{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", technology = \"unknown\" and tissue_curation_coarse = \"Hematopoietic System\"", "rows": [[24784, "SRR25502048", "SRX21232930", "SRS18488024", "SRP453114", "PRJNA1001808", "The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger", "GSE239949", "Transcriptome Analysis", "From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.", null, "pubmed:28382966", null, "Sample 15 05316 MCK mut3", "GSM7678168", null, "tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing", "Sample 15 05316 MCK mut3", "Data were QC\u2019d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample", "lyz+  mpx+ granulocytes", null, "RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.", null, "cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf", "GSM7678168", "GSM7678168: Sample 15 05316 MCK mut3; Danio rerio; RNA Seq", "GSM7678168 r1", "GSM7678168", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP453114", null, null, "15-05316_MCK_mut3_GTGCTT_L002_R1_001.fastq.gz 15-05316_MCK_mut3_GTGCTT_L002_R2_001.fastq.gz", "fastq fastq", 4329868620.0, 20618422.0, "GSM7678168 r1", "0:105 1:105", "A:1075032412;C:1077085067;G:1119735718;T:1057797736;N:217687", 105, 105, null, null, 1075032412, 1077085067, 1119735718, 1057797736, 217687, "SRX21232930", "SRS18488024", "SRA1685493", "Rural Clinical Sciences, La Trobe University", "Rural Clinical Sciences, La Trobe University", 2, 0.78961, 0.91048, 0.20166, 0.23232, 0.81556, 0.81115, 0.59478, 0.59379, 105, 105, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-08-03", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [24785, "SRR25502049", "SRX21232929", "SRS18488023", "SRP453114", "PRJNA1001808", "The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger", "GSE239949", "Transcriptome Analysis", "From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.", null, "pubmed:28382966", null, "Sample 15 05316 MCK mut2", "GSM7678167", null, "tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing", "Sample 15 05316 MCK mut2", "Data were QC\u2019d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample", "lyz+  mpx+ granulocytes", null, "RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.", null, "cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf", "GSM7678167", "GSM7678167: Sample 15 05316 MCK mut2; Danio rerio; RNA Seq", "GSM7678167 r1", "GSM7678167", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP453114", null, null, "15-05316_MCK_mut2_ACCTCA_L002_R1_001.fastq.gz 15-05316_MCK_mut2_ACCTCA_L002_R2_001.fastq.gz", "fastq fastq", 4444374270.0, 21163687.0, "GSM7678167 r1", "0:105 1:105", "A:1114919906;C:1098541058;G:1145427151;T:1085262902;N:223253", 105, 105, null, null, 1114919906, 1098541058, 1145427151, 1085262902, 223253, "SRX21232929", "SRS18488023", "SRA1685493", "Rural Clinical Sciences, La Trobe University", "Rural Clinical Sciences, La Trobe University", 2, 0.74961, 0.90068, 0.18596, 0.22057, 0.81115, 0.80754, 0.5829, 0.58615, 105, 105, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-08-03", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [24786, "SRR25502050", "SRX21232928", "SRS18488022", "SRP453114", "PRJNA1001808", "The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger", "GSE239949", "Transcriptome Analysis", "From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.", null, "pubmed:28382966", null, "Sample 15 05316 MCK mut1", "GSM7678166", null, "tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing", "Sample 15 05316 MCK mut1", "Data were QC\u2019d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample", "lyz+  mpx+ granulocytes", null, "RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.", null, "cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf", "GSM7678166", "GSM7678166: Sample 15 05316 MCK mut1; Danio rerio; RNA Seq", "GSM7678166 r1", "GSM7678166", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP453114", null, null, "15-05316_MCK_mut1_GCACTA_L002_R1_001.fastq.gz 15-05316_MCK_mut1_GCACTA_L002_R2_001.fastq.gz", "fastq fastq", 4459467180.0, 21235558.0, "GSM7678166 r1", "0:105 1:105", "A:1206908747;C:1012207561;G:1060393698;T:1179731376;N:225798", 105, 105, null, null, 1206908747, 1012207561, 1060393698, 1179731376, 225798, "SRX21232928", "SRS18488022", "SRA1685493", "Rural Clinical Sciences, La Trobe University", "Rural Clinical Sciences, La Trobe University", 2, 0.75719, 0.88462, 0.20719, 0.24095, 0.78559, 0.77914, 0.50538, 0.55691, 105, 105, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-08-03", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [24787, "SRR25502051", "SRX21232927", "SRS18488021", "SRP453114", "PRJNA1001808", "The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger", "GSE239949", "Transcriptome Analysis", "From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.", null, "pubmed:28382966", null, "Sample 15 05315 MCK WT3", "GSM7678165", null, "tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing", "Sample 15 05315 MCK WT3", "Data were QC\u2019d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample", "lyz+  mpx+ granulocytes", null, "RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.", null, "cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf", "GSM7678165", "GSM7678165: Sample 15 05315 MCK WT3; Danio rerio; RNA Seq", "GSM7678165 r1", "GSM7678165", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP453114", null, null, "15-05315_MCK_WT3_AGTGAG_L002_R1_001.fastq.gz 15-05315_MCK_WT3_AGTGAG_L002_R2_001.fastq.gz", "fastq fastq", 3925329240.0, 18692044.0, "GSM7678165 r1", "0:105 1:105", "A:1022654212;C:930239389;G:973328942;T:998905803;N:200894", 105, 105, null, null, 1022654212, 930239389, 973328942, 998905803, 200894, "SRX21232927", "SRS18488021", "SRA1685493", "Rural Clinical Sciences, La Trobe University", "Rural Clinical Sciences, La Trobe University", 2, 0.75647, 0.89377, 0.19165, 0.22718, 0.81057, 0.80501, 0.51173, 0.54819, 105, 105, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-08-03", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [24788, "SRR25502052", "SRX21232926", "SRS18488020", "SRP453114", "PRJNA1001808", "The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger", "GSE239949", "Transcriptome Analysis", "From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.", null, "pubmed:28382966", null, "Sample 15 05314 MCK WT2", "GSM7678164", null, "tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing", "Sample 15 05314 MCK WT2", "Data were QC\u2019d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample", "lyz+  mpx+ granulocytes", null, "RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.", null, "cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf", "GSM7678164", "GSM7678164: Sample 15 05314 MCK WT2; Danio rerio; RNA Seq", "GSM7678164 r1", "GSM7678164", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP453114", null, null, "15-05314_MCK_WT2_TGGTGA_L002_R2_001.fastq.gz 15-05314_MCK_WT2_TGGTGA_L002_R1_001.fastq.gz", "fastq fastq", 4100489820.0, 19526142.0, "GSM7678164 r1", "0:105 1:105", "A:1022482319;C:1016090490;G:1063619365;T:998086417;N:211229", 105, 105, null, null, 1022482319, 1016090490, 1063619365, 998086417, 211229, "SRX21232926", "SRS18488020", "SRA1685493", "Rural Clinical Sciences, La Trobe University", "Rural Clinical Sciences, La Trobe University", 2, 0.76378, 0.90522, 0.20093, 0.23619, 0.82467, 0.82049, 0.57261, 0.562, 105, 105, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-08-03", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [24789, "SRR25502053", "SRX21232925", "SRS18488019", "SRP453114", "PRJNA1001808", "The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger", "GSE239949", "Transcriptome Analysis", "From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.", null, "pubmed:28382966", null, "Sample 15 05313 MCK WT1", "GSM7678163", null, "tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing", "Sample 15 05313 MCK WT1", "Data were QC\u2019d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample", "lyz+  mpx+ granulocytes", null, "RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.", null, "cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf", "GSM7678163", "GSM7678163: Sample 15 05313 MCK WT1; Danio rerio; RNA Seq", "GSM7678163 r1", "GSM7678163", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP453114", null, null, "15-05313_MCK_WT1_AACCAG_L002_R1_001.fastq.gz 15-05313_MCK_WT1_AACCAG_L002_R2_001.fastq.gz", "fastq fastq", 4135721100.0, 19693910.0, "GSM7678163 r1", "0:105 1:105", "A:1048700719;C:1014162128;G:1070155053;T:1002495763;N:207437", 105, 105, null, null, 1048700719, 1014162128, 1070155053, 1002495763, 207437, "SRX21232925", "SRS18488019", "SRA1685493", "Rural Clinical Sciences, La Trobe University", "Rural Clinical Sciences, La Trobe University", 2, 0.70974, 0.9073, 0.1771, 0.22534, 0.82483, 0.81625, 0.56311, 0.55183, 105, 105, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-08-03", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [31522, "SRR28418937", "SRX24023264", "SRS20817617", "SRP497230", "PRJNA1090848", "Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq]", "GSE262188", "Transcriptome Analysis", "Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however  the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision  its dynamic and role in HSPC development is poorly investigated. Here  we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably  PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions  which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then  conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors  such as PU.1 .", null, "pubmed:38886858", null, "HPSC rep3 RNA seq 3month", "GSM8159257", null, "source name:hematopoietic stem cell|tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry|geo loc name:missing|collection date:missing", "HPSC rep3 RNA seq 3month", "The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering  high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "hematopoietic stem cell", null, "Briefly  \u223c10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 \u03bcl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1\u00d7  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 \u03bcM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina", null, "tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry", "GSM8159257", "GSM8159257: HPSC rep3 RNA seq 3month; Danio rerio; RNA Seq", "GSM8159257 r1", "GSM8159257", "1", "Briefly  \u223c10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 \u03bcl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1\u00d7  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 \u03bcM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP497230", null, "loader:fastq load.py", "RNA-seq_Adult_HPSC_rep3_R1.fq.gz RNA-seq_Adult_HPSC_rep3_R2.fq.gz", "fastq fastq", 11621758500.0, 38739195.0, "GSM8159257 r1", "0:150 1:150", "A:3144084931;C:2632272493;G:2693165513;T:3151802925;N:432638", 150, 150, null, null, 3144084931, 2632272493, 2693165513, 3151802925, 432638, "SRX24023264", "SRS20817617", "SRA1831889", "South China University of Technology", "South China University of Technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-21", "Adult", "Adult", "Blood", "Hematopoietic System"], [31523, "SRR28418938", "SRX24023263", "SRS20817616", "SRP497230", "PRJNA1090848", "Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq]", "GSE262188", "Transcriptome Analysis", "Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however  the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision  its dynamic and role in HSPC development is poorly investigated. Here  we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably  PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions  which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then  conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors  such as PU.1 .", null, "pubmed:38886858", null, "HPSC rep2 RNA seq 3month", "GSM8159256", null, "source name:hematopoietic stem cell|tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry|geo loc name:missing|collection date:missing", "HPSC rep2 RNA seq 3month", "The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering  high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "hematopoietic stem cell", null, "Briefly  \u223c10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 \u03bcl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1\u00d7  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 \u03bcM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina", null, "tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry", "GSM8159256", "GSM8159256: HPSC rep2 RNA seq 3month; Danio rerio; RNA Seq", "GSM8159256 r1", "GSM8159256", "1", "Briefly  \u223c10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 \u03bcl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1\u00d7  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 \u03bcM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP497230", null, "loader:fastq load.py", "RNA-seq_Adult_HPSC_rep2_R1.fq.gz RNA-seq_Adult_HPSC_rep2_R2.fq.gz", "fastq fastq", 9951217200.0, 33170724.0, "GSM8159256 r1", "0:150 1:150", "A:2755384814;C:2209586340;G:2237522365;T:2748523249;N:200432", 150, 150, null, null, 2755384814, 2209586340, 2237522365, 2748523249, 200432, "SRX24023263", "SRS20817616", "SRA1831889", "South China University of Technology", "South China University of Technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-21", "Adult", "Adult", "Blood", "Hematopoietic System"], [31524, "SRR28418939", "SRX24023262", "SRS20817615", "SRP497230", "PRJNA1090848", "Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq]", "GSE262188", "Transcriptome Analysis", "Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however  the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision  its dynamic and role in HSPC development is poorly investigated. Here  we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably  PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions  which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then  conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors  such as PU.1 .", null, "pubmed:38886858", null, "HPSC rep1 RNA seq 3month", "GSM8159255", null, "source name:hematopoietic stem cell|tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry|geo loc name:missing|collection date:missing", "HPSC rep1 RNA seq 3month", "The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering  high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "hematopoietic stem cell", null, "Briefly  \u223c10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 \u03bcl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1\u00d7  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 \u03bcM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina", null, "tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry", "GSM8159255", "GSM8159255: HPSC rep1 RNA seq 3month; Danio rerio; RNA Seq", "GSM8159255 r1", "GSM8159255", "1", "Briefly  \u223c10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 \u03bcl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1\u00d7  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 \u03bcM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP497230", null, "loader:fastq load.py", "RNA-seq_Adult_HPSC_rep1_R1.fq.gz RNA-seq_Adult_HPSC_rep1_R2.fq.gz", "fastq fastq", 11096617200.0, 36988724.0, "GSM8159255 r1", "0:150 1:150", "A:3071303610;C:2460399138;G:2510824334;T:3053621175;N:468943", 150, 150, null, null, 3071303610, 2460399138, 2510824334, 3053621175, 468943, "SRX24023262", "SRS20817615", "SRA1831889", "South China University of Technology", "South China University of Technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-21", "Adult", "Adult", "Blood", "Hematopoietic System"], [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\u00b0C to mild 18\u00b0C and severe 10\u00b0C 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 \u2018negative regulation of endopeptidase activity\u2019 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", null, "pubmed:26227973", null, "spleen10", "GSM1523053", null, "source name:spleen|tissue:spleen|temperature:10\u00b0C|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", null, "tissue:spleen|temperature:10\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523053", "GSM1523053: spleen10; Danio rerio; RNA Seq", "GSM1523053", null, "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", null, "SRP048807", null, null, "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, null, null, 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", null, "China", "2014-10-09", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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\u00b0C to mild 18\u00b0C and severe 10\u00b0C 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 \u2018negative regulation of endopeptidase activity\u2019 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", null, "pubmed:26227973", null, "spleen18", "GSM1523052", null, "source name:spleen|tissue:spleen|temperature:18\u00b0C|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", null, "tissue:spleen|temperature:18\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523052", "GSM1523052: spleen18; Danio rerio; RNA Seq", "GSM1523052", null, "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", null, "SRP048807", null, null, "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, null, null, 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", null, "China", "2014-10-09", "Adult", "Adult", "Spleen", "Hematopoietic System"], [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\u00b0C to mild 18\u00b0C and severe 10\u00b0C 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 \u2018negative regulation of endopeptidase activity\u2019 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", null, "pubmed:26227973", null, "spleen28", "GSM1523051", null, "source name:spleen|tissue:spleen|temperature:28\u00b0C|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", null, "tissue:spleen|temperature:28\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523051", "GSM1523051: spleen28; Danio rerio; RNA Seq", "GSM1523051", null, "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", null, "SRP048807", null, null, "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, null, null, 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", null, "China", "2014-10-09", "Adult", "Adult", "Spleen", "Hematopoietic System"], [38293, "SRR1647684", "SRX756919", "SRS742121", "SRP049663", "PRJNA266803", "Spring Varaemia of Carp Virus SVCV infection of adult zebrafish", "GSE63133", "Transcriptome Analysis", "During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 \u00b5L SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.", null, "pubmed:25535281", null, "24S", "GSM1541908", null, "source name:spleen|tissue:spleen|disease state:24h post SVCV infection", "24S", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "spleen", null, "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:spleen|disease state:24h post SVCV infection", "GSM1541908", "GSM1541908: 24S; Danio rerio; RNA Seq", "GSM1541908", null, "1", "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1541908", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049663", null, null, "24S_ATGTCA_L003_R1.fastq", "fastq", 1207014756.0, 23666956.0, "GSM1541908 r1", "0:51", "A:316359100;C:290453604;G:283305513;T:316815698;N:80841", 51, null, null, null, 316359100, 290453604, 283305513, 316815698, 80841, "SRX756919", "SRS742121", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.91158, null, 0.09021, null, 0.70867, null, 0.46907, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Spleen", "Hematopoietic System"], [38294, "SRR1647683", "SRX756918", "SRS742119", "SRP049663", "PRJNA266803", "Spring Varaemia of Carp Virus SVCV infection of adult zebrafish", "GSE63133", "Transcriptome Analysis", "During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 \u00b5L SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.", null, "pubmed:25535281", null, "6S", "GSM1541907", null, "source name:spleen|tissue:spleen|disease state:6h post SVCV infection", "6S", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "spleen", null, "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:spleen|disease state:6h post SVCV infection", "GSM1541907", "GSM1541907: 6S; Danio rerio; RNA Seq", "GSM1541907", null, "1", "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1541907", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049663", null, null, "6S_AGTTCC_L003_R1.fastq", "fastq", 1251006540.0, 24529540.0, "GSM1541907 r1", "0:51", "A:323805792;C:303846999;G:297418642;T:325862442;N:72665", 51, null, null, null, 323805792, 303846999, 297418642, 325862442, 72665, "SRX756918", "SRS742119", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.92105, null, 0.09005, null, 0.71273, null, 0.46937, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Spleen", "Hematopoietic System"], [38295, "SRR1647682", "SRX756917", "SRS742118", "SRP049663", "PRJNA266803", "Spring Varaemia of Carp Virus SVCV infection of adult zebrafish", "GSE63133", "Transcriptome Analysis", "During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 \u00b5L SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.", null, "pubmed:25535281", null, "0S", "GSM1541906", null, "source name:spleen|tissue:spleen|disease state:un infected", "0S", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "spleen", null, "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:spleen|disease state:un infected", "GSM1541906", "GSM1541906: 0S; Danio rerio; RNA Seq", "GSM1541906", null, "1", "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1541906", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049663", null, null, "0S_AGTCAA_L003_R1.fastq", "fastq", 1155087372.0, 22648772.0, "GSM1541906 r1", "0:51", "A:301183546;C:279328135;G:272663981;T:301834798;N:76912", 51, null, null, null, 301183546, 279328135, 272663981, 301834798, 76912, "SRX756917", "SRS742118", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.91841, null, 0.09679, null, 0.70546, null, 0.47624, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Spleen", "Hematopoietic System"], [39665, "SRR2027911", "SRX1029315", "SRS937775", "SRP058376", "PRJNA284108", "RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures", "GSE68920", "Transcriptome Analysis", "We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28\u00b0C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.", null, "pubmed:31832066", null, "6dpf mpeg1:mCherryPosMmarinumGFPPos rep3", "GSM1686459", null, "source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "6dpf mpeg1:mCherryPosMmarinumGFPPos rep3", "Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample", "zebra fish larvae", "Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 1 x 50 nucleotides.", "Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5\u00b0C in egg water 60\u00b5g/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich", "tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "GSM1686459", "GSM1686459: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep3; Danio rerio; RNA Seq", "GSM1686459", null, "1", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 1 x 50 nucleotides.", "GEO Accession:GSM1686459", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058376", null, null, "ZFG-14-09_06_ATTCCT_L003_R1_001.fastq.gz", "fastq", 988427889.0, 19380939.0, "GSM1686459 r1", "0:51", "A:322268594;C:166925867;G:171531103;T:327506982;N:195343", 51, null, null, null, 322268594, 166925867, 171531103, 327506982, 195343, "SRX1029315", "SRS937775", "SRA268539", "GEO", "Institute of Biology, Leiden University", 1, 0.6999, null, 0.24019, null, 0.85358, null, 0.56832, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Netherlands", "2015-05-15", "Larval", "Larval", "Blood", "Hematopoietic System"], [39666, "SRR2027910", "SRX1029314", "SRS937773", "SRP058376", "PRJNA284108", "RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures", "GSE68920", "Transcriptome Analysis", "We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28\u00b0C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.", null, "pubmed:31832066", null, "6dpf mpeg1:mCherryPosMmarinumGFPPos rep2", "GSM1686458", null, "source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "6dpf mpeg1:mCherryPosMmarinumGFPPos rep2", "Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample", "zebra fish larvae", "Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 1 x 50 nucleotides.", "Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5\u00b0C in egg water 60\u00b5g/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich", "tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "GSM1686458", "GSM1686458: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep2; Danio rerio; RNA Seq", "GSM1686458", null, "1", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 1 x 50 nucleotides.", "GEO Accession:GSM1686458", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058376", null, null, "ZFG-14-09_05_ACTGAT_L003_R1_001.fastq.gz", "fastq", 846771207.0, 16603357.0, "GSM1686458 r1", "0:51", "A:268435928;C:150903620;G:153931870;T:273331733;N:168056", 51, null, null, null, 268435928, 150903620, 153931870, 273331733, 168056, "SRX1029314", "SRS937773", "SRA268539", "GEO", "Institute of Biology, Leiden University", 1, 0.72025, null, 0.17943, null, 0.87937, null, 0.5683, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Netherlands", "2015-05-15", "Larval", "Larval", "Blood", "Hematopoietic System"], [39667, "SRR2027909", "SRX1029313", "SRS937774", "SRP058376", "PRJNA284108", "RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures", "GSE68920", "Transcriptome Analysis", "We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28\u00b0C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.", null, "pubmed:31832066", null, "6dpf mpeg1:mCherryPosMmarinumGFPPos rep1", "GSM1686457", null, "source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "6dpf mpeg1:mCherryPosMmarinumGFPPos rep1", "Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample", "zebra fish larvae", "Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 1 x 50 nucleotides.", "Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5\u00b0C in egg water 60\u00b5g/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich", "tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "GSM1686457", "GSM1686457: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep1; Danio rerio; RNA Seq", "GSM1686457", null, "1", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 1 x 50 nucleotides.", "GEO Accession:GSM1686457", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058376", null, null, "ZFG-14-09_04_GAGTGG_L003_R1_001.fastq.gz", "fastq", 807459642.0, 15832542.0, "GSM1686457 r1", "0:51", "A:260516660;C:140425216;G:145411663;T:260942267;N:163836", 51, null, null, null, 260516660, 140425216, 145411663, 260942267, 163836, "SRX1029313", "SRS937774", "SRA268539", "GEO", "Institute of Biology, Leiden University", 1, 0.7097, null, 0.17187, null, 0.93304, null, 0.64092, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Netherlands", "2015-05-15", "Larval", "Larval", "Blood", "Hematopoietic System"], [39668, "SRR2027908", "SRX1029312", "SRS937776", "SRP058376", "PRJNA284108", "RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures", "GSE68920", "Transcriptome Analysis", "We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28\u00b0C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.", null, "pubmed:31832066", null, "6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3", "GSM1686456", null, "source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3", "Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample", "zebra fish larvae", "Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 1 x 50 nucleotides.", "Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5\u00b0C in egg water 60\u00b5g/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich", "tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "GSM1686456", "GSM1686456: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3; Danio rerio; RNA Seq", "GSM1686456", null, "1", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 1 x 50 nucleotides.", "GEO Accession:GSM1686456", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058376", null, null, "ZFG-14-09_03_CGTACG_L003_R1_001.fastq.gz", "fastq", 1523483526.0, 29872226.0, "GSM1686456 r1", "0:51", "A:499019794;C:267493952;G:277264815;T:479405699;N:299266", 51, null, null, null, 499019794, 267493952, 277264815, 479405699, 299266, "SRX1029312", "SRS937776", "SRA268539", "GEO", "Institute of Biology, Leiden University", 1, 0.67328, null, 0.15117, null, 0.91179, null, 0.54858, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Netherlands", "2015-05-15", "Larval", "Larval", "Blood", "Hematopoietic System"], [39669, "SRR2027907", "SRX1029311", "SRS937777", "SRP058376", "PRJNA284108", "RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures", "GSE68920", "Transcriptome Analysis", "We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28\u00b0C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.", null, "pubmed:31832066", null, "6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2", "GSM1686455", null, "source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2", "Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample", "zebra fish larvae", "Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 1 x 50 nucleotides.", "Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5\u00b0C in egg water 60\u00b5g/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich", "tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "GSM1686455", "GSM1686455: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2; Danio rerio; RNA Seq", "GSM1686455", null, "1", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 1 x 50 nucleotides.", "GEO Accession:GSM1686455", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058376", null, null, "ZFG-14-09_02_GTTTCG_L003_R1_001.fastq.gz", "fastq", 938675094.0, 18405394.0, "GSM1686455 r1", "0:51", "A:284384359;C:173449465;G:178039777;T:302612825;N:188668", 51, null, null, null, 284384359, 173449465, 178039777, 302612825, 188668, "SRX1029311", "SRS937777", "SRA268539", "GEO", "Institute of Biology, Leiden University", 1, 0.72884, null, 0.14723, null, 0.90767, null, 0.57414, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Netherlands", "2015-05-15", "Larval", "Larval", "Blood", "Hematopoietic System"], [39670, "SRR2027906", "SRX1029310", "SRS937778", "SRP058376", "PRJNA284108", "RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures", "GSE68920", "Transcriptome Analysis", "We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28\u00b0C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.", null, "pubmed:31832066", null, "6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1", "GSM1686454", null, "source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1", "Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample", "zebra fish larvae", "Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 1 x 50 nucleotides.", "Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5\u00b0C in egg water 60\u00b5g/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich", "tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "GSM1686454", "GSM1686454: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1; Danio rerio; RNA Seq", "GSM1686454", null, "1", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 1 x 50 nucleotides.", "GEO Accession:GSM1686454", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058376", null, null, "ZFG-14-09_01_GTGGCC_L003_R1_001.fastq.gz", "fastq", 1248324348.0, 24476948.0, "GSM1686454 r1", "0:51", "A:391067882;C:223380294;G:229132022;T:404526410;N:217740", 51, null, null, null, 391067882, 223380294, 229132022, 404526410, 217740, "SRX1029310", "SRS937778", "SRA268539", "GEO", "Institute of Biology, Leiden University", 1, 0.70232, null, 0.14257, null, 0.92894, null, 0.59305, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Netherlands", "2015-05-15", "Larval", "Larval", "Blood", "Hematopoietic System"], [40807, "SRR3381847", "SRX1704280", "SRS1396343", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 3 blood", "GSM2122871", null, "source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "Treated 3 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "GSM2122871", "GSM2122871: Treated 3 blood; Danio rerio; RNA Seq", "GSM2122871", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122871", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s6_1_GSLv3-7_38_SL139795.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_38_SL139795.fastq.gz", "fastq fastq", 1349428600.0, 13494286.0, "GSM2122871 r1", "0:50 1:50", "A:391483366;C:283353944;G:288253777;T:386190051;N:147462", 50, 50, null, null, 391483366, 283353944, 288253777, 386190051, 147462, "SRX1704280", "SRS1396343", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.88853, 0.89204, 0.22815, 0.23941, 0.73917, 0.73979, 0.53637, 0.53893, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40808, "SRR3381848", "SRX1704280", "SRS1396343", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 3 blood", "GSM2122871", null, "source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "Treated 3 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "GSM2122871", "GSM2122871: Treated 3 blood; Danio rerio; RNA Seq", "GSM2122871", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122871", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s5_1_GSLv3-7_38_SL139795.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_38_SL139795.fastq.gz", "fastq fastq", 1020366100.0, 10203661.0, "GSM2122871 r2", "0:50 1:50", "A:296023946;C:213173706;G:215342808;T:295806226;N:19414", 50, 50, null, null, 296023946, 213173706, 215342808, 295806226, 19414, "SRX1704280", "SRS1396343", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.88792, 0.89203, 0.21382, 0.24279, 0.7652, 0.7444, 0.53618, 0.54254, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40809, "SRR3381849", "SRX1704280", "SRS1396343", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 3 blood", "GSM2122871", null, "source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "Treated 3 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "GSM2122871", "GSM2122871: Treated 3 blood; Danio rerio; RNA Seq", "GSM2122871", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122871", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s6_1_GSLv3-7_38_SL139795.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_38_SL139795.fastq.gz", "fastq fastq", 1008129000.0, 10081290.0, "GSM2122871 r3", "0:50 1:50", "A:292536545;C:210308039;G:212529262;T:292736486;N:18668", 50, 50, null, null, 292536545, 210308039, 212529262, 292736486, 18668, "SRX1704280", "SRS1396343", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.88682, 0.89249, 0.21573, 0.24321, 0.7657, 0.74456, 0.53948, 0.54456, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40810, "SRR3381850", "SRX1704280", "SRS1396343", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 3 blood", "GSM2122871", null, "source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "Treated 3 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "GSM2122871", "GSM2122871: Treated 3 blood; Danio rerio; RNA Seq", "GSM2122871", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122871", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s5_1_GSLv3-7_38_SL139795.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_38_SL139795.fastq.gz", "fastq fastq", 1348814000.0, 13488140.0, "GSM2122871 r4", "0:50 1:50", "A:391186639;C:283404571;G:288274584;T:385756613;N:191593", 50, 50, null, null, 391186639, 283404571, 288274584, 385756613, 191593, "SRX1704280", "SRS1396343", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.88673, 0.89303, 0.22875, 0.24107, 0.74276, 0.74134, 0.53585, 0.54514, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40811, "SRR3381843", "SRX1704279", "SRS1396344", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 2 blood", "GSM2122870", null, "source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "Treated 2 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "GSM2122870", "GSM2122870: Treated 2 blood; Danio rerio; RNA Seq", "GSM2122870", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122870", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s6_1_GSLv3-7_37_SL139794.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_37_SL139794.fastq.gz", "fastq fastq", 1251398700.0, 12513987.0, "GSM2122870 r1", "0:50 1:50", "A:383059535;C:243111832;G:248681985;T:376401618;N:143730", 50, 50, null, null, 383059535, 243111832, 248681985, 376401618, 143730, "SRX1704279", "SRS1396344", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.86725, 0.86597, 0.35725, 0.37228, 0.74312, 0.73961, 0.53136, 0.53663, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40812, "SRR3381844", "SRX1704279", "SRS1396344", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 2 blood", "GSM2122870", null, "source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "Treated 2 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "GSM2122870", "GSM2122870: Treated 2 blood; Danio rerio; RNA Seq", "GSM2122870", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122870", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s5_1_GSLv3-7_37_SL139794.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_37_SL139794.fastq.gz", "fastq fastq", 959597100.0, 9595971.0, "GSM2122870 r2", "0:50 1:50", "A:294644349;C:184893976;G:188222172;T:291818696;N:17907", 50, 50, null, null, 294644349, 184893976, 188222172, 291818696, 17907, "SRX1704279", "SRS1396344", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.86953, 0.86626, 0.33903, 0.3765, 0.77264, 0.74432, 0.53426, 0.53782, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40813, "SRR3381845", "SRX1704279", "SRS1396344", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 2 blood", "GSM2122870", null, "source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "Treated 2 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "GSM2122870", "GSM2122870: Treated 2 blood; Danio rerio; RNA Seq", "GSM2122870", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122870", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s5_1_GSLv3-7_37_SL139794.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_37_SL139794.fastq.gz", "fastq fastq", 1245250000.0, 12452500.0, "GSM2122870 r3", "0:50 1:50", "A:381219052;C:241987476;G:247543915;T:374295403;N:204154", 50, 50, null, null, 381219052, 241987476, 247543915, 374295403, 204154, "SRX1704279", "SRS1396344", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.86789, 0.86686, 0.35484, 0.37206, 0.74119, 0.73679, 0.50299, 0.53759, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40814, "SRR3381846", "SRX1704279", "SRS1396344", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 2 blood", "GSM2122870", null, "source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "Treated 2 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "GSM2122870", "GSM2122870: Treated 2 blood; Danio rerio; RNA Seq", "GSM2122870", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122870", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s6_1_GSLv3-7_37_SL139794.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_37_SL139794.fastq.gz", "fastq fastq", 950337100.0, 9503371.0, "GSM2122870 r4", "0:50 1:50", "A:291821125;C:182753545;G:186179426;T:289565320;N:17684", 50, 50, null, null, 291821125, 182753545, 186179426, 289565320, 17684, "SRX1704279", "SRS1396344", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.86635, 0.86476, 0.34245, 0.3786, 0.77309, 0.74474, 0.50694, 0.53099, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40815, "SRR3381839", "SRX1704278", "SRS1396345", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 1 blood", "GSM2122869", null, "source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "Treated 1 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "GSM2122869", "GSM2122869: Treated 1 blood; Danio rerio; RNA Seq", "GSM2122869", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s5_1_GSLv3-7_36_SL139793.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_36_SL139793.fastq.gz", "fastq fastq", 1067516000.0, 10675160.0, "GSM2122869 r1", "0:50 1:50", "A:289362409;C:244764167;G:247658920;T:285596522;N:133982", 50, 50, null, null, 289362409, 244764167, 247658920, 285596522, 133982, "SRX1704278", "SRS1396345", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.90704, 0.92219, 0.1113, 0.11316, 0.73645, 0.73746, 0.52358, 0.53128, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40816, "SRR3381840", "SRX1704278", "SRS1396345", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 1 blood", "GSM2122869", null, "source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "Treated 1 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "GSM2122869", "GSM2122869: Treated 1 blood; Danio rerio; RNA Seq", "GSM2122869", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s5_1_GSLv3-7_36_SL139793.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_36_SL139793.fastq.gz", "fastq fastq", 802301400.0, 8023014.0, "GSM2122869 r2", "0:50 1:50", "A:216222361;C:183743858;G:183958773;T:218361744;N:14664", 50, 50, null, null, 216222361, 183743858, 183958773, 218361744, 14664, "SRX1704278", "SRS1396345", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.90734, 0.92073, 0.10828, 0.11414, 0.75816, 0.74156, 0.52518, 0.53162, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40817, "SRR3381841", "SRX1704278", "SRS1396345", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 1 blood", "GSM2122869", null, "source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "Treated 1 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "GSM2122869", "GSM2122869: Treated 1 blood; Danio rerio; RNA Seq", "GSM2122869", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s6_1_GSLv3-7_36_SL139793.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_36_SL139793.fastq.gz", "fastq fastq", 1068410400.0, 10684104.0, "GSM2122869 r3", "0:50 1:50", "A:289709397;C:244889156;G:247758297;T:285941886;N:111664", 50, 50, null, null, 289709397, 244889156, 247758297, 285941886, 111664, "SRX1704278", "SRS1396345", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.90673, 0.9217, 0.11124, 0.11262, 0.73779, 0.73819, 0.52628, 0.53419, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40818, "SRR3381842", "SRX1704278", "SRS1396345", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 1 blood", "GSM2122869", null, "source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "Treated 1 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol", "GSM2122869", "GSM2122869: Treated 1 blood; Danio rerio; RNA Seq", "GSM2122869", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s6_1_GSLv3-7_36_SL139793.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_36_SL139793.fastq.gz", "fastq fastq", 792180400.0, 7921804.0, "GSM2122869 r4", "0:50 1:50", "A:213515752;C:181199374;G:181507201;T:215943851;N:14222", 50, 50, null, null, 213515752, 181199374, 181507201, 215943851, 14222, "SRX1704278", "SRS1396345", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.90574, 0.92099, 0.11022, 0.11558, 0.75773, 0.74158, 0.52565, 0.52697, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40819, "SRR3381835", "SRX1704277", "SRS1396346", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 3 blood", "GSM2122868", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 3 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122868", "GSM2122868: Control 3 blood; Danio rerio; RNA Seq", "GSM2122868", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s6_1_GSLv3-7_35_SL139792.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_35_SL139792.fastq.gz", "fastq fastq", 1006437300.0, 10064373.0, "GSM2122868 r1", "0:50 1:50", "A:270736589;C:231073543;G:230348781;T:274259695;N:18692", 50, 50, null, null, 270736589, 231073543, 230348781, 274259695, 18692, "SRX1704277", "SRS1396346", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.89576, 0.91552, 0.11015, 0.11108, 0.77108, 0.75708, 0.52238, 0.55295, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40820, "SRR3381836", "SRX1704277", "SRS1396346", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 3 blood", "GSM2122868", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 3 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122868", "GSM2122868: Control 3 blood; Danio rerio; RNA Seq", "GSM2122868", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s5_1_GSLv3-7_35_SL139792.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_35_SL139792.fastq.gz", "fastq fastq", 1019872300.0, 10198723.0, "GSM2122868 r2", "0:50 1:50", "A:274310405;C:234397316;G:233653220;T:277492635;N:18724", 50, 50, null, null, 274310405, 234397316, 233653220, 277492635, 18724, "SRX1704277", "SRS1396346", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.89872, 0.91671, 0.10908, 0.10998, 0.76848, 0.7559, 0.55678, 0.52913, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40821, "SRR3381837", "SRX1704277", "SRS1396346", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 3 blood", "GSM2122868", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 3 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122868", "GSM2122868: Control 3 blood; Danio rerio; RNA Seq", "GSM2122868", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s6_1_GSLv3-7_35_SL139792.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_35_SL139792.fastq.gz", "fastq fastq", 1350419100.0, 13504191.0, "GSM2122868 r3", "0:50 1:50", "A:365416324;C:310498635;G:312632921;T:361739733;N:131487", 50, 50, null, null, 365416324, 310498635, 312632921, 361739733, 131487, "SRX1704277", "SRS1396346", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.89828, 0.91602, 0.11147, 0.11073, 0.74941, 0.75053, 0.54012, 0.53979, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40822, "SRR3381838", "SRX1704277", "SRS1396346", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 3 blood", "GSM2122868", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 3 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122868", "GSM2122868: Control 3 blood; Danio rerio; RNA Seq", "GSM2122868", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s5_1_GSLv3-7_35_SL139792.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_35_SL139792.fastq.gz", "fastq fastq", 1352817900.0, 13528179.0, "GSM2122868 r4", "0:50 1:50", "A:366001448;C:311109301;G:313269573;T:362247619;N:189959", 50, 50, null, null, 366001448, 311109301, 313269573, 362247619, 189959, "SRX1704277", "SRS1396346", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.89762, 0.91702, 0.11094, 0.1109, 0.74864, 0.7498, 0.53153, 0.55731, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40823, "SRR3381831", "SRX1704276", "SRS1396347", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 2 blood", "GSM2122867", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 2 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122867", "GSM2122867: Control 2 blood; Danio rerio; RNA Seq", "GSM2122867", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122867", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s5_1_GSLv3-7_34_SL139791.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_34_SL139791.fastq.gz", "fastq fastq", 1320276500.0, 13202765.0, "GSM2122867 r1", "0:50 1:50", "A:347340148;C:314346533;G:315984111;T:342435896;N:169812", 50, 50, null, null, 347340148, 314346533, 315984111, 342435896, 169812, "SRX1704276", "SRS1396347", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.92673, 0.93522, 0.1474, 0.1486, 0.77695, 0.77822, 0.5491, 0.55404, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40824, "SRR3381832", "SRX1704276", "SRS1396347", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 2 blood", "GSM2122867", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 2 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122867", "GSM2122867: Control 2 blood; Danio rerio; RNA Seq", "GSM2122867", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122867", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s6_1_GSLv3-7_34_SL139791.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_34_SL139791.fastq.gz", "fastq fastq", 980312400.0, 9803124.0, "GSM2122867 r2", "0:50 1:50", "A:256051139;C:233456025;G:232307447;T:258480444;N:17345", 50, 50, null, null, 256051139, 233456025, 232307447, 258480444, 17345, "SRX1704276", "SRS1396347", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.92686, 0.9359, 0.1445, 0.14733, 0.79537, 0.78244, 0.55823, 0.5607, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40825, "SRR3381833", "SRX1704276", "SRS1396347", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 2 blood", "GSM2122867", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 2 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122867", "GSM2122867: Control 2 blood; Danio rerio; RNA Seq", "GSM2122867", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122867", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s5_1_GSLv3-7_34_SL139791.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_34_SL139791.fastq.gz", "fastq fastq", 996477700.0, 9964777.0, "GSM2122867 r3", "0:50 1:50", "A:260257795;C:237526121;G:236299803;T:262375630;N:18351", 50, 50, null, null, 260257795, 237526121, 236299803, 262375630, 18351, "SRX1704276", "SRS1396347", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.9292, 0.93713, 0.143, 0.14889, 0.79531, 0.7834, 0.55615, 0.55279, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40826, "SRR3381834", "SRX1704276", "SRS1396347", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 2 blood", "GSM2122867", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 2 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122867", "GSM2122867: Control 2 blood; Danio rerio; RNA Seq", "GSM2122867", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122867", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s6_1_GSLv3-7_34_SL139791.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_34_SL139791.fastq.gz", "fastq fastq", 1319184300.0, 13191843.0, "GSM2122867 r4", "0:50 1:50", "A:347098468;C:314043165;G:315610117;T:342302442;N:130108", 50, 50, null, null, 347098468, 314043165, 315610117, 342302442, 130108, "SRX1704276", "SRS1396347", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.92671, 0.93595, 0.14826, 0.14877, 0.77792, 0.77873, 0.55524, 0.5557, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40827, "SRR3381825", "SRX1704275", "SRS1396348", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 1 blood", "GSM2122866", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 1 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122866", "GSM2122866: Control 1 blood; Danio rerio; RNA Seq", "GSM2122866", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s6_1_GSLv3-7_33_SL139790.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_33_SL139790.fastq.gz", "fastq fastq", 692276000.0, 6922760.0, "GSM2122866 r1", "0:50 1:50", "A:191405813;C:153586292;G:152965257;T:194306049;N:12589", 50, 50, null, null, 191405813, 153586292, 152965257, 194306049, 12589, "SRX1704275", "SRS1396348", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.9083, 0.91142, 0.16578, 0.17743, 0.75789, 0.74221, 0.55181, 0.54476, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40828, "SRR3381826", "SRX1704275", "SRS1396348", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 1 blood", "GSM2122866", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 1 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122866", "GSM2122866: Control 1 blood; Danio rerio; RNA Seq", "GSM2122866", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s5_1_GSLv3-7_33_SL139790.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_33_SL139790.fastq.gz", "fastq fastq", 911479300.0, 9114793.0, "GSM2122866 r2", "0:50 1:50", "A:253240601;C:202627238;G:203390297;T:252105631;N:115533", 50, 50, null, null, 253240601, 202627238, 203390297, 252105631, 115533, "SRX1704275", "SRS1396348", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.90729, 0.91334, 0.17307, 0.1777, 0.73316, 0.73419, 0.55981, 0.56826, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40829, "SRR3381827", "SRX1704275", "SRS1396348", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 1 blood", "GSM2122866", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 1 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122866", "GSM2122866: Control 1 blood; Danio rerio; RNA Seq", "GSM2122866", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s6_1_GSLv3-7_33_SL139790.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_33_SL139790.fastq.gz", "fastq fastq", 910041600.0, 9100416.0, "GSM2122866 r3", "0:50 1:50", "A:252924440;C:202200821;G:202972517;T:251856107;N:87715", 50, 50, null, null, 252924440, 202200821, 202972517, 251856107, 87715, "SRX1704275", "SRS1396348", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.90819, 0.91345, 0.17288, 0.17678, 0.73582, 0.73448, 0.55482, 0.56579, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40830, "SRR3381828", "SRX1704275", "SRS1396348", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 1 blood", "GSM2122866", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 1 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122866", "GSM2122866: Control 1 blood; Danio rerio; RNA Seq", "GSM2122866", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s5_1_GSLv3-7_33_SL139790.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_33_SL139790.fastq.gz", "fastq fastq", 701940200.0, 7019402.0, "GSM2122866 r4", "0:50 1:50", "A:194036996;C:155992188;G:155284640;T:196613376;N:13000", 50, 50, null, null, 194036996, 155992188, 155284640, 196613376, 13000, "SRX1704275", "SRS1396348", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.90959, 0.91386, 0.16429, 0.17705, 0.75544, 0.7391, 0.548, 0.57224, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40831, "SRR3381829", "SRX1704275", "SRS1396348", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 1 blood", "GSM2122866", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 1 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122866", "GSM2122866: Control 1 blood; Danio rerio; RNA Seq", "GSM2122866", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DKGANXX_s8_1_GSLv3-7_33_SL139790.fastq.gz C8DKGANXX_s8_2_GSLv3-7_33_SL139790.fastq.gz", "fastq fastq", 1596331500.0, 15963315.0, "GSM2122866 r5", "0:50 1:50", "A:444854958;C:353331559;G:354367449;T:442888766;N:888768", 50, 50, null, null, 444854958, 353331559, 354367449, 442888766, 888768, "SRX1704275", "SRS1396348", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.90554, 0.91175, 0.17327, 0.17968, 0.73669, 0.73728, 0.55044, 0.5651, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [40832, "SRR3381830", "SRX1704275", "SRS1396348", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 1 blood", "GSM2122866", null, "source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "Control 1 blood", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "whole blood  DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO", "GSM2122866", "GSM2122866: Control 1 blood; Danio rerio; RNA Seq", "GSM2122866", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DKGANXX_s7_1_GSLv3-7_33_SL139790.fastq.gz C8DKGANXX_s7_2_GSLv3-7_33_SL139790.fastq.gz", "fastq fastq", 1600754600.0, 16007546.0, "GSM2122866 r6", "0:50 1:50", "A:446178544;C:354456079;G:355435947;T:443937350;N:746680", 50, 50, null, null, 446178544, 354456079, 355435947, 443937350, 746680, "SRX1704275", "SRS1396348", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.90709, 0.91238, 0.17011, 0.17723, 0.74054, 0.73994, 0.55938, 0.55607, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Blood", "Hematopoietic System"], [47583, "SRR6661157", "SRX3638253", "SRS2904504", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplWTPHZ 3", "GSM2975201", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "SplWTPHZ 3", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975201", "GSM2975201: SplWTPHZ 3; Danio rerio; RNA Seq", "GSM2975201", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975201", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplWTPHZ_3.fastq.gz", "fastq", 863137362.0, 16924262.0, "GSM2975201 r1", "0:51", "A:243029420;C:186621398;G:190769119;T:242704294;N:13131", 51, null, null, null, 243029420, 186621398, 190769119, 242704294, 13131, "SRX3638253", "SRS2904504", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.94871, null, 0.18797, null, 0.7289, null, 0.48689, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47584, "SRR6661156", "SRX3638252", "SRS2904503", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplWTPHZ 2", "GSM2975200", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "SplWTPHZ 2", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975200", "GSM2975200: SplWTPHZ 2; Danio rerio; RNA Seq", "GSM2975200", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975200", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplWTPHZ_2.fastq.gz", "fastq", 748057494.0, 14667794.0, "GSM2975200 r1", "0:51", "A:212731080;C:159238564;G:163993235;T:212082953;N:11662", 51, null, null, null, 212731080, 159238564, 163993235, 212082953, 11662, "SRX3638252", "SRS2904503", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.94641, null, 0.22364, null, 0.7264, null, 0.48998, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47585, "SRR6661155", "SRX3638251", "SRS2904502", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplWTPHZ 1", "GSM2975199", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "SplWTPHZ 1", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975199", "GSM2975199: SplWTPHZ 1; Danio rerio; RNA Seq", "GSM2975199", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975199", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplWTPHZ_1.fastq.gz", "fastq", 771862917.0, 15134567.0, "GSM2975199 r1", "0:51", "A:220317243;C:164032479;G:167543123;T:219958265;N:11807", 51, null, null, null, 220317243, 164032479, 167543123, 219958265, 11807, "SRX3638251", "SRS2904502", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.94835, null, 0.1926, null, 0.71453, null, 0.48677, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47586, "SRR6661154", "SRX3638250", "SRS2904501", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplWT 3", "GSM2975198", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "SplWT 3", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975198", "GSM2975198: SplWT 3; Danio rerio; RNA Seq", "GSM2975198", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975198", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplWT_3.fastq.gz", "fastq", 815973888.0, 15999488.0, "GSM2975198 r1", "0:51", "A:236186435;C:169473350;G:175246943;T:235055142;N:12018", 51, null, null, null, 236186435, 169473350, 175246943, 235055142, 12018, "SRX3638250", "SRS2904501", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.94554, null, 0.25855, null, 0.71873, null, 0.54675, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47587, "SRR6661153", "SRX3638249", "SRS2904499", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplWT 2", "GSM2975197", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "SplWT 2", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975197", "GSM2975197: SplWT 2; Danio rerio; RNA Seq", "GSM2975197", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975197", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplWT_2.fastq.gz", "fastq", 909644262.0, 17836162.0, "GSM2975197 r1", "0:51", "A:259661486;C:192636111;G:198048163;T:259284494;N:14008", 51, null, null, null, 259661486, 192636111, 198048163, 259284494, 14008, "SRX3638249", "SRS2904499", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.94781, null, 0.22979, null, 0.69962, null, 0.49839, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47588, "SRR6661152", "SRX3638248", "SRS2904500", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplWT 1", "GSM2975196", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "SplWT 1", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975196", "GSM2975196: SplWT 1; Danio rerio; RNA Seq", "GSM2975196", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975196", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplWT_1.fastq.gz", "fastq", 888755274.0, 17426574.0, "GSM2975196 r1", "0:51", "A:241072815;C:200347978;G:205733626;T:241587449;N:13406", 51, null, null, null, 241072815, 200347978, 205733626, 241587449, 13406, "SRX3638248", "SRS2904500", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.95759, null, 0.1342, null, 0.72918, null, 0.52233, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47589, "SRR6661151", "SRX3638247", "SRS2904498", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplDKOPHZ 3", "GSM2975195", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "SplDKOPHZ 3", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975195", "GSM2975195: SplDKOPHZ 3; Danio rerio; RNA Seq", "GSM2975195", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975195", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplDKOPHZ_3.fastq.gz", "fastq", 881441160.0, 17283160.0, "GSM2975195 r1", "0:51", "A:243254581;C:194198200;G:199055092;T:244919975;N:13312", 51, null, null, null, 243254581, 194198200, 199055092, 244919975, 13312, "SRX3638247", "SRS2904498", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.90441, null, 0.14881, null, 0.71447, null, 0.51129, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47590, "SRR6661150", "SRX3638246", "SRS2904497", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplDKOPHZ 2", "GSM2975194", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "SplDKOPHZ 2", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975194", "GSM2975194: SplDKOPHZ 2; Danio rerio; RNA Seq", "GSM2975194", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975194", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplDKOPHZ_2.fastq.gz", "fastq", 795840414.0, 15604714.0, "GSM2975194 r1", "0:51", "A:229921467;C:166126021;G:170186584;T:229594266;N:12076", 51, null, null, null, 229921467, 166126021, 170186584, 229594266, 12076, "SRX3638246", "SRS2904497", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.88657, null, 0.23556, null, 0.7194, null, 0.51207, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47591, "SRR6661149", "SRX3638245", "SRS2904495", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplDKOPHZ 1", "GSM2975193", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "SplDKOPHZ 1", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975193", "GSM2975193: SplDKOPHZ 1; Danio rerio; RNA Seq", "GSM2975193", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975193", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplDKOPHZ_1.fastq.gz", "fastq", 788951436.0, 15469636.0, "GSM2975193 r1", "0:51", "A:217408862;C:175236911;G:178930271;T:217363444;N:11948", 51, null, null, null, 217408862, 175236911, 178930271, 217363444, 11948, "SRX3638245", "SRS2904495", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.90945, null, 0.10065, null, 0.72468, null, 0.48596, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47592, "SRR6661148", "SRX3638244", "SRS2904496", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplDKO 3", "GSM2975192", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "SplDKO 3", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975192", "GSM2975192: SplDKO 3; Danio rerio; RNA Seq", "GSM2975192", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975192", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplDKO_3.fastq.gz", "fastq", 732609543.0, 14364893.0, "GSM2975192 r1", "0:51", "A:209020386;C:154988652;G:160405898;T:208183578;N:11029", 51, null, null, null, 209020386, 154988652, 160405898, 208183578, 11029, "SRX3638244", "SRS2904496", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.88228, null, 0.23609, null, 0.72529, null, 0.50392, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47593, "SRR6661147", "SRX3638243", "SRS2904493", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplDKO 2", "GSM2975191", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "SplDKO 2", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975191", "GSM2975191: SplDKO 2; Danio rerio; RNA Seq", "GSM2975191", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975191", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplDKO_2.fastq.gz", "fastq", 747985635.0, 14666385.0, "GSM2975191 r1", "0:51", "A:209892939;C:160527969;G:165683955;T:211869190;N:11582", 51, null, null, null, 209892939, 160527969, 165683955, 211869190, 11582, "SRX3638243", "SRS2904493", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.90267, null, 0.20054, null, 0.7249, null, 0.53668, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [47594, "SRR6661146", "SRX3638242", "SRS2904494", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "SplDKO 1", "GSM2975190", null, "source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "SplDKO 1", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975190", "GSM2975190: SplDKO 1; Danio rerio; RNA Seq", "GSM2975190", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975190", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "SplDKO_1.fastq.gz", "fastq", 724574391.0, 14207341.0, "GSM2975190 r1", "0:51", "A:207549130;C:151913145;G:156789401;T:208311727;N:10988", 51, null, null, null, 207549130, 151913145, 156789401, 208311727, 10988, "SRX3638242", "SRS2904494", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.89742, null, 0.2275, null, 0.71547, null, 0.5072, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49188, "SRR7785379", "SRX4640375", "SRS3738589", "SRP159583", "PRJNA489308", "Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis", "PRJNA489308", "Other", "Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.", null, null, null, null, "H67", null, "breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:wild type|replicate:replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "H67", "H67", "H67", "Wild type zebrafish control 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP159583", null, null, "H67_S2_L001_R2_001.fastq.gz H67_S2_L001_R1_001.fastq.gz", "fastq fastq", 18477819300.0, 61592731.0, "H67 S2 L001 R2 001.fastq.gz", "0:150 1:150", "A:4887782016;C:4375793599;G:4438933003;T:4775205744;N:104938", 150, 150, null, null, 4887782016, 4375793599, 4438933003, 4775205744, 104938, "SRX4640375", "SRS3738589", "SRA766519", "Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology", "Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University", 2, 0.93322, 0.93319, 0.06946, 0.06963, 0.6747, 0.68083, 0.47183, 0.47148, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-09-20", "Adult", "Adult", "Blood", "Hematopoietic System"], [49189, "SRR7785380", "SRX4640374", "SRS3738594", "SRP159583", "PRJNA489308", "Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis", "PRJNA489308", "Other", "Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.", null, null, null, null, "H66", null, "breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:wild type|replicate:replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "H66", "H66", "H66", "Wild type zebrafish control 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP159583", null, null, "H66_S1_L001_R2_001.fastq.gz H66_S1_L001_R1_001.fastq.gz", "fastq fastq", 20487126300.0, 68290421.0, "H66 S1 L001 R2 001.fastq.gz", "0:150 1:150", "A:5445452582;C:4824876569;G:4904146081;T:5312533433;N:117635", 150, 150, null, null, 5445452582, 4824876569, 4904146081, 5312533433, 117635, "SRX4640374", "SRS3738594", "SRA766519", "Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology", "Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University", 2, 0.93306, 0.9336, 0.08694, 0.08764, 0.66687, 0.6734, 0.46489, 0.47008, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-09-20", "Adult", "Adult", "Blood", "Hematopoietic System"], [49190, "SRR7785381", "SRX4640373", "SRS3738593", "SRP159583", "PRJNA489308", "Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis", "PRJNA489308", "Other", "Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.", null, null, null, null, "H124", null, "breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:Tol2 EVI 1 EGFP transgenic|replicate:replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "H124", "H124", "H124", "Tol2 EVI 1 EGFP transgenic zebrafish sample 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP159583", null, null, "H124_S1_L001_R1_001.fastq.gz H124_S1_L001_R2_001.fastq.gz", "fastq fastq", 13178593800.0, 43928646.0, "H124 S1 L001 R1 001.fastq.gz", "0:150 1:150", "A:3507220604;C:3103991247;G:3164157369;T:3403051995;N:172585", 150, 150, null, null, 3507220604, 3103991247, 3164157369, 3403051995, 172585, "SRX4640373", "SRS3738593", "SRA766519", "Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology", "Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University", 2, 0.94147, 0.94277, 0.08109, 0.08136, 0.69483, 0.70011, 0.47542, 0.47593, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-09-20", "Adult", "Adult", "Blood", "Hematopoietic System"], [49191, "SRR7785382", "SRX4640372", "SRS3738592", "SRP159583", "PRJNA489308", "Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis", "PRJNA489308", "Other", "Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.", null, null, null, null, "H93", null, "breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:wild type|replicate:replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "H93", "H93", "H93", "Wild type zebrafish control 3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP159583", null, null, "H93_S3_L001_R1_001.fastq.gz H93_S3_L001_R2_001.fastq.gz", "fastq fastq", 18197379600.0, 60657932.0, "H93 S3 L001 R1 001.fastq.gz", "0:150 1:150", "A:4814246240;C:4308418881;G:4375398316;T:4699211054;N:105109", 150, 150, null, null, 4814246240, 4308418881, 4375398316, 4699211054, 105109, "SRX4640372", "SRS3738592", "SRA766519", "Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology", "Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University", 2, 0.9312, 0.93173, 0.07454, 0.07498, 0.67065, 0.6773, 0.46807, 0.47334, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-09-20", "Adult", "Adult", "Blood", "Hematopoietic System"], [49192, "SRR7785383", "SRX4640371", "SRS3738590", "SRP159583", "PRJNA489308", "Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis", "PRJNA489308", "Other", "Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.", null, null, null, null, "H126", null, "breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:Tol2 EVI 1 EGFP transgenic|replicate:replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "H126", "H126", "H126", "Tol2 EVI 1 EGFP transgenic zebrafish sample 3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP159583", null, null, "H126_S3_L001_R1_001.fastq.gz H126_S3_L001_R2_001.fastq.gz", "fastq fastq", 14979601800.0, 49932006.0, "H126 S3 L001 R2 001.fastq.gz", "0:150 1:150", "A:3961375940;C:3551410264;G:3640700651;T:3825918931;N:196014", 150, 150, null, null, 3961375940, 3551410264, 3640700651, 3825918931, 196014, "SRX4640371", "SRS3738590", "SRA766519", "Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology", "Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University", 2, 0.93717, 0.93908, 0.05823, 0.05891, 0.70552, 0.71256, 0.46146, 0.45779, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-09-20", "Adult", "Adult", "Blood", "Hematopoietic System"], [49193, "SRR7785384", "SRX4640370", "SRS3738588", "SRP159583", "PRJNA489308", "Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis", "PRJNA489308", "Other", "Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.", null, null, null, null, "H125", null, "breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:Tol2 EVI 1 EGFP transgenic|replicate:replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "H125", "H125", "H125", "Tol2 EVI 1 EGFP transgenic zebrafish sample 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP159583", null, null, "H125_S2_L001_R1_001.fastq.gz H125_S2_L001_R2_001.fastq.gz", "fastq fastq", 16012998000.0, 53376660.0, "H125 S2 L001 R1 001.fastq.gz", "0:150 1:150", "A:4365269809;C:3662731840;G:3768367416;T:4216409682;N:219253", 150, 150, null, null, 4365269809, 3662731840, 3768367416, 4216409682, 219253, "SRX4640370", "SRS3738588", "SRA766519", "Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology", "Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University", 2, 0.9402, 0.94198, 0.09449, 0.09528, 0.71999, 0.72512, 0.46106, 0.47624, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-04", "Adult", "Adult", "Blood", "Hematopoietic System"], [49748, "SRR8040452", "SRX4870965", "SRS3925946", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps5 RNA seq", "GSM3427234", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32lps5 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427234", "GSM3427234: t32lps5 RNA seq; Danio rerio; RNA Seq", "GSM3427234", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427234", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2525095950.0, 33667946.0, "GSM3427234 r1", "0:75 1:0", "A:654325529;C:574214700;G:560979222;T:735543925;N:32574", 75, 0, null, null, 654325529, 574214700, 560979222, 735543925, 32574, "SRX4870965", "SRS3925946", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.94279, null, 0.11158, null, 0.7739, null, 0.56131, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49749, "SRR8040451", "SRX4870964", "SRS3925945", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps4 RNA seq", "GSM3427233", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32lps4 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427233", "GSM3427233: t32lps4 RNA seq; Danio rerio; RNA Seq", "GSM3427233", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427233", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2324475900.0, 30993012.0, "GSM3427233 r1", "0:75 1:0", "A:593299460;C:533734154;G:526980483;T:670430972;N:30831", 75, 0, null, null, 593299460, 533734154, 526980483, 670430972, 30831, "SRX4870964", "SRS3925945", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.9455, null, 0.10812, null, 0.78046, null, 0.55958, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49750, "SRR8040450", "SRX4870962", "SRS3925943", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps3 RNA seq", "GSM3427232", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32lps3 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427232", "GSM3427232: t32lps3 RNA seq; Danio rerio; RNA Seq", "GSM3427232", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427232", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2390945250.0, 31879270.0, "GSM3427232 r1", "0:75 1:0", "A:620617289;C:546536575;G:538087155;T:685671110;N:33121", 75, 0, null, null, 620617289, 546536575, 538087155, 685671110, 33121, "SRX4870962", "SRS3925943", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.94216, null, 0.12594, null, 0.74925, null, 0.54113, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49751, "SRR8040449", "SRX4870961", "SRS3925942", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps2 RNA seq", "GSM3427231", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32lps2 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427231", "GSM3427231: t32lps2 RNA seq; Danio rerio; RNA Seq", "GSM3427231", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427231", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2372211900.0, 31629492.0, "GSM3427231 r1", "0:75 1:0", "A:609244327;C:553579722;G:546387461;T:662968297;N:32093", 75, 0, null, null, 609244327, 553579722, 546387461, 662968297, 32093, "SRX4870961", "SRS3925942", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.91064, null, 0.09975, null, 0.7318, null, 0.52325, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49752, "SRR8040448", "SRX4870960", "SRS3925941", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32lps1 RNA seq", "GSM3427230", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32lps1 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427230", "GSM3427230: t32lps1 RNA seq; Danio rerio; RNA Seq", "GSM3427230", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427230", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2601300000.0, 34684000.0, "GSM3427230 r1", "0:75 1:0", "A:696279292;C:582818011;G:571718581;T:750447755;N:36361", 75, 0, null, null, 696279292, 582818011, 571718581, 750447755, 36361, "SRX4870960", "SRS3925941", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.93957, null, 0.13624, null, 0.74641, null, 0.53521, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49753, "SRR8040447", "SRX4870959", "SRS3925940", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct10 RNA seq", "GSM3427229", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32ct10 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427229", "GSM3427229: t32ct10 RNA seq; Danio rerio; RNA Seq", "GSM3427229", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427229", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2206367925.0, 29418239.0, "GSM3427229 r1", "0:75 1:0", "A:564695219;C:513292663;G:507293808;T:621057423;N:28812", 75, 0, null, null, 564695219, 513292663, 507293808, 621057423, 28812, "SRX4870959", "SRS3925940", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.94594, null, 0.10744, null, 0.75511, null, 0.39959, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49754, "SRR8040446", "SRX4870958", "SRS3925939", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct8 RNA seq", "GSM3427228", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32ct8 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427228", "GSM3427228: t32ct8 RNA seq; Danio rerio; RNA Seq", "GSM3427228", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427228", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2160654900.0, 28808732.0, "GSM3427228 r1", "0:75 1:0", "A:560268124;C:491395956;G:494788088;T:614174312;N:28420", 75, 0, null, null, 560268124, 491395956, 494788088, 614174312, 28420, "SRX4870958", "SRS3925939", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.91437, null, 0.1131, null, 0.74661, null, 0.54441, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49755, "SRR8040445", "SRX4870957", "SRS3925938", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct6 RNA seq", "GSM3427227", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32ct6 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427227", "GSM3427227: t32ct6 RNA seq; Danio rerio; RNA Seq", "GSM3427227", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427227", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2175448725.0, 29005983.0, "GSM3427227 r1", "0:75 1:0", "A:588911336;C:487829921;G:471925092;T:626753522;N:28854", 75, 0, null, null, 588911336, 487829921, 471925092, 626753522, 28854, "SRX4870957", "SRS3925938", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.93789, null, 0.14514, null, 0.73839, null, 0.51589, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49756, "SRR8040444", "SRX4870956", "SRS3925937", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct3 RNA seq", "GSM3427226", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32ct3 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427226", "GSM3427226: t32ct3 RNA seq; Danio rerio; RNA Seq", "GSM3427226", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427226", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2350450425.0, 31339339.0, "GSM3427226 r1", "0:75 1:0", "A:612558543;C:533417342;G:511898107;T:692543546;N:32887", 75, 0, null, null, 612558543, 533417342, 511898107, 692543546, 32887, "SRX4870956", "SRS3925937", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.88939, null, 0.13696, null, 0.74649, null, 0.5071, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49757, "SRR8040443", "SRX4870955", "SRS3925936", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t32ct2 RNA seq", "GSM3427225", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t32ct2 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427225", "GSM3427225: t32ct2 RNA seq; Danio rerio; RNA Seq", "GSM3427225", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427225", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2500728150.0, 33343042.0, "GSM3427225 r1", "0:75 1:0", "A:663109698;C:565815864;G:564300306;T:707468578;N:33704", 75, 0, null, null, 663109698, 565815864, 564300306, 707468578, 33704, "SRX4870955", "SRS3925936", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.92821, null, 0.27272, null, 0.71969, null, 0.48781, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49758, "SRR8040442", "SRX4870954", "SRS3925988", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps8 RNA seq", "GSM3427224", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28lps8 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427224", "GSM3427224: t28lps8 RNA seq; Danio rerio; RNA Seq", "GSM3427224", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427224", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2342903700.0, 31238716.0, "GSM3427224 r1", "0:75 1:0", "A:613986696;C:535703169;G:527411229;T:665771221;N:31385", 75, 0, null, null, 613986696, 535703169, 527411229, 665771221, 31385, "SRX4870954", "SRS3925988", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.92238, null, 0.11108, null, 0.75223, null, 0.54609, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49759, "SRR8040441", "SRX4870953", "SRS3925935", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps4 RNA seq", "GSM3427223", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28lps4 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427223", "GSM3427223: t28lps4 RNA seq; Danio rerio; RNA Seq", "GSM3427223", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427223", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2009201550.0, 26789354.0, "GSM3427223 r1", "0:75 1:0", "A:503118595;C:466998217;G:461838042;T:577221133;N:25563", 75, 0, null, null, 503118595, 466998217, 461838042, 577221133, 25563, "SRX4870953", "SRS3925935", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.85044, null, 0.10362, null, 0.78149, null, 0.59209, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49760, "SRR8040440", "SRX4870952", "SRS3925934", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps3 RNA seq", "GSM3427222", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28lps3 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427222", "GSM3427222: t28lps3 RNA seq; Danio rerio; RNA Seq", "GSM3427222", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427222", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2262918375.0, 30172245.0, "GSM3427222 r1", "0:75 1:0", "A:557712391;C:559312209;G:525961809;T:619902191;N:29775", 75, 0, null, null, 557712391, 559312209, 525961809, 619902191, 29775, "SRX4870952", "SRS3925934", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.75792, null, 0.0861, null, 0.77977, null, 0.47016, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49761, "SRR8040439", "SRX4870951", "SRS3925933", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps2 RNA seq", "GSM3427221", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28lps2 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427221", "GSM3427221: t28lps2 RNA seq; Danio rerio; RNA Seq", "GSM3427221", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427221", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2362744425.0, 31503259.0, "GSM3427221 r1", "0:75 1:0", "A:605359081;C:550864600;G:543725417;T:662762619;N:32708", 75, 0, null, null, 605359081, 550864600, 543725417, 662762619, 32708, "SRX4870951", "SRS3925933", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.92027, null, 0.10164, null, 0.7403, null, 0.52342, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49762, "SRR8040438", "SRX4870950", "SRS3925932", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28lps1 RNA seq", "GSM3427220", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28lps1 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427220", "GSM3427220: t28lps1 RNA seq; Danio rerio; RNA Seq", "GSM3427220", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427220", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2219433000.0, 29592440.0, "GSM3427220 r1", "0:75 1:0", "A:559427934;C:519857518;G:513429485;T:626687457;N:30606", 75, 0, null, null, 559427934, 519857518, 513429485, 626687457, 30606, "SRX4870950", "SRS3925932", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.89861, null, 0.09731, null, 0.76889, null, 0.4978, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49763, "SRR8040437", "SRX4870949", "SRS3925931", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct7 RNA seq", "GSM3427219", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28ct7 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427219", "GSM3427219: t28ct7 RNA seq; Danio rerio; RNA Seq", "GSM3427219", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427219", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2329584075.0, 31061121.0, "GSM3427219 r1", "0:75 1:0", "A:624440550;C:517755267;G:499439713;T:687917841;N:30704", 75, 0, null, null, 624440550, 517755267, 499439713, 687917841, 30704, "SRX4870949", "SRS3925931", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.88755, null, 0.13982, null, 0.75739, null, 0.56552, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49764, "SRR8040436", "SRX4870948", "SRS3925930", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct5 RNA seq", "GSM3427218", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28ct5 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427218", "GSM3427218: t28ct5 RNA seq; Danio rerio; RNA Seq", "GSM3427218", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427218", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2116347225.0, 28217963.0, "GSM3427218 r1", "0:75 1:0", "A:549735276;C:488049942;G:477129323;T:601405177;N:27507", 75, 0, null, null, 549735276, 488049942, 477129323, 601405177, 27507, "SRX4870948", "SRS3925930", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.94198, null, 0.11445, null, 0.75487, null, 0.53068, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49765, "SRR8040435", "SRX4870947", "SRS3925929", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct3 RNA seq", "GSM3427217", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28ct3 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427217", "GSM3427217: t28ct3 RNA seq; Danio rerio; RNA Seq", "GSM3427217", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427217", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2689388775.0, 35858517.0, "GSM3427217 r1", "0:75 1:0", "A:723021338;C:600600385;G:595495733;T:770233672;N:37647", 75, 0, null, null, 723021338, 600600385, 595495733, 770233672, 37647, "SRX4870947", "SRS3925929", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.9433, null, 0.12005, null, 0.75175, null, 0.52805, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49766, "SRR8040434", "SRX4870946", "SRS3925927", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct2 RNA seq", "GSM3427216", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28ct2 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427216", "GSM3427216: t28ct2 RNA seq; Danio rerio; RNA Seq", "GSM3427216", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427216", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2358123450.0, 31441646.0, "GSM3427216 r1", "0:75 1:0", "A:608599109;C:548957677;G:537939593;T:662594226;N:32845", 75, 0, null, null, 608599109, 548957677, 537939593, 662594226, 32845, "SRX4870946", "SRS3925927", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.93343, null, 0.09904, null, 0.73701, null, 0.50221, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49767, "SRR8040433", "SRX4870945", "SRS3925928", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t28ct1 RNA seq", "GSM3427215", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t28ct1 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427215", "GSM3427215: t28ct1 RNA seq; Danio rerio; RNA Seq", "GSM3427215", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427215", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2340413625.0, 31205515.0, "GSM3427215 r1", "0:75 1:0", "A:601455783;C:547481954;G:534319560;T:657124045;N:32283", 75, 0, null, null, 601455783, 547481954, 534319560, 657124045, 32283, "SRX4870945", "SRS3925928", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.91963, null, 0.11224, null, 0.7363, null, 0.52602, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49768, "SRR8040432", "SRX4870944", "SRS3925926", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps8 RNA seq", "GSM3427214", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24lps8 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427214", "GSM3427214: t24lps8 RNA seq; Danio rerio; RNA Seq", "GSM3427214", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427214", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 1914339900.0, 25524532.0, "GSM3427214 r1", "0:75 1:0", "A:512209644;C:432894621;G:420067370;T:549142945;N:25320", 75, 0, null, null, 512209644, 432894621, 420067370, 549142945, 25320, "SRX4870944", "SRS3925926", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.92034, null, 0.12782, null, 0.73777, null, 0.53097, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49769, "SRR8040431", "SRX4870943", "SRS3925925", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps4 RNA seq", "GSM3427213", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24lps4 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427213", "GSM3427213: t24lps4 RNA seq; Danio rerio; RNA Seq", "GSM3427213", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427213", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2137202850.0, 28496038.0, "GSM3427213 r1", "0:75 1:0", "A:542475947;C:498947754;G:490366774;T:605383850;N:28525", 75, 0, null, null, 542475947, 498947754, 490366774, 605383850, 28525, "SRX4870943", "SRS3925925", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.91347, null, 0.09882, null, 0.75763, null, 0.46833, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49770, "SRR8040430", "SRX4870942", "SRS3925924", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps3 RNA seq", "GSM3427212", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24lps3 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427212", "GSM3427212: t24lps3 RNA seq; Danio rerio; RNA Seq", "GSM3427212", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427212", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2514206700.0, 33522756.0, "GSM3427212 r1", "0:75 1:0", "A:663829025;C:573707517;G:558298485;T:718336661;N:35012", 75, 0, null, null, 663829025, 573707517, 558298485, 718336661, 35012, "SRX4870942", "SRS3925924", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.93997, null, 0.11968, null, 0.74241, null, 0.53459, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49771, "SRR8040429", "SRX4870941", "SRS3925923", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps2 RNA seq", "GSM3427211", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24lps2 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427211", "GSM3427211: t24lps2 RNA seq; Danio rerio; RNA Seq", "GSM3427211", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427211", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2502607650.0, 33368102.0, "GSM3427211 r1", "0:75 1:0", "A:659207653;C:572452612;G:556598074;T:714314698;N:34613", 75, 0, null, null, 659207653, 572452612, 556598074, 714314698, 34613, "SRX4870941", "SRS3925923", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.92032, null, 0.12899, null, 0.7441, null, 0.52707, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49772, "SRR8040428", "SRX4870940", "SRS3925921", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24lps1 RNA seq", "GSM3427210", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24lps1 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427210", "GSM3427210: t24lps1 RNA seq; Danio rerio; RNA Seq", "GSM3427210", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427210", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2301013650.0, 30680182.0, "GSM3427210 r1", "0:75 1:0", "A:600014931;C:531214958;G:529006695;T:640746698;N:30368", 75, 0, null, null, 600014931, 531214958, 529006695, 640746698, 30368, "SRX4870940", "SRS3925921", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.94819, null, 0.10959, null, 0.74706, null, 0.44871, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49773, "SRR8040427", "SRX4870939", "SRS3925922", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct8 RNA seq", "GSM3427209", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24ct8 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427209", "GSM3427209: t24ct8 RNA seq; Danio rerio; RNA Seq", "GSM3427209", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427209", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2196418725.0, 29285583.0, "GSM3427209 r1", "0:75 1:0", "A:573278624;C:504375268;G:494497295;T:624238861;N:28677", 75, 0, null, null, 573278624, 504375268, 494497295, 624238861, 28677, "SRX4870939", "SRS3925922", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.94225, null, 0.11903, null, 0.75051, null, 0.55244, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49774, "SRR8040426", "SRX4870938", "SRS3925919", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct5 RNA seq", "GSM3427208", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24ct5 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427208", "GSM3427208: t24ct5 RNA seq; Danio rerio; RNA Seq", "GSM3427208", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427208", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2267199975.0, 30229333.0, "GSM3427208 r1", "0:75 1:0", "A:584789099;C:523482900;G:517770578;T:641127463;N:29935", 75, 0, null, null, 584789099, 523482900, 517770578, 641127463, 29935, "SRX4870938", "SRS3925919", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.88505, null, 0.11534, null, 0.74566, null, 0.55279, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49775, "SRR8040425", "SRX4870937", "SRS3925920", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct4 RNA seq", "GSM3427207", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24ct4 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427207", "GSM3427207: t24ct4 RNA seq; Danio rerio; RNA Seq", "GSM3427207", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427207", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2127502425.0, 28366699.0, "GSM3427207 r1", "0:75 1:0", "A:543019165;C:503067510;G:498801425;T:582586507;N:27818", 75, 0, null, null, 543019165, 503067510, 498801425, 582586507, 27818, "SRX4870937", "SRS3925920", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.9223, null, 0.07915, null, 0.72401, null, 0.51588, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49776, "SRR8040424", "SRX4870936", "SRS3925917", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct3 RNA seq", "GSM3427206", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24ct3 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427206", "GSM3427206: t24ct3 RNA seq; Danio rerio; RNA Seq", "GSM3427206", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427206", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2708072025.0, 36107627.0, "GSM3427206 r1", "0:75 1:0", "A:672991238;C:642923577;G:634295347;T:757824608;N:37255", 75, 0, null, null, 672991238, 642923577, 634295347, 757824608, 37255, "SRX4870936", "SRS3925917", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.95238, null, 0.09, null, 0.75513, null, 0.52869, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [49777, "SRR8040423", "SRX4870935", "SRS3925918", "SRP165277", "PRJNA495917", "Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish", "GSE121163", "Transcriptome Analysis", "Zebrafish eggs were collected at 28 \u00b0C  and split into three embryonic incubation temperature groups 24 \u00b0C  28 \u00b0C  32 \u00b0C. When larvae reaching first feeding  the incubation temperature of larvae from 24 \u00b0C and 32 \u00b0C was gradually changed to 28 \u00b0C  and all fish were kept at 28 \u00b0C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 \u00b5l of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 \u00b5l phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 \u00b0C vs 28 \u00b0C; 32 \u00b0C vs 28 \u00b0C  and between LPS treatment and control within each temperature group 24 \u00b0C LPS vs control; 28 \u00b0C LPS vs control; 32 \u00b0C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 \u00b0C embryonic incubation temperature compared to fish kept at constant 28 \u00b0C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 \u00b0C embryonic incubation temperature compared to fish kept at 28 \u00b0C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 \u00b0C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 \u00b0C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 \u00b0C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 \u00b0C  28 \u00b0C  32 \u00b0C.", "parent bioproject:PRJNA495914", null, null, "t24ct2 RNA seq", "GSM3427205", null, "tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf", "t24ct2 RNA seq", "Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library", "spleen", "Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 \u03bcl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 \u00b0C.", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "Zebrafish adults were maintained in a recirculating aquatic system at 28 \u00b1 0.5 \u00b0C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 \u00b1 0.5 \u00b0C  28 \u00b1 0.5 \u00b0C or 32 \u00b1 0.5 \u00b0C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.", "strain:AB|developmental stage:adult|age:100 dpf", "GSM3427205", "GSM3427205: t24ct2 RNA seq; Danio rerio; RNA Seq", "GSM3427205", null, "1", "Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 \u03bcl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 \u00b0C for 30 min  centrifuged at 3 000 \u00d7 g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 \u03bcl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 \u03bcl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 \u00b0C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 \u00b0C for 30 s  1 cycle; 98 \u00b0C for 10 s  65 \u00b0C for 75 s  14 cycles; 65 \u00b0C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.", "GEO Accession:GSM3427205", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP165277", null, null, null, null, 2495119875.0, 33268265.0, "GSM3427205 r1", "0:75 1:0", "A:627918584;C:589525055;G:590001770;T:687639074;N:35392", 75, 0, null, null, 627918584, 589525055, 590001770, 687639074, 35392, "SRX4870935", "SRS3925918", "SRA793499", "GEO", "Faculty of Biosciences and Aquaculture, Nord University", 1, 0.95519, null, 0.08888, null, 0.74746, null, 0.44744, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2018-10-12", "Adult", "Adult", "Spleen", "Hematopoietic System"], [51876, "SRR8922974", "SRX5704273", "SRS4643334", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: WT6", "GSM3728533", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "erythroid cells: WT6", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "GSM3728533", "GSM3728533: erythroid cells: WT6; Danio rerio; RNA Seq", "GSM3728533", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728533", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_TAGCTT_LWT6.1_val_1.fq.gz J633_AHFHNLBGX2_TAGCTT_LWT6.2_val_2.fq.gz", "fastq fastq", 8611605345.0, 32335443.0, "GSM3728533 r1", "0:133.59 1:132.74", "A:1724489451;C:2542199793;G:2626828499;T:1716562999;N:1524603", 133, 132, null, null, 1724489451, 2542199793, 2626828499, 1716562999, 1524603, "SRX5704273", "SRS4643334", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.91241, 0.96131, 0.10384, 0.10826, 0.77761, 0.7767, 0.69985, 0.69519, 128, 128, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51877, "SRR8922973", "SRX5704272", "SRS4643333", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: WT5", "GSM3728532", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "erythroid cells: WT5", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "GSM3728532", "GSM3728532: erythroid cells: WT5; Danio rerio; RNA Seq", "GSM3728532", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728532", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_TGACCA_LWT5.1_val_1.fq.gz J633_AHFHNLBGX2_TGACCA_LWT5.2_val_2.fq.gz", "fastq fastq", 8110446942.0, 28906836.0, "GSM3728532 r1", "0:140.70 1:139.87", "A:1479901358;C:2533764326;G:2613647627;T:1481710129;N:1423502", 140, 139, null, null, 1479901358, 2533764326, 2613647627, 1481710129, 1423502, "SRX5704272", "SRS4643333", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.92578, 0.97511, 0.09182, 0.09201, 0.80503, 0.80324, 0.76985, 0.7675, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51878, "SRR8922972", "SRX5704271", "SRS4643332", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: WT4", "GSM3728531", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "erythroid cells: WT4", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "GSM3728531", "GSM3728531: erythroid cells: WT4; Danio rerio; RNA Seq", "GSM3728531", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728531", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_TTAGGC_LWT4.2_val_2.fq.gz J633_AHFHNLBGX2_TTAGGC_LWT4.1_val_1.fq.gz", "fastq fastq", 8627466135.0, 32957109.0, "GSM3728531 r1", "0:131.12 1:130.66", "A:1686521982;C:2592728511;G:2670950174;T:1675745501;N:1519967", 131, 130, null, null, 1686521982, 2592728511, 2670950174, 1675745501, 1519967, "SRX5704271", "SRS4643332", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.91773, 0.96731, 0.11151, 0.1134, 0.78792, 0.78597, 0.73657, 0.73692, 104, 104, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51879, "SRR8922971", "SRX5704270", "SRS4643331", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: WT3", "GSM3728530", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "erythroid cells: WT3", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "GSM3728530", "GSM3728530: erythroid cells: WT3; Danio rerio; RNA Seq", "GSM3728530", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728530", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_CGATGT_LWT3.2_val_2.fq.gz J633_AHFHNLBGX2_CGATGT_LWT3.1_val_1.fq.gz", "fastq fastq", 7675701402.0, 28099783.0, "GSM3728530 r1", "0:136.90 1:136.26", "A:1496106079;C:2307580110;G:2386093773;T:1484556287;N:1365153", 136, 136, null, null, 1496106079, 2307580110, 2386093773, 1484556287, 1365153, "SRX5704270", "SRS4643331", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.91833, 0.96754, 0.10771, 0.10822, 0.80135, 0.80158, 0.76757, 0.7524, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51880, "SRR8922970", "SRX5704269", "SRS4643330", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: WT2", "GSM3728529", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "erythroid cells: WT2", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "GSM3728529", "GSM3728529: erythroid cells: WT2; Danio rerio; RNA Seq", "GSM3728529", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728529", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_ATCACG_LWT2.2_val_2.fq.gz J633_AHFHNLBGX2_ATCACG_LWT2.1_val_1.fq.gz", "fastq fastq", 8749226933.0, 32236600.0, "GSM3728529 r1", "0:135.97 1:135.43", "A:1818348438;C:2523018672;G:2595068272;T:1811215171;N:1576380", 135, 135, null, null, 1818348438, 2523018672, 2595068272, 1811215171, 1576380, "SRX5704269", "SRS4643330", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.91533, 0.96543, 0.12825, 0.13005, 0.77394, 0.77344, 0.70772, 0.67993, 143, 143, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"]], "truncated": false, 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