{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"bulk\" and tissue_curation = \"Embryo Imprecise\"", "rows": [[28690, "SRR26535341", "SRX22238472", "SRS19292733", "SRP468564", "PRJNA1032461", "A syngeneic spontaneous zebrafish model oftp53 deficient  EGFRviii  and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo", "GSE246295", "Transcriptome Analysis", "To build a patient relevantin vivomodel of human glioblastoma  we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life  with a gene expression signature similar to human glioblastoma of the mesenchymal subtype  along with a strong inflammatory component. Within early stage tumor lesions  and in an intact and endogenous tumor microenvironment  we visualized infiltration of phagocytic cells  as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages  suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore  CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context  while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether  we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging  high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation  with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains  we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells.  EGFRviii derived tumors were induced by microinjection of EGFRviii  PI3KCAH1047R  and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS  PI3KCAH1047R  GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3  KPG 1 3  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "Pooled EPS brains  mScarlet ve Sorted Cells", "GSM7866396", null, "source name:Sorted Cells|strain:CG1 p53null|tissue:Sorted Cells|geo loc name:missing|collection date:missing", "Pooled EPS brains  mScarlet ve Sorted Cells", "Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A \u201cdecoy aware\u201d index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23  with entries manually added for GFP  mScarlet  EGFRviii  KRAS  and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments:  r    seqBias    mp  3    validateMappings    rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.", "Sorted Cells", "Fertilized embryos injected with either EPS or KPG construct mix", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina  according to manufacturer\u2019s recommendations", "Zebrafish were housed and reared following approved animal use protocol", "strain:CG1 p53null|tissue:Sorted Cells", "GSM7866396", "GSM7866396: Pooled EPS brains  mScarlet ve Sorted Cells; Danio rerio; RNA Seq", "GSM7866396 r1", "GSM7866396", "1", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina  according to manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "loader:fastq load.py", "CS_Neg.fastq.gz", "fastq", 6384313020.0, 63211020.0, "GSM7866396 r1", "0:101", "A:1646899028;C:1504048934;G:1428638008;T:1804712211;N:14839", 101, null, null, null, 1646899028, 1504048934, 1428638008, 1804712211, 14839, "SRX22238472", "SRS19292733", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94094, null, 0.14273, null, 0.67416, null, 0.48471, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28691, "SRR26535342", "SRX22238471", "SRS19292732", "SRP468564", "PRJNA1032461", "A syngeneic spontaneous zebrafish model oftp53 deficient  EGFRviii  and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo", "GSE246295", "Transcriptome Analysis", "To build a patient relevantin vivomodel of human glioblastoma  we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life  with a gene expression signature similar to human glioblastoma of the mesenchymal subtype  along with a strong inflammatory component. Within early stage tumor lesions  and in an intact and endogenous tumor microenvironment  we visualized infiltration of phagocytic cells  as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages  suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore  CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context  while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether  we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging  high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation  with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains  we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells.  EGFRviii derived tumors were induced by microinjection of EGFRviii  PI3KCAH1047R  and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS  PI3KCAH1047R  GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3  KPG 1 3  alongside three control brains from injected siblings who did not develop tumors CTRL 1 3  were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition  resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.", null, "pubmed:39052000", null, "Pooled EPS brains  mScarlet+ve Sorted Cells", "GSM7866395", null, "source name:Sorted Cells|strain:CG1 p53null|tissue:Sorted Cells|geo loc name:missing|collection date:missing", "Pooled EPS brains  mScarlet+ve Sorted Cells", "Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A \u201cdecoy aware\u201d index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23  with entries manually added for GFP  mScarlet  EGFRviii  KRAS  and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments:  r    seqBias    mp  3    validateMappings    rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.", "Sorted Cells", "Fertilized embryos injected with either EPS or KPG construct mix", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina  according to manufacturer\u2019s recommendations", "Zebrafish were housed and reared following approved animal use protocol", "strain:CG1 p53null|tissue:Sorted Cells", "GSM7866395", "GSM7866395: Pooled EPS brains  mScarlet+ve Sorted Cells; Danio rerio; RNA Seq", "GSM7866395 r1", "GSM7866395", "1", "Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina  according to manufacturer's recommendations", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "loader:fastq load.py", "CS_Pos.fastq.gz", "fastq", 6221936027.0, 61603327.0, "GSM7866395 r1", "0:101", "A:1586867899;C:1467436044;G:1398048259;T:1769569401;N:14424", 101, null, null, null, 1586867899, 1467436044, 1398048259, 1769569401, 14424, "SRX22238471", "SRS19292732", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.88463, null, 0.14567, null, 0.69126, null, 0.48428, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2023-10-26", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38348, "SRR1785168", "SRX864139", "SRS834998", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "sphere cells rep1", "GSM1600044", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:sphere cells", "sphere cells rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:sphere cells", "GSM1600044", "GSM1600044: sphere cells rep1; Danio rerio; RNA Seq", "GSM1600044", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600044", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W10T_1.fastq.gz", "fastq", 9786365912.0, 96894712.0, "GSM1600044 r1", "0:101", "A:2573654910;C:2329556867;G:2311713480;T:2571211477;N:229178", 101, null, null, null, 2573654910, 2329556867, 2311713480, 2571211477, 229178, "SRX864139", "SRS834998", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.95572, null, 0.05587, null, 0.73657, null, 0.48128, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38349, "SRR1785167", "SRX864138", "SRS834995", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "1000 cell rep1", "GSM1600043", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:1000 cells", "1000 cell rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:1000 cells", "GSM1600043", "GSM1600043: 1000 cell rep1; Danio rerio; RNA Seq", "GSM1600043", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600043", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W9T_1.fastq.gz", "fastq", 8394219282.0, 83111082.0, "GSM1600043 r1", "0:101", "A:2195214424;C:2012486651;G:1991514912;T:2194810285;N:193010", 101, null, null, null, 2195214424, 2012486651, 1991514912, 2194810285, 193010, "SRX864138", "SRS834995", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.95627, null, 0.02474, null, 0.75761, null, 0.47804, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38350, "SRR1785166", "SRX864137", "SRS834994", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "256 cell rep1", "GSM1600042", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:256 cell", "256 cell rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:256 cell", "GSM1600042", "GSM1600042: 256 cell rep1; Danio rerio; RNA Seq", "GSM1600042", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600042", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W8T_1.fastq.gz", "fastq", 7155728901.0, 70848801.0, "GSM1600042 r1", "0:101", "A:1868886025;C:1718971317;G:1698634177;T:1869072256;N:165126", 101, null, null, null, 1868886025, 1718971317, 1698634177, 1869072256, 165126, "SRX864137", "SRS834994", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.95828, null, 0.02188, null, 0.76307, null, 0.47861, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38351, "SRR1785165", "SRX864136", "SRS835002", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "128 cell rep1", "GSM1600041", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:128 cell", "128 cell rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:128 cell", "GSM1600041", "GSM1600041: 128 cell rep1; Danio rerio; RNA Seq", "GSM1600041", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600041", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W7T_1.fastq.gz", "fastq", 11606209465.0, 114912965.0, "GSM1600041 r1", "0:101", "A:2959737203;C:2867533898;G:2855568487;T:2922947397;N:422480", 101, null, null, null, 2959737203, 2867533898, 2855568487, 2922947397, 422480, "SRX864136", "SRS835002", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.95887, null, 0.01798, null, 0.76824, null, 0.47695, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38352, "SRR1785164", "SRX864135", "SRS834996", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "64 cell rep1", "GSM1600040", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:64 cell", "64 cell rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:64 cell", "GSM1600040", "GSM1600040: 64 cell rep1; Danio rerio; RNA Seq", "GSM1600040", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600040", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W6T_1.fastq.gz", "fastq", 8895665799.0, 88075899.0, "GSM1600040 r1", "0:101", "A:2214065560;C:2252759233;G:2253964784;T:2174045976;N:830246", 101, null, null, null, 2214065560, 2252759233, 2253964784, 2174045976, 830246, "SRX864135", "SRS834996", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.96228, null, 0.0252, null, 0.77481, null, 0.4855, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38353, "SRR1785163", "SRX864134", "SRS834991", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "16 cell rep1", "GSM1600039", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:16 cell", "16 cell rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:16 cell", "GSM1600039", "GSM1600039: 16 cell rep1; Danio rerio; RNA Seq", "GSM1600039", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600039", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W5T_1.fastq.gz", "fastq", 8981816880.0, 88928880.0, "GSM1600039 r1", "0:101", "A:2337146004;C:2178908640;G:2150713936;T:2314829776;N:218524", 101, null, null, null, 2337146004, 2178908640, 2150713936, 2314829776, 218524, "SRX864134", "SRS834991", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.94918, null, 0.02746, null, 0.76264, null, 0.50197, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38354, "SRR1785162", "SRX864133", "SRS834990", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "4 cell rep1", "GSM1600038", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:4 cell", "4 cell rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:4 cell", "GSM1600038", "GSM1600038: 4 cell rep1; Danio rerio; RNA Seq", "GSM1600038", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600038", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W4T_1.fastq.gz", "fastq", 13975600381.0, 138372281.0, "GSM1600038 r1", "0:101", "A:3535785422;C:3493456274;G:3501455121;T:3443583783;N:1319781", 101, null, null, null, 3535785422, 3493456274, 3501455121, 3443583783, 1319781, "SRX864133", "SRS834990", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.96034, null, 0.01453, null, 0.80397, null, 0.48159, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38355, "SRR1785161", "SRX864132", "SRS834993", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "1 cell rep1", "GSM1600037", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:1 cell", "1 cell rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:1 cell", "GSM1600037", "GSM1600037: 1 cell rep1; Danio rerio; RNA Seq", "GSM1600037", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600037", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W3T_1.fastq.gz", "fastq", 4678817425.0, 46324925.0, "GSM1600037 r1", "0:101", "A:1226268061;C:1122155105;G:1116587571;T:1213657606;N:149082", 101, null, null, null, 1226268061, 1122155105, 1116587571, 1213657606, 149082, "SRX864132", "SRS834993", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.95665, null, 0.0188, null, 0.83631, null, 0.49048, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38356, "SRR1785160", "SRX864131", "SRS834992", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "oocyte cells rep1", "GSM1600036", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:oocyte cells", "oocyte cells rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:oocyte cells", "GSM1600036", "GSM1600036: oocyte cells rep1; Danio rerio; RNA Seq", "GSM1600036", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600036", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W2T_1.fastq.gz", "fastq", 6479637628.0, 64154828.0, "GSM1600036 r1", "0:101", "A:1673078599;C:1583189342;G:1563072444;T:1660074744;N:222499", 101, null, null, null, 1673078599, 1583189342, 1563072444, 1660074744, 222499, "SRX864131", "SRS834992", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.96179, null, 0.02299, null, 0.80052, null, 0.48738, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38357, "SRR1785159", "SRX864130", "SRS834997", "SRP053099", "PRJNA274362", "Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio", "GSE65556", "Transcriptome Analysis", "RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio", null, null, null, "sperm cells rep1", "GSM1600035", null, "tissue:Danio embryo cells|developmental stage:embryo|cell type:sperm cells", "sperm cells rep1", "Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage", "Danio embryo cells", null, "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", null, "developmental stage:embryo|cell type:sperm cells", "GSM1600035", "GSM1600035: sperm cells rep1; Danio rerio; RNA Seq", "GSM1600035", null, "1", "RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.", "GEO Accession:GSM1600035", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP053099", null, null, "W1T_1.fastq.gz", "fastq", 5332672841.0, 52798741.0, "GSM1600035 r1", "0:101", "A:1401445230;C:1274787038;G:1282323111;T:1373844821;N:272641", 101, null, null, null, 1401445230, 1274787038, 1282323111, 1373844821, 272641, "SRX864130", "SRS834997", "SRA236187", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.92774, null, 0.08051, null, 0.66204, null, 0.5063, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-02-03", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52139, "SRR8945527", "SRX5725657", "SRS4663725", "SRP193485", "PRJNA534270", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 2]", "GSE130200", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Cre Injected 2", "GSM3733699", null, "tissue:Embryo|genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with Cre to induce recombinase", "Cre Injected 2", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC 0.11.8 Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Trimmomatic version 0.36 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Only reads longer than 15 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11 using STAR 2.6.0c with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.14.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 12.04.2018 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danrer11 / GRCz11 Supplementary files format and content: The tab delimited matrix with DESeq normalized counts.", "Embryo", "Fish embryos raised at 28 \u030aC were subject to a 37 \u030aC heat shock for 1 hr by replacing the egg water with pre warmed 37 \u030aC egg water starting at different time points  and then keeping them in a 37 \u030aC incubator.", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with cre at the one cell stage and uninjected  were grown in E3 medium at xxx\u00b0C until tailbud stage.", "genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with Cre to induce recombinase", "GSM3733699", "GSM3733699: Cre Injected 2; Danio rerio; RNA Seq", "GSM3733699", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733699", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193485", null, null, "Marass_RNA_lib_inj_2.fastq.gz", "fastq", 1318624367.0, 17749685.0, "GSM3733699 r1", "0:74.29 1:0", "A:320435609;C:333825364;G:380093353;T:284207932;N:62109", 74, 0, null, null, 320435609, 333825364, 380093353, 284207932, 62109, "SRX5725657", "SRS4663725", "SRA878585", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.93022, null, 0.12203, null, 0.75935, null, 0.65366, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52140, "SRR8945526", "SRX5725656", "SRS4663727", "SRP193485", "PRJNA534270", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 2]", "GSE130200", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Cre Injected 1", "GSM3733698", null, "tissue:Embryo|genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with Cre to induce recombinase", "Cre Injected 1", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC 0.11.8 Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Trimmomatic version 0.36 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Only reads longer than 15 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11 using STAR 2.6.0c with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.14.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 12.04.2018 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danrer11 / GRCz11 Supplementary files format and content: The tab delimited matrix with DESeq normalized counts.", "Embryo", "Fish embryos raised at 28 \u030aC were subject to a 37 \u030aC heat shock for 1 hr by replacing the egg water with pre warmed 37 \u030aC egg water starting at different time points  and then keeping them in a 37 \u030aC incubator.", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with cre at the one cell stage and uninjected  were grown in E3 medium at xxx\u00b0C until tailbud stage.", "genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with Cre to induce recombinase", "GSM3733698", "GSM3733698: Cre Injected 1; Danio rerio; RNA Seq", "GSM3733698", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733698", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193485", null, null, "Marass_RNA_lib_inj_1.fastq.gz", "fastq", 1238690565.0, 16655617.0, "GSM3733698 r1", "0:74.37 1:0", "A:308225901;C:304528449;G:340420680;T:285472238;N:43297", 74, 0, null, null, 308225901, 304528449, 340420680, 285472238, 43297, "SRX5725656", "SRS4663727", "SRA878585", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.91996, null, 0.17266, null, 0.75308, null, 0.62697, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52141, "SRR8945525", "SRX5725655", "SRS4663726", "SRP193485", "PRJNA534270", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 2]", "GSE130200", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Uninjected 2", "GSM3733697", null, "tissue:Embryo|genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298", "Uninjected 2", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC 0.11.8 Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Trimmomatic version 0.36 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Only reads longer than 15 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11 using STAR 2.6.0c with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.14.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 12.04.2018 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danrer11 / GRCz11 Supplementary files format and content: The tab delimited matrix with DESeq normalized counts.", "Embryo", "Fish embryos raised at 28 \u030aC were subject to a 37 \u030aC heat shock for 1 hr by replacing the egg water with pre warmed 37 \u030aC egg water starting at different time points  and then keeping them in a 37 \u030aC incubator.", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with cre at the one cell stage and uninjected  were grown in E3 medium at xxx\u00b0C until tailbud stage.", "genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298", "GSM3733697", "GSM3733697: Uninjected 2; Danio rerio; RNA Seq", "GSM3733697", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733697", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193485", null, null, "Marass_RNA_lib_Ab_2.fastq.gz", "fastq", 1403915686.0, 18892344.0, "GSM3733697 r1", "0:74.31 1:0", "A:317311926;C:374434129;G:413852871;T:298232684;N:84076", 74, 0, null, null, 317311926, 374434129, 413852871, 298232684, 84076, "SRX5725655", "SRS4663726", "SRA878585", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.92665, null, 0.1128, null, 0.75929, null, 0.67981, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52142, "SRR8945524", "SRX5725654", "SRS4663724", "SRP193485", "PRJNA534270", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 2]", "GSE130200", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Uninjected 1", "GSM3733696", null, "tissue:Embryo|genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298", "Uninjected 1", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC 0.11.8 Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Trimmomatic version 0.36 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Only reads longer than 15 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11 using STAR 2.6.0c with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.14.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 12.04.2018 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danrer11 / GRCz11 Supplementary files format and content: The tab delimited matrix with DESeq normalized counts.", "Embryo", "Fish embryos raised at 28 \u030aC were subject to a 37 \u030aC heat shock for 1 hr by replacing the egg water with pre warmed 37 \u030aC egg water starting at different time points  and then keeping them in a 37 \u030aC incubator.", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with cre at the one cell stage and uninjected  were grown in E3 medium at xxx\u00b0C until tailbud stage.", "genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298", "GSM3733696", "GSM3733696: Uninjected 1; Danio rerio; RNA Seq", "GSM3733696", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733696", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193485", null, null, "Marass_RNA_lib_Ab_1.fastq.gz", "fastq", 1439519955.0, 19389235.0, "GSM3733696 r1", "0:74.24 1:0", "A:306530355;C:398952556;G:440224503;T:293709258;N:103283", 74, 0, null, null, 306530355, 398952556, 440224503, 293709258, 103283, "SRX5725654", "SRS4663724", "SRA878585", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.93162, null, 0.10646, null, 0.76627, null, 0.68572, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52143, "SRR8945523", "SRX5725653", "SRS4663723", "SRP193484", "PRJNA534271", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 1]", "GSE130199", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of wild type and npas4l bns297/bns297 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Npas4l KO 2", "GSM3733690", null, "tissue:Embryo|genotype:npas4l bns297/bns297", "Npas4l KO 2", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer10 GRCz10.90 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danRer10 Supplementary files format and content: The tab delimited matrix shows DESeq normalized counts.", "Embryo", null, "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Wild type AB embryos and npas4lbns297/bns297  were grown in E3 medium at 28\u00b0C until 6 somite stage.", "genotype:npas4l bns297/bns297", "GSM3733690", "GSM3733690: Npas4l KO 2; Danio rerio; RNA Seq", "GSM3733690", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733690", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193484", null, null, "NPAS4L-KO_2.fastq.gz", "fastq", 2188145091.0, 30480884.0, "GSM3733690 r1", "0:71.79 1:0", "A:565091244;C:556088129;G:587566739;T:479372691;N:26288", 71, 0, null, null, 565091244, 556088129, 587566739, 479372691, 26288, "SRX5725653", "SRS4663723", "SRA878584", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.93251, null, 0.36429, null, 0.79344, null, 0.7597, null, 70, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52144, "SRR8945522", "SRX5725652", "SRS4663722", "SRP193484", "PRJNA534271", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 1]", "GSE130199", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of wild type and npas4l bns297/bns297 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Npas4l KO 1", "GSM3733689", null, "tissue:Embryo|genotype:npas4l bns297/bns297", "Npas4l KO 1", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer10 GRCz10.90 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danRer10 Supplementary files format and content: The tab delimited matrix shows DESeq normalized counts.", "Embryo", null, "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Wild type AB embryos and npas4lbns297/bns297  were grown in E3 medium at 28\u00b0C until 6 somite stage.", "genotype:npas4l bns297/bns297", "GSM3733689", "GSM3733689: Npas4l KO 1; Danio rerio; RNA Seq", "GSM3733689", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733689", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193484", null, null, "NPAS4L-KO_1.fastq.gz", "fastq", 2433253496.0, 33687089.0, "GSM3733689 r1", "0:72.23 1:0", "A:593060668;C:644801659;G:698633749;T:496734812;N:22608", 72, 0, null, null, 593060668, 644801659, 698633749, 496734812, 22608, "SRX5725652", "SRS4663722", "SRA878584", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.95463, null, 0.30956, null, 0.82254, null, 0.78357, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52145, "SRR8945521", "SRX5725651", "SRS4663720", "SRP193484", "PRJNA534271", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 1]", "GSE130199", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of wild type and npas4l bns297/bns297 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "WT 2", "GSM3733688", null, "tissue:Embryo|genotype:wild type", "WT 2", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer10 GRCz10.90 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danRer10 Supplementary files format and content: The tab delimited matrix shows DESeq normalized counts.", "Embryo", null, "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Wild type AB embryos and npas4lbns297/bns297  were grown in E3 medium at 28\u00b0C until 6 somite stage.", "genotype:wild type", "GSM3733688", "GSM3733688: WT 2; Danio rerio; RNA Seq", "GSM3733688", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733688", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193484", null, null, "WT_2.fastq.gz", "fastq", 2431837029.0, 33941204.0, "GSM3733688 r1", "0:71.65 1:0", "A:605500316;C:637722247;G:683241300;T:505342978;N:30188", 71, 0, null, null, 605500316, 637722247, 683241300, 505342978, 30188, "SRX5725651", "SRS4663720", "SRA878584", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.94056, null, 0.3147, null, 0.80892, null, 0.75935, null, 37, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52146, "SRR8945520", "SRX5725650", "SRS4663721", "SRP193484", "PRJNA534271", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 1]", "GSE130199", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of wild type and npas4l bns297/bns297 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "WT 1", "GSM3733687", null, "tissue:Embryo|genotype:wild type", "WT 1", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer10 GRCz10.90 using STAR 2.4.0a with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danRer10 Supplementary files format and content: The tab delimited matrix shows DESeq normalized counts.", "Embryo", null, "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Wild type AB embryos and npas4lbns297/bns297  were grown in E3 medium at 28\u00b0C until 6 somite stage.", "genotype:wild type", "GSM3733687", "GSM3733687: WT 1; Danio rerio; RNA Seq", "GSM3733687", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733687", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193484", null, null, "WT_1.fastq.gz", "fastq", 2100118003.0, 29339428.0, "GSM3733687 r1", "0:71.58 1:0", "A:512913868;C:558713165;G:598879366;T:429576279;N:35325", 71, 0, null, null, 512913868, 558713165, 598879366, 429576279, 35325, "SRX5725650", "SRS4663721", "SRA878584", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.94426, null, 0.30979, null, 0.80417, null, 0.76724, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68502, "SRR18074848", "SRX14226378", "SRS12047703", "SRP358067", "PRJNA803151", "mRNA aging shapes the Cap2 methylome in mammalian mRNA", "GSE196043", "Other", "The mRNA cap structure is a major site of dynamic mRNA methylation.  mRNA caps exist in either the Cap1 or Cap2 form  depending on the presence of 2' O methylation on the first  or both the first and second transcribed nucleotide  respectively.  However  the identity of Cap2 containing mRNAs and the function of Cap2 are unclear.  Here we describe CLAM Cap Seq  a method for transcriptome wide mapping and quantification of Cap2.  We find that unlike other epitranscriptomic modifications  Cap2 can occur on all mRNAs.  Cap2 is formed through a slow continuous conversion of mRNAs from Cap1 to Cap2 as mRNAs age in the cytosol.  As a result  Cap2 is enriched on long lived mRNAs.  We find that large increases in the abundance of Cap1 leads to activation of RIG I  especially in conditions where RIG I expression is increased.  The methylation of Cap1 to Cap2 markedly reduces the ability of RNAs to bind and activate RIG I.  We find that the slow Cap2 methylation rate allows Cap2 to accumulate on host mRNAs yet ensures that low Cap2 levels occur on newly expressed viral RNAs.  Overall  these results reveal an immunostimulatory role for Cap1  and that Cap2 functions to reduce activation of the innate immune response. Overall design: We developed next generation sequencing methods for quantification of Cap2 methylation in bulk mRNA CapTag seq  as well as in individual mRNAs in a transcriptome wide manner CLAM Cap seq. Furthermore  we developed tools for measuring translation and stability of transcript start nucleotide TSN mRNA isoforms by combining polysome profiling and actinomycin D treatment with TSS seq transcription start site sequencing.", null, "pubmed:36725932", null, "Zebrafish CapQuant seq 2", "GSM5907184", null, "source name:48 hpf embryo|cell line/tissue:whole|genotype:wild type A/B|purification:oligodT25 beads", "Zebrafish CapQuant seq 2", "Removal of low quality reads and three prime end adapter trimming was performed with flexbar v2.5. Removal of duplicated reads was accomplished with pyFastqDuplicateRemover.py within the pyCRAC package v1.3.2. Read trimming was performed using seqtk package v1.3. Read alignement to fly  mouse or human genome was conducted using Bowtie v1.2.3. five prime end read coverage was calculated per each genomic position using BEDTools v2.28.0. Genome build: Drosohila melanogaster; dm6  Mus musculus; mm10  Homo sapiens; hg38.", "48 hpf embryo", null, "CapTag seq Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  PolyA+ RNA was isolated from total RNA using magnetic oligodT25 beads NEB.", "Zebrafish AB line embryos were maintained in E3 medium at 28 degrees and staged as previously described Kimmel et al.  Developmental Dynamics  1995.", "cell line/tissue:whole|genotype:wild type A/B|purification:oligodT25 beads", "GSM5907184", "GSM5907184: Zebrafish CapQuant seq 2; Danio rerio; OTHER", "GSM5907184 r1", "GSM5907184", "1", "CapTag seq Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  PolyA+ RNA was isolated from total RNA using magnetic oligodT25 beads NEB.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP358067", null, null, "Zebrafish_CQS2_R1.fastq.gz", "fastq", 658260009.0, 12907059.0, "GSM5907184 r1", "0:51 1:0", "A:158463141;C:142984303;G:213148834;T:143656235;N:7496", 51, 0, null, null, 158463141, 142984303, 213148834, 143656235, 7496, "SRX14226378", "SRS12047703", "SRA1545466", "Pharmacology, Weill Cornell Medicine", "Pharmacology, Weill Cornell Medicine", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-02-18", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68503, "SRR18074849", "SRX14226377", "SRS12047702", "SRP358067", "PRJNA803151", "mRNA aging shapes the Cap2 methylome in mammalian mRNA", "GSE196043", "Other", "The mRNA cap structure is a major site of dynamic mRNA methylation.  mRNA caps exist in either the Cap1 or Cap2 form  depending on the presence of 2' O methylation on the first  or both the first and second transcribed nucleotide  respectively.  However  the identity of Cap2 containing mRNAs and the function of Cap2 are unclear.  Here we describe CLAM Cap Seq  a method for transcriptome wide mapping and quantification of Cap2.  We find that unlike other epitranscriptomic modifications  Cap2 can occur on all mRNAs.  Cap2 is formed through a slow continuous conversion of mRNAs from Cap1 to Cap2 as mRNAs age in the cytosol.  As a result  Cap2 is enriched on long lived mRNAs.  We find that large increases in the abundance of Cap1 leads to activation of RIG I  especially in conditions where RIG I expression is increased.  The methylation of Cap1 to Cap2 markedly reduces the ability of RNAs to bind and activate RIG I.  We find that the slow Cap2 methylation rate allows Cap2 to accumulate on host mRNAs yet ensures that low Cap2 levels occur on newly expressed viral RNAs.  Overall  these results reveal an immunostimulatory role for Cap1  and that Cap2 functions to reduce activation of the innate immune response. Overall design: We developed next generation sequencing methods for quantification of Cap2 methylation in bulk mRNA CapTag seq  as well as in individual mRNAs in a transcriptome wide manner CLAM Cap seq. Furthermore  we developed tools for measuring translation and stability of transcript start nucleotide TSN mRNA isoforms by combining polysome profiling and actinomycin D treatment with TSS seq transcription start site sequencing.", null, "pubmed:36725932", null, "Zebrafish CapQuant seq 1", "GSM5907183", null, "source name:48 hpf embryo|cell line/tissue:whole|genotype:wild type A/B|purification:oligodT25 beads", "Zebrafish CapQuant seq 1", "Removal of low quality reads and three prime end adapter trimming was performed with flexbar v2.5. Removal of duplicated reads was accomplished with pyFastqDuplicateRemover.py within the pyCRAC package v1.3.2. Read trimming was performed using seqtk package v1.3. Read alignement to fly  mouse or human genome was conducted using Bowtie v1.2.3. five prime end read coverage was calculated per each genomic position using BEDTools v2.28.0. Genome build: Drosohila melanogaster; dm6  Mus musculus; mm10  Homo sapiens; hg38.", "48 hpf embryo", null, "CapTag seq Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  PolyA+ RNA was isolated from total RNA using magnetic oligodT25 beads NEB.", "Zebrafish AB line embryos were maintained and staged as previously described Kimmel et al.  Developmental Dynamics  1995.", "cell line/tissue:whole|genotype:wild type A/B|purification:oligodT25 beads", "GSM5907183", "GSM5907183: Zebrafish CapQuant seq 1; Danio rerio; OTHER", "GSM5907183 r1", "GSM5907183", "1", "CapTag seq Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  PolyA+ RNA was isolated from total RNA using magnetic oligodT25 beads NEB.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP358067", null, null, "Zebrafish_CQS1_R1.fastq.gz", "fastq", 1636691694.0, 32091994.0, "GSM5907183 r1", "0:51 1:0", "A:394187895;C:355520591;G:529426272;T:357424863;N:132073", 51, 0, null, null, 394187895, 355520591, 529426272, 357424863, 132073, "SRX14226377", "SRS12047702", "SRA1545466", "Pharmacology, Weill Cornell Medicine", "Pharmacology, Weill Cornell Medicine", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-02-18", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [72263, "SRR22398713", "SRX18368432", "SRS15854864", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "wt cp25 4", "GSM6754861", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:2.5|mdibl id:WT +2.5 4|conc ng ul:138.222|a 260s280:2.11|a 260s230:1.69|sequence count:53490826", "wt cp25 4", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype WT|developmental stage:5 dpf embryo|time:2.5|mdibl id:WT +2.5 4|conc ng ul:138.222|a 260s280:2.11|a 260s230:1.69|sequence count:53490826", "GSM6754861", "GSM6754861: wt cp25 4; Danio rerio; RNA Seq", "GSM6754861 r1", "GSM6754861", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "wt_cp25_4_R1.fastq.gz", "fastq", 3971633541.0, 53490826.0, "GSM6754861 r1", "0:74.25 1:0", "A:1007182228;C:929484142;G:892507427;T:1142079615;N:380129", 74, 0, null, null, 1007182228, 929484142, 892507427, 1142079615, 380129, "SRX18368432", "SRS15854864", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94921, null, 0.1103, null, 0.66513, null, 0.48762, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72264, "SRR22398716", "SRX18368431", "SRS15854863", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "wt cp25 3", "GSM6754860", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:2.5|mdibl id:WT +2.5 3|conc ng ul:107.595|a 260s280:2.14|a 260s230:1.34|sequence count:55925525", "wt cp25 3", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype WT|developmental stage:5 dpf embryo|time:2.5|mdibl id:WT +2.5 3|conc ng ul:107.595|a 260s280:2.14|a 260s230:1.34|sequence count:55925525", "GSM6754860", "GSM6754860: wt cp25 3; Danio rerio; RNA Seq", "GSM6754860 r1", "GSM6754860", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "wt_cp25_3_R1.fastq.gz", "fastq", 4151847256.0, 55925525.0, "GSM6754860 r1", "0:74.24 1:0", "A:1050577660;C:974197737;G:936600779;T:1190080560;N:390520", 74, 0, null, null, 1050577660, 974197737, 936600779, 1190080560, 390520, "SRX18368431", "SRS15854863", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94795, null, 0.10889, null, 0.66732, null, 0.48527, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72265, "SRR22398714", "SRX18368430", "SRS15854862", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "wt cp25 2", "GSM6754859", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:2.5|mdibl id:WT +2.5 2|conc ng ul:117.806|a 260s280:2.13|a 260s230:0.82|sequence count:58067253", "wt cp25 2", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype WT|developmental stage:5 dpf embryo|time:2.5|mdibl id:WT +2.5 2|conc ng ul:117.806|a 260s280:2.13|a 260s230:0.82|sequence count:58067253", "GSM6754859", "GSM6754859: wt cp25 2; Danio rerio; RNA Seq", "GSM6754859 r1", "GSM6754859", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "wt_cp25_2_R1.fastq.gz", "fastq", 4309818874.0, 58067253.0, "GSM6754859 r1", "0:74.22 1:0", "A:1114944612;C:990370711;G:956027483;T:1248075089;N:400979", 74, 0, null, null, 1114944612, 990370711, 956027483, 1248075089, 400979, "SRX18368430", "SRS15854862", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94404, null, 0.12016, null, 0.66732, null, 0.47887, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72266, "SRR22398715", "SRX18368429", "SRS15854861", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "wt cp25 1", "GSM6754858", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:2.5|mdibl id:WT +2.5 1|conc ng ul:127.291|a 260s280:2.15|a 260s230:0.94|sequence count:59428413", "wt cp25 1", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype WT|developmental stage:5 dpf embryo|time:2.5|mdibl id:WT +2.5 1|conc ng ul:127.291|a 260s280:2.15|a 260s230:0.94|sequence count:59428413", "GSM6754858", "GSM6754858: wt cp25 1; Danio rerio; RNA Seq", "GSM6754858 r1", "GSM6754858", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "wt_cp25_1_R1.fastq.gz", "fastq", 4407739857.0, 59428413.0, "GSM6754858 r1", "0:74.17 1:0", "A:1137830012;C:1015732103;G:975339556;T:1278384440;N:453746", 74, 0, null, null, 1137830012, 1015732103, 975339556, 1278384440, 453746, "SRX18368429", "SRS15854861", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94356, null, 0.12239, null, 0.67543, null, 0.48843, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72267, "SRR22398717", "SRX18368428", "SRS15854860", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "ko cp25 4", "GSM6754857", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:2.5|mdibl id:KO +2.5 4|conc ng ul:163.39|a 260s280:2.11|a 260s230:2.03|sequence count:46388653", "ko cp25 4", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype Klf9  / |developmental stage:5 dpf embryo|time:2.5|mdibl id:KO +2.5 4|conc ng ul:163.39|a 260s280:2.11|a 260s230:2.03|sequence count:46388653", "GSM6754857", "GSM6754857: ko cp25 4; Danio rerio; RNA Seq", "GSM6754857 r1", "GSM6754857", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "ko_cp25_4_R1.fastq.gz", "fastq", 3446442454.0, 46388653.0, "GSM6754857 r1", "0:74.29 1:0", "A:885382304;C:794319275;G:763794659;T:1002667835;N:278381", 74, 0, null, null, 885382304, 794319275, 763794659, 1002667835, 278381, "SRX18368428", "SRS15854860", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94513, null, 0.1161, null, 0.66598, null, 0.4967, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72268, "SRR22398718", "SRX18368427", "SRS15854859", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "ko cp25 3", "GSM6754856", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:2.5|mdibl id:KO +2.5 3|conc ng ul:119.387|a 260s280:2.09|a 260s230:2.25|sequence count:58009227", "ko cp25 3", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype Klf9  / |developmental stage:5 dpf embryo|time:2.5|mdibl id:KO +2.5 3|conc ng ul:119.387|a 260s280:2.09|a 260s230:2.25|sequence count:58009227", "GSM6754856", "GSM6754856: ko cp25 3; Danio rerio; RNA Seq", "GSM6754856 r1", "GSM6754856", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "ko_cp25_3_R1.fastq.gz", "fastq", 4311994952.0, 58009227.0, "GSM6754856 r1", "0:74.33 1:0", "A:1098005222;C:1005030862;G:965223116;T:1243452005;N:283747", 74, 0, null, null, 1098005222, 1005030862, 965223116, 1243452005, 283747, "SRX18368427", "SRS15854859", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94673, null, 0.11276, null, 0.66847, null, 0.49233, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72269, "SRR22398726", "SRX18368426", "SRS15854858", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "ko cp25 2", "GSM6754855", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:2.5|mdibl id:KO +2.5 2|conc ng ul:105.565|a 260s280:2.12|a 260s230:0.98|sequence count:49990819", "ko cp25 2", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype Klf9  / |developmental stage:5 dpf embryo|time:2.5|mdibl id:KO +2.5 2|conc ng ul:105.565|a 260s280:2.12|a 260s230:0.98|sequence count:49990819", "GSM6754855", "GSM6754855: ko cp25 2; Danio rerio; RNA Seq", "GSM6754855 r1", "GSM6754855", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "ko_cp25_2_R1.fastq.gz", "fastq", 3706388155.0, 49990819.0, "GSM6754855 r1", "0:74.14 1:0", "A:948025653;C:857558445;G:827401541;T:1072813059;N:589457", 74, 0, null, null, 948025653, 857558445, 827401541, 1072813059, 589457, "SRX18368426", "SRS15854858", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.9446, null, 0.12345, null, 0.66902, null, 0.49658, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72270, "SRR22398719", "SRX18368425", "SRS15854857", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "ko cp25 1", "GSM6754854", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:2.5|mdibl id:KO +2.5 1|conc ng ul:109.491|a 260s280:2.11|a 260s230:1.42|sequence count:47621085", "ko cp25 1", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype Klf9  / |developmental stage:5 dpf embryo|time:2.5|mdibl id:KO +2.5 1|conc ng ul:109.491|a 260s280:2.11|a 260s230:1.42|sequence count:47621085", "GSM6754854", "GSM6754854: ko cp25 1; Danio rerio; RNA Seq", "GSM6754854 r1", "GSM6754854", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "ko_cp25_1_R1.fastq.gz", "fastq", 3535345923.0, 47621085.0, "GSM6754854 r1", "0:74.24 1:0", "A:912664803;C:814365640;G:784261393;T:1023651094;N:402993", 74, 0, null, null, 912664803, 814365640, 784261393, 1023651094, 402993, "SRX18368425", "SRS15854857", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94483, null, 0.12372, null, 0.67058, null, 0.49227, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72271, "SRR22398725", "SRX18368424", "SRS15854856", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "wt bz00 4", "GSM6754853", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:0|mdibl id:WT 0 4|conc ng ul:143.511|a 260s280:2.13|a 260s230:1.57|sequence count:61583000", "wt bz00 4", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype WT|developmental stage:5 dpf embryo|time:0|mdibl id:WT 0 4|conc ng ul:143.511|a 260s280:2.13|a 260s230:1.57|sequence count:61583000", "GSM6754853", "GSM6754853: wt bz00 4; Danio rerio; RNA Seq", "GSM6754853 r1", "GSM6754853", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "wt_bz00_4_R1.fastq.gz", "fastq", 4558041252.0, 61583000.0, "GSM6754853 r1", "0:74.01 1:0", "A:1174813850;C:1053099181;G:1012107824;T:1316617074;N:1403323", 74, 0, null, null, 1174813850, 1053099181, 1012107824, 1316617074, 1403323, "SRX18368424", "SRS15854856", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94572, null, 0.12348, null, 0.67448, null, 0.4873, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72272, "SRR22398720", "SRX18368423", "SRS15854855", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "wt bz00 3", "GSM6754852", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:0|mdibl id:WT 0 3|conc ng ul:138.681|a 260s280:2.13|a 260s230:1.54|sequence count:58341062", "wt bz00 3", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype WT|developmental stage:5 dpf embryo|time:0|mdibl id:WT 0 3|conc ng ul:138.681|a 260s280:2.13|a 260s230:1.54|sequence count:58341062", "GSM6754852", "GSM6754852: wt bz00 3; Danio rerio; RNA Seq", "GSM6754852 r1", "GSM6754852", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "wt_bz00_3_R1.fastq.gz", "fastq", 4324729722.0, 58341062.0, "GSM6754852 r1", "0:74.13 1:0", "A:1096278358;C:1014112739;G:973246126;T:1240721487;N:371012", 74, 0, null, null, 1096278358, 1014112739, 973246126, 1240721487, 371012, "SRX18368423", "SRS15854855", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94897, null, 0.11731, null, 0.66835, null, 0.48302, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72273, "SRR22398724", "SRX18368422", "SRS15854854", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "wt bz00 2", "GSM6754851", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:0|mdibl id:WT 0 2|conc ng ul:135.007|a 260s280:2.13|a 260s230:0.98|sequence count:49196377", "wt bz00 2", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype WT|developmental stage:5 dpf embryo|time:0|mdibl id:WT 0 2|conc ng ul:135.007|a 260s280:2.13|a 260s230:0.98|sequence count:49196377", "GSM6754851", "GSM6754851: wt bz00 2; Danio rerio; RNA Seq", "GSM6754851 r1", "GSM6754851", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "wt_bz00_2_R1.fastq.gz", "fastq", 3643049767.0, 49196377.0, "GSM6754851 r1", "0:74.05 1:0", "A:925447169;C:847530454;G:817481959;T:1051509088;N:1081097", 74, 0, null, null, 925447169, 847530454, 817481959, 1051509088, 1081097, "SRX18368422", "SRS15854854", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94762, null, 0.1071, null, 0.66149, null, 0.48635, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72274, "SRR22398721", "SRX18368421", "SRS15854853", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "wt bz00 1", "GSM6754850", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:0|mdibl id:WT 0 1|conc ng ul:149.394|a 260s280:2.12|a 260s230:1.12|sequence count:55724803", "wt bz00 1", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype WT|developmental stage:5 dpf embryo|time:0|mdibl id:WT 0 1|conc ng ul:149.394|a 260s280:2.12|a 260s230:1.12|sequence count:55724803", "GSM6754850", "GSM6754850: wt bz00 1; Danio rerio; RNA Seq", "GSM6754850 r1", "GSM6754850", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "wt_bz00_1_R1.fastq.gz", "fastq", 4132217260.0, 55724803.0, "GSM6754850 r1", "0:74.15 1:0", "A:1065785685;C:951791352;G:916868354;T:1197414078;N:357791", 74, 0, null, null, 1065785685, 951791352, 916868354, 1197414078, 357791, "SRX18368421", "SRS15854853", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94384, null, 0.11036, null, 0.66253, null, 0.48713, null, 73, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72275, "SRR22398722", "SRX18368420", "SRS15854852", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "ko bz00 3", "GSM6754848", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:0|mdibl id:KO 0 3|conc ng ul:125.073|a 260s280:2.13|a 260s230:0.54|sequence count:43888003", "ko bz00 3", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype Klf9  / |developmental stage:5 dpf embryo|time:0|mdibl id:KO 0 3|conc ng ul:125.073|a 260s280:2.13|a 260s230:0.54|sequence count:43888003", "GSM6754848", "GSM6754848: ko bz00 3; Danio rerio; RNA Seq", "GSM6754848 r1", "GSM6754848", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "ko_bz00_3_R1.fastq.gz", "fastq", 3261925759.0, 43888003.0, "GSM6754848 r1", "0:74.32 1:0", "A:829455673;C:763869126;G:729279622;T:939176246;N:145092", 74, 0, null, null, 829455673, 763869126, 729279622, 939176246, 145092, "SRX18368420", "SRS15854852", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94701, null, 0.12716, null, 0.67004, null, 0.50296, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72276, "SRR22398723", "SRX18368419", "SRS15854851", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "ko bz00 4", "GSM6754849", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:0|mdibl id:KO 0 4|conc ng ul:126.704|a 260s280:2.12|a 260s230:1.91|sequence count:46608771", "ko bz00 4", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype Klf9  / |developmental stage:5 dpf embryo|time:0|mdibl id:KO 0 4|conc ng ul:126.704|a 260s280:2.12|a 260s230:1.91|sequence count:46608771", "GSM6754849", "GSM6754849: ko bz00 4; Danio rerio; RNA Seq", "GSM6754849 r1", "GSM6754849", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "ko_bz00_4_R1.fastq.gz", "fastq", 3465408347.0, 46608771.0, "GSM6754849 r1", "0:74.35 1:0", "A:882442105;C:807154063;G:770576357;T:1004932656;N:303166", 74, 0, null, null, 882442105, 807154063, 770576357, 1004932656, 303166, "SRX18368419", "SRS15854851", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94561, null, 0.12587, null, 0.6672, null, 0.48039, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72277, "SRR22398727", "SRX18368418", "SRS15854850", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "ko bz00 2", "GSM6754847", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:0|mdibl id:KO 0 2|conc ng ul:123.215|a 260s280:2.12|a 260s230:1.67|sequence count:43789649", "ko bz00 2", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype Klf9  / |developmental stage:5 dpf embryo|time:0|mdibl id:KO 0 2|conc ng ul:123.215|a 260s280:2.12|a 260s230:1.67|sequence count:43789649", "GSM6754847", "GSM6754847: ko bz00 2; Danio rerio; RNA Seq", "GSM6754847 r1", "GSM6754847", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "ko_bz00_2_R1.fastq.gz", "fastq", 3253450441.0, 43789649.0, "GSM6754847 r1", "0:74.30 1:0", "A:839107458;C:748950160;G:719943086;T:945309012;N:140725", 74, 0, null, null, 839107458, 748950160, 719943086, 945309012, 140725, "SRX18368418", "SRS15854850", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94525, null, 0.12477, null, 0.67028, null, 0.49471, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72278, "SRR22398734", "SRX18368417", "SRS15854849", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "ko bz00 1", "GSM6754846", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time:0|mdibl id:KO 0 1|conc ng ul:138.474|a 260s280:2.15|a 260s230:1.58|sequence count:63322040", "ko bz00 1", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype Klf9  / |developmental stage:5 dpf embryo|time:0|mdibl id:KO 0 1|conc ng ul:138.474|a 260s280:2.15|a 260s230:1.58|sequence count:63322040", "GSM6754846", "GSM6754846: ko bz00 1; Danio rerio; RNA Seq", "GSM6754846 r1", "GSM6754846", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "ko_bz00_1_R1.fastq.gz", "fastq", 4702919348.0, 63322040.0, "GSM6754846 r1", "0:74.27 1:0", "A:1208884586;C:1089826557;G:1044501432;T:1359302369;N:404404", 74, 0, null, null, 1208884586, 1089826557, 1044501432, 1359302369, 404404, "SRX18368417", "SRS15854849", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94777, null, 0.12221, null, 0.67708, null, 0.49392, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72279, "SRR22398728", "SRX18368416", "SRS15854848", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "wt am30 4", "GSM6754845", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time: 3|mdibl id:WT  3 4|conc ng ul:134.487|a 260s280:2.15|a 260s230:1.39|sequence count:63356407", "wt am30 4", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype WT|developmental stage:5 dpf embryo|time: 3|mdibl id:WT  3 4|conc ng ul:134.487|a 260s280:2.15|a 260s230:1.39|sequence count:63356407", "GSM6754845", "GSM6754845: wt am30 4; Danio rerio; RNA Seq", "GSM6754845 r1", "GSM6754845", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "wt_am30_4_R1.fastq.gz", "fastq", 4707868699.0, 63356407.0, "GSM6754845 r1", "0:74.31 1:0", "A:1203701452;C:1089432799;G:1048996672;T:1364846807;N:890969", 74, 0, null, null, 1203701452, 1089432799, 1048996672, 1364846807, 890969, "SRX18368416", "SRS15854848", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94701, null, 0.11284, null, 0.66714, null, 0.48591, null, 73, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72280, "SRR22398733", "SRX18368415", "SRS15854847", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "wt am30 3", "GSM6754844", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time: 3|mdibl id:WT  3 3|conc ng ul:133.341|a 260s280:2.07|a 260s230:1.29|sequence count:67175079", "wt am30 3", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype WT|developmental stage:5 dpf embryo|time: 3|mdibl id:WT  3 3|conc ng ul:133.341|a 260s280:2.07|a 260s230:1.29|sequence count:67175079", "GSM6754844", "GSM6754844: wt am30 3; Danio rerio; RNA Seq", "GSM6754844 r1", "GSM6754844", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "wt_am30_3_R1.fastq.gz", "fastq", 4993030085.0, 67175079.0, "GSM6754844 r1", "0:74.33 1:0", "A:1275030845;C:1160279340;G:1117068336;T:1440349025;N:302539", 74, 0, null, null, 1275030845, 1160279340, 1117068336, 1440349025, 302539, "SRX18368415", "SRS15854847", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94645, null, 0.11554, null, 0.66724, null, 0.46708, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72281, "SRR22398729", "SRX18368414", "SRS15854846", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "wt am30 2", "GSM6754843", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time: 3|mdibl id:WT  3 2|conc ng ul:144.163|a 260s280:2.11|a 260s230:1.41|sequence count:64202767", "wt am30 2", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype WT|developmental stage:5 dpf embryo|time: 3|mdibl id:WT  3 2|conc ng ul:144.163|a 260s280:2.11|a 260s230:1.41|sequence count:64202767", "GSM6754843", "GSM6754843: wt am30 2; Danio rerio; RNA Seq", "GSM6754843 r1", "GSM6754843", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "wt_am30_2_R1.fastq.gz", "fastq", 4774624628.0, 64202767.0, "GSM6754843 r1", "0:74.37 1:0", "A:1226843673;C:1106688102;G:1065434365;T:1375454118;N:204370", 74, 0, null, null, 1226843673, 1106688102, 1065434365, 1375454118, 204370, "SRX18368414", "SRS15854846", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94652, null, 0.12306, null, 0.66951, null, 0.49383, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72282, "SRR22398732", "SRX18368413", "SRS15854845", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "wt am30 1", "GSM6754842", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time: 3|mdibl id:WT  3 1|conc ng ul:123.886|a 260s280:2.1|a 260s230:1.65|sequence count:57588838", "wt am30 1", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype WT|developmental stage:5 dpf embryo|time: 3|mdibl id:WT  3 1|conc ng ul:123.886|a 260s280:2.1|a 260s230:1.65|sequence count:57588838", "GSM6754842", "GSM6754842: wt am30 1; Danio rerio; RNA Seq", "GSM6754842 r1", "GSM6754842", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "wt_am30_1_R1.fastq.gz", "fastq", 4279904253.0, 57588838.0, "GSM6754842 r1", "0:74.32 1:0", "A:1108696635;C:979371472;G:944355461;T:1247033388;N:447297", 74, 0, null, null, 1108696635, 979371472, 944355461, 1247033388, 447297, "SRX18368413", "SRS15854845", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94514, null, 0.11835, null, 0.66981, null, 0.4881, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72283, "SRR22398730", "SRX18368412", "SRS15854844", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "ko am30 4", "GSM6754841", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time: 3|mdibl id:KO  3 4|conc ng ul:146.811|a 260s280:2.13|a 260s230:1.64|sequence count:45580367", "ko am30 4", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype Klf9  / |developmental stage:5 dpf embryo|time: 3|mdibl id:KO  3 4|conc ng ul:146.811|a 260s280:2.13|a 260s230:1.64|sequence count:45580367", "GSM6754841", "GSM6754841: ko am30 4; Danio rerio; RNA Seq", "GSM6754841 r1", "GSM6754841", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "ko_am30_4_R1.fastq.gz", "fastq", 3387836215.0, 45580367.0, "GSM6754841 r1", "0:74.33 1:0", "A:878994756;C:771715446;G:742146109;T:994764227;N:215677", 74, 0, null, null, 878994756, 771715446, 742146109, 994764227, 215677, "SRX18368412", "SRS15854844", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94286, null, 0.12355, null, 0.6731, null, 0.48888, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72284, "SRR22398731", "SRX18368411", "SRS15854843", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "ko am30 3", "GSM6754840", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time: 3|mdibl id:KO  3 3|conc ng ul:130.202|a 260s280:2.11|a 260s230:1.82|sequence count:45716196", "ko am30 3", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype Klf9  / |developmental stage:5 dpf embryo|time: 3|mdibl id:KO  3 3|conc ng ul:130.202|a 260s280:2.11|a 260s230:1.82|sequence count:45716196", "GSM6754840", "GSM6754840: ko am30 3; Danio rerio; RNA Seq", "GSM6754840 r1", "GSM6754840", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "ko_am30_3_R1.fastq.gz", "fastq", 3397790979.0, 45716196.0, "GSM6754840 r1", "0:74.32 1:0", "A:874671145;C:781147028;G:750987590;T:990652325;N:332891", 74, 0, null, null, 874671145, 781147028, 750987590, 990652325, 332891, "SRX18368411", "SRS15854843", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94685, null, 0.12013, null, 0.67247, null, 0.49487, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72285, "SRR22398735", "SRX18368410", "SRS15854842", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "ko am30 2", "GSM6754839", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time: 3|mdibl id:KO  3 2|conc ng ul:153.06|a 260s280:2.13|a 260s230:1.88|sequence count:61815409", "ko am30 2", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype Klf9  / |developmental stage:5 dpf embryo|time: 3|mdibl id:KO  3 2|conc ng ul:153.06|a 260s280:2.13|a 260s230:1.88|sequence count:61815409", "GSM6754839", "GSM6754839: ko am30 2; Danio rerio; RNA Seq", "GSM6754839 r1", "GSM6754839", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "ko_am30_2_R1.fastq.gz", "fastq", 4591792497.0, 61815409.0, "GSM6754839 r1", "0:74.28 1:0", "A:1166498576;C:1070326771;G:1027221078;T:1327476945;N:269127", 74, 0, null, null, 1166498576, 1070326771, 1027221078, 1327476945, 269127, "SRX18368410", "SRS15854842", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94781, null, 0.11355, null, 0.66864, null, 0.49723, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [72286, "SRR22398736", "SRX18368409", "SRS15854841", "SRP409542", "PRJNA904806", "Bulk RNA seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber lights on", "GSE218687", "Transcriptome Analysis", "Kr\u00fcppel like factor 9 Klf9 is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 dpf dpf. However  klf9 expression oscillates diurnally  and the time point that was sampled corresponded to its expression nadir. To determine if klf9 /  function varies with time of day  we performed bulk RNA seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9 /  mutation that we reported previously are robust to time of day  the mutation has additional effects that manifest only at the predawn time point. We used a published single cell atlas of zebrafish development to map the effects of the klf9 /  mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs liver  pancreas  and intestine and decreased representation of genes associated with differentiating neurons  blood  and somites. Measurements from confocally imaged larvae suggest that overrepresentation of liver genes in klf9 /  mutants is due to development of enlarged livers. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish klf9 /  mutant larvae vs wild type at three times of day.  Klf9  /  knockouts were generated through CRISPR  creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon  as previously described in Gans et al  Scientific Reports 10  11415 2020. https://doi.org/10.1038/s41598 020 68040 z", null, null, null, "ko am30 1", "GSM6754838", null, "source name:larvae|tissue:larvae|developmental stage:5 dpf embryo|time: 3|mdibl id:KO  3 1|conc ng ul:166.574|a 260s280:1.94|a 260s230:1.16|sequence count:50914883", "ko am30 1", "Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: \"  fastqc args '  noextract'\"  \"  illumina\"  \"  length 1 35\"  \"  length 2 35\"  \"  stringency 1\"  \"  length 20\"  and \"  quality 20\". Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command \u201crsem calculate expression\u201d with options: \"  keep intermediate files\"  \"  star gzipped read file\"  \" p 64\"  \"  estimate rspd\"  \"  append names\"  \"  output genome bam\"  and \"  star\". This run used 64 threads with the option to estimate the read start position distribution RSPD from the data instead of the default uniform RPSD and the option to output a BAM formatted file of read alignments in genomic coordinates. Counts were formatted into a count matrix with tximport using default options. Due to concerns regarding potential confounding experimental variables  this experiment was repeated with improved collection protocols  yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two  so the two were \"merged\" into one by taking the sum of transcript counts from corresponding samples with respect to time  replicate number  and genetics from the two runs. The transcripts from this experiment were aligned to Ensembl gene IDs Danio rerio  101. For downstream analysis  it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID  so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name  effectively removing gene duplicates from the count matrix. Principal Components Analysis PCA was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core Massacci  2020. Differential Expression Analysis was performed between wildtype and klf9  /  samples in the count matrix with the MDIBL Bioinformatics Core\u2019s DESeq2 R script  using R version 4.0.3 and DESeq2 version 1.30.1. In addition to PC1 being used as a covariate  time was used as a covariant to isolate the time independent effect of the klf9 knockout. The time dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9  /  samples. Assembly: Zebrafish genome v11  as obtained from Ensembl release 101  and preprocessed with rsem prepare reference  using STAR\u2019s genomeGenerate option  using STAR v 2.7.5c Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components Supplementary files format and content: jcoffman 008.ZTp2.5.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 2.5 hours post lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.ZTm3.DEseq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at the time point 3 hours before lights on.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.gene.counts.tsv; tab separated values.  RSEM estimated count matrix at the gene level  with removal of duplicate genes as described above Supplementary files format and content: jcoffman 008.ZT.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT  at lights on zeitgeber time.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression. Supplementary files format and content: jcoffman 008.PC1 time.DESeq2 out.tsv; tab separated values  DESeq2 output table for comparison of Klf9  /  vs Wildtype control WT across all time points.  The first principal component  which was associated with a technical affect of replicates was included as a covariate in the regression  as was the time of day. Supplementary files format and content: jcoffman 008.rlog.tsv; DESeq normalized count matrix  using the rlog regularized log2 function", "larvae", null, "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", "Zebrafish were klf9 /  mutants derived from the AB strain  and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory  and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly  fertilized eggs were collected in the morning  disinfected and at 4 hpf placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.", "tissue:larvae|genotype Klf9  / |developmental stage:5 dpf embryo|time: 3|mdibl id:KO  3 1|conc ng ul:166.574|a 260s280:1.94|a 260s230:1.16|sequence count:50914883", "GSM6754838", "GSM6754838: ko am30 1; Danio rerio; RNA Seq", "GSM6754838 r1", "GSM6754838", "1", "At  3  0  and 2.5 hours zeitgeber time onset of the light phase in the incubator on day 5 post fertilization  four biological replicates of klf9 /  mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes  media was removed  and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over 10 minutes. Frozen samples were stored at  80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit Qiagen 74134. For each set of four biological replicate samples  RLT Plus lysis buffer plus beta mercaptoethanol  per kit instructions was added to each sample immediately upon its retrieval from the freezer  and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing\u2014i.e.  passed though Qiashredder columns Qiagen 79654  bound  washed  and eluted per kit instructions. RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single end sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP409542", null, null, "ko_am30_1_R1.fastq.gz", "fastq", 3786315387.0, 50914883.0, "GSM6754838 r1", "0:74.37 1:0", "A:965927215;C:875465462;G:846443972;T:1098110795;N:367943", 74, 0, null, null, 965927215, 875465462, 846443972, 1098110795, 367943, "SRX18368409", "SRS15854841", "SRA1546501", "Bioinformatics Core, MDI Biological Laboratory", "Bioinformatics Core, MDI Biological Laboratory", 1, 0.94574, null, 0.11829, null, 0.66574, null, 0.4914, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-11-23", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [74329, "SRR23635030", "SRX19518333", "SRS16905710", "SRP425040", "PRJNA939370", "The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq]", "GSE226182", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "KO  replicate 2  bulk RNAseq", "GSM7067524", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  replicate 2  bulk RNAseq", "Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample", "embryo", null, "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067524", "GSM7067524: KO  replicate 2  bulk RNAseq; Danio rerio; RNA Seq", "GSM7067524 r1", "GSM7067524", "1", "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "DNBSEQ", "DNBSEQ-G400", null, "SRP425040", null, null, "KO2.fastq.gz", "fastq", 4188284200.0, 41882842.0, "GSM7067524 r1", "0:100", "A:1066992737;C:1011357361;G:1055554148;T:1041284278;N:13095676", 100, null, null, null, 1066992737, 1011357361, 1055554148, 1041284278, 13095676, "SRX19518333", "SRS16905710", "SRA1597336", "Yunnan University", "Yunnan University", 1, 0.88647, null, 0.07541, null, 0.7237, null, 0.47069, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74330, "SRR23635031", "SRX19518332", "SRS16905709", "SRP425040", "PRJNA939370", "The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq]", "GSE226182", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "KO  replicate 1  bulk RNAseq", "GSM7067523", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  replicate 1  bulk RNAseq", "Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample", "embryo", null, "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067523", "GSM7067523: KO  replicate 1  bulk RNAseq; Danio rerio; RNA Seq", "GSM7067523 r1", "GSM7067523", "1", "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "DNBSEQ", "DNBSEQ-G400", null, "SRP425040", null, null, "KO1.fastq.gz", "fastq", 4181083400.0, 41810834.0, "GSM7067523 r1", "0:100", "A:1077414361;C:996554293;G:1053357384;T:1040649776;N:13107586", 100, null, null, null, 1077414361, 996554293, 1053357384, 1040649776, 13107586, "SRX19518332", "SRS16905709", "SRA1597336", "Yunnan University", "Yunnan University", 1, 0.87685, null, 0.07522, null, 0.72699, null, 0.48859, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74331, "SRR23635032", "SRX19518331", "SRS16905708", "SRP425040", "PRJNA939370", "The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq]", "GSE226182", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "WT  replicate 2  bulk RNAseq", "GSM7067522", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing", "WT  replicate 2  bulk RNAseq", "Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample", "embryo", null, "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "tissue:embryo|age:48 hpf|genotype:wild type", "GSM7067522", "GSM7067522: WT  replicate 2  bulk RNAseq; Danio rerio; RNA Seq", "GSM7067522 r1", "GSM7067522", "1", "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "DNBSEQ", "DNBSEQ-G400", null, "SRP425040", null, null, "WT2.fastq.gz", "fastq", 1435167700.0, 14351677.0, "GSM7067522 r1", "0:100", "A:371412640;C:334204906;G:351277070;T:371684263;N:6588821", 100, null, null, null, 371412640, 334204906, 351277070, 371684263, 6588821, "SRX19518331", "SRS16905708", "SRA1597336", "Yunnan University", "Yunnan University", 1, 0.83841, null, 0.15087, null, 0.71417, null, 0.50982, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74332, "SRR23635033", "SRX19518330", "SRS16905707", "SRP425040", "PRJNA939370", "The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq]", "GSE226182", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies  343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "WT  replicate 1  bulk RNAseq", "GSM7067521", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing", "WT  replicate 1  bulk RNAseq", "Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression  for each Sample", "embryo", null, "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "tissue:embryo|age:48 hpf|genotype:wild type", "GSM7067521", "GSM7067521: WT  replicate 1  bulk RNAseq; Danio rerio; RNA Seq", "GSM7067521 r1", "GSM7067521", "1", "RNA was extracted by TRNzol method  and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "DNBSEQ", "DNBSEQ-G400", null, "SRP425040", null, null, "WT1.fastq.gz", "fastq", 1961618800.0, 19616188.0, "GSM7067521 r1", "0:100", "A:518460045;C:447438337;G:477081234;T:509513188;N:9125996", 100, null, null, null, 518460045, 447438337, 477081234, 509513188, 9125996, "SRX19518330", "SRS16905707", "SRA1597336", "Yunnan University", "Yunnan University", 1, 0.81315, null, 0.14097, null, 0.72342, null, 0.50905, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [75396, "SRR24497420", "SRX20282374", "SRS17609397", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 DN replicate3", "GSM7321058", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N|geo loc name:missing|collection date:missing", "Mcpip1 DN replicate3", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N", "GSM7321058", "GSM7321058: Mcpip1 DN replicate3; Danio rerio; RNA Seq", "GSM7321058 r1", "GSM7321058", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "DN_C24.fastq.gz", "fastq", 4215951250.0, 27509986.0, "GSM7321058 r1", "0:153.25", "A:1174686445;C:999279135;G:1076390086;T:965595584;N:0", 153, null, null, null, 1174686445, 999279135, 1076390086, 965595584, 0, "SRX20282374", "SRS17609397", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.7271, null, 0.04079, null, 0.77583, null, 0.48331, null, 128, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [75397, "SRR24497423", "SRX20282373", "SRS17609396", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 DN replicate2", "GSM7321057", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N|geo loc name:missing|collection date:missing", "Mcpip1 DN replicate2", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N", "GSM7321057", "GSM7321057: Mcpip1 DN replicate2; Danio rerio; RNA Seq", "GSM7321057 r1", "GSM7321057", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "DN_B16.fastq.gz", "fastq", 4150646040.0, 29771678.0, "GSM7321057 r1", "0:139.42", "A:1158168842;C:981804106;G:1077873702;T:932799390;N:0", 139, null, null, null, 1158168842, 981804106, 1077873702, 932799390, 0, "SRX20282373", "SRS17609396", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.83432, null, 0.03292, null, 0.77068, null, 0.48489, null, 149, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [75398, "SRR24497421", "SRX20282372", "SRS17609394", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 DN replicate1", "GSM7321056", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N|geo loc name:missing|collection date:missing", "Mcpip1 DN replicate1", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N", "GSM7321056", "GSM7321056: Mcpip1 DN replicate1; Danio rerio; RNA Seq", "GSM7321056 r1", "GSM7321056", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "DN_A8.fastq.gz", "fastq", 3405374389.0, 22617333.0, "GSM7321056 r1", "0:150.56", "A:943415180;C:825787941;G:885910600;T:750260668;N:0", 150, null, null, null, 943415180, 825787941, 885910600, 750260668, 0, "SRX20282372", "SRS17609394", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.85916, null, 0.04442, null, 0.78344, null, 0.48648, null, 177, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [75399, "SRR24497422", "SRX20282371", "SRS17609395", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 WT replicate3", "GSM7321055", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1|geo loc name:missing|collection date:missing", "Mcpip1 WT replicate3", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1", "GSM7321055", "GSM7321055: Mcpip1 WT replicate3; Danio rerio; RNA Seq", "GSM7321055 r1", "GSM7321055", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "WT_C23.fastq.gz", "fastq", 3644157793.0, 27473010.0, "GSM7321055 r1", "0:132.65", "A:1014320322;C:878841963;G:948316248;T:802679260;N:0", 132, null, null, null, 1014320322, 878841963, 948316248, 802679260, 0, "SRX20282371", "SRS17609395", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.88531, null, 0.03151, null, 0.75101, null, 0.49337, null, 123, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [75400, "SRR24497424", "SRX20282370", "SRS17609393", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 WT replicate2", "GSM7321054", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1|geo loc name:missing|collection date:missing", "Mcpip1 WT replicate2", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1", "GSM7321054", "GSM7321054: Mcpip1 WT replicate2; Danio rerio; RNA Seq", "GSM7321054 r1", "GSM7321054", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "WT_B15.fastq.gz", "fastq", 4930632556.0, 30493682.0, "GSM7321054 r1", "0:161.69", "A:1385638764;C:1206486517;G:1269832302;T:1068674973;N:0", 161, null, null, null, 1385638764, 1206486517, 1269832302, 1068674973, 0, "SRX20282370", "SRS17609393", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.86405, null, 0.03935, null, 0.78324, null, 0.49971, null, 107, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [75401, "SRR24497425", "SRX20282369", "SRS17609392", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 WT replicate1", "GSM7321053", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1|geo loc name:missing|collection date:missing", "Mcpip1 WT replicate1", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1", "GSM7321053", "GSM7321053: Mcpip1 WT replicate1; Danio rerio; RNA Seq", "GSM7321053 r1", "GSM7321053", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "WT_A7.fastq.gz", "fastq", 4888312783.0, 29414563.0, "GSM7321053 r1", "0:166.19", "A:1356799075;C:1172146709;G:1273947582;T:1085419417;N:0", 166, null, null, null, 1356799075, 1172146709, 1273947582, 1085419417, 0, "SRX20282369", "SRS17609392", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.82661, null, 0.05547, null, 0.7751, null, 0.49668, null, 188, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 56, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_layout\" = :p0 and \"technology\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "bulk", "p2": "Embryo Imprecise"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 54, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&experiment.library_strategy=OTHER", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 56, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise", "results": [{"value": "cDNA", "label": "cDNA", "count": 54, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&experiment.library_selection=cDNA", "selected": false}, {"value": "other", "label": "other", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&experiment.library_selection=other", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 56, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=bulk&tissue_curation=Embryo+Imprecise", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 46, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&experiment.platform=ILLUMINA", "selected": false}, {"value": "ION_TORRENT", "label": "ION_TORRENT", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&experiment.platform=ION_TORRENT", "selected": false}, {"value": "DNBSEQ", "label": "DNBSEQ", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&experiment.platform=DNBSEQ", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise", "results": [{"value": "Embryo", "label": "Embryo", "count": 26, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&devstage_curation_coarse=Embryo", "selected": false}, {"value": "Larval", "label": "Larval", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&devstage_curation_coarse=Larval", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&devstage_curation_coarse=Multi-stage", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise", "results": [{"value": "Larval", "label": "Larval", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&devstage_curation=Larval", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&devstage_curation=Multi-stage", "selected": false}, {"value": "Hatching", "label": "Hatching", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&devstage_curation=Hatching", "selected": false}, {"value": "Blastula", "label": "Blastula", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&devstage_curation=Blastula", "selected": false}, {"value": "Segmentation", "label": "Segmentation", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&devstage_curation=Segmentation", "selected": false}, {"value": "Cleavage", "label": "Cleavage", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&devstage_curation=Cleavage", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&devstage_curation=Undetermined", "selected": false}, {"value": "Zygote", "label": "Zygote", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&devstage_curation=Zygote", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 56, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise&tissue_curation_coarse=All+anatomical+structures", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise", "results": [{"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 56, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk&tissue_curation=Embryo+Imprecise", "results": [{"value": "bulk", "label": "bulk", "count": 56, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Embryo+Imprecise", "selected": true}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 84.50680300120439}