34556579   Spleen2 GSM5237139   source name:zebrafish spleen|genotype:wild type|tissue:spleen|strain:TLAB Spleen2 Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM zebrafish spleen   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|tissue:spleen|strain:TLAB GSM5237139 GSM5237139: Spleen2; Danio rerio; RNA Seq GSM5237139   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM5237139 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP314470     Spleen2.fastq fastq 1372663100.0 13726631.0 GSM5237139 r1 0:100 A:303080845;C:392345861;G:369765807;T:307418421;N:52166 100       303080845 392345861 369765807 307418421 52166 SRX10579915 SRS8684383 SRA1217576 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96541   0.18478   0.78565   0.60522   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2021-04-12 Undetermined Undetermined Spleen Hematopoietic System
63897 63897 SRR14213369 SRX10579914 SRS8684382 SRP314470 PRJNA721381 RNA Seq from zebrafish adult tissues GSE171906 Transcriptome Analysis The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.   pubmed:34556579   Spleen1 GSM5237138   source name:zebrafish spleen|genotype:wild type|tissue:spleen|strain:TLAB Spleen1 Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM zebrafish spleen   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|tissue:spleen|strain:TLAB GSM5237138 GSM5237138: Spleen1; Danio rerio; RNA Seq GSM5237138   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM5237138 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP314470     Spleen1.fastq fastq 2268815600.0 22688156.0 GSM5237138 r1 0:100 A:570901318;C:562128594;G:552921437;T:582778510;N:85741 100       570901318 562128594 552921437 582778510 85741 SRX10579914 SRS8684382 SRA1217576 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.93633   0.14981   0.72825   0.52073   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2021-04-12 Undetermined Undetermined Spleen Hematopoietic System

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