{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Hatching\" and tissue_curation = \"Multi-tissue\"", "rows": [[29909, "SRR27592934", "SRX23261746", "SRS20163710", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep11", "GSM8020192", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep11", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types", "GSM8020192", "GSM8020192: deaf1  2 dpf  rep11; Danio rerio; RNA Seq", "GSM8020192 r1", "GSM8020192", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-wt_D28_S56_R1_001.fastq.gz", "fastq", 4475806200.0, 44758062.0, "GSM8020192 r1", "0:100", "A:1106171674;C:1156870042;G:1092472583;T:1120212338;N:79563", 100, null, null, null, 1106171674, 1156870042, 1092472583, 1120212338, 79563, "SRX23261746", "SRS20163710", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29910, "SRR27592935", "SRX23261745", "SRS20163711", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep10", "GSM8020191", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep10", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types", "GSM8020191", "GSM8020191: deaf1  2 dpf  rep10; Danio rerio; RNA Seq", "GSM8020191 r1", "GSM8020191", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-wt_D27_S55_R1_001.fastq.gz", "fastq", 4001586700.0, 40015867.0, "GSM8020191 r1", "0:100", "A:1000059012;C:1020300240;G:981249122;T:999909425;N:68901", 100, null, null, null, 1000059012, 1020300240, 981249122, 999909425, 68901, "SRX23261745", "SRS20163711", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29911, "SRR27592936", "SRX23261744", "SRS20163709", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep9", "GSM8020190", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep9", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types", "GSM8020190", "GSM8020190: deaf1  2 dpf  rep9; Danio rerio; RNA Seq", "GSM8020190 r1", "GSM8020190", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-wt_D26_S54_R1_001.fastq.gz", "fastq", 3716740300.0, 37167403.0, "GSM8020190 r1", "0:100", "A:930732486;C:940157658;G:908687307;T:937097122;N:65727", 100, null, null, null, 930732486, 940157658, 908687307, 937097122, 65727, "SRX23261744", "SRS20163709", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29912, "SRR27592937", "SRX23261743", "SRS20163708", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep8", "GSM8020189", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep8", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous", "GSM8020189", "GSM8020189: deaf1  2 dpf  rep8; Danio rerio; RNA Seq", "GSM8020189 r1", "GSM8020189", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-hom_D25_S53_R1_001.fastq.gz", "fastq", 3741485000.0, 37414850.0, "GSM8020189 r1", "0:100", "A:929440558;C:958986044;G:914039968;T:938952561;N:65869", 100, null, null, null, 929440558, 958986044, 914039968, 938952561, 65869, "SRX23261743", "SRS20163708", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29913, "SRR27592938", "SRX23261742", "SRS20163707", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep7", "GSM8020188", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep7", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous", "GSM8020188", "GSM8020188: deaf1  2 dpf  rep7; Danio rerio; RNA Seq", "GSM8020188 r1", "GSM8020188", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-hom_D24_S52_R1_001.fastq.gz", "fastq", 2971991400.0, 29719914.0, "GSM8020188 r1", "0:100", "A:738636815;C:755836125;G:729168292;T:748297854;N:52314", 100, null, null, null, 738636815, 755836125, 729168292, 748297854, 52314, "SRX23261742", "SRS20163707", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29914, "SRR27592939", "SRX23261741", "SRS20163706", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep6", "GSM8020187", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep6", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous", "GSM8020187", "GSM8020187: deaf1  2 dpf  rep6; Danio rerio; RNA Seq", "GSM8020187 r1", "GSM8020187", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-hom_D23_S51_R1_001.fastq.gz", "fastq", 4134397800.0, 41343978.0, "GSM8020187 r1", "0:100", "A:1032735373;C:1051188374;G:1016197596;T:1034203095;N:73362", 100, null, null, null, 1032735373, 1051188374, 1016197596, 1034203095, 73362, "SRX23261741", "SRS20163706", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29915, "SRR27592940", "SRX23261740", "SRS20163705", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep5", "GSM8020186", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep5", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous", "GSM8020186", "GSM8020186: deaf1  2 dpf  rep5; Danio rerio; RNA Seq", "GSM8020186 r1", "GSM8020186", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-hom_D22_S50_R1_001.fastq.gz", "fastq", 3631624500.0, 36316245.0, "GSM8020186 r1", "0:100", "A:901094303;C:929956244;G:893844528;T:906664233;N:65192", 100, null, null, null, 901094303, 929956244, 893844528, 906664233, 65192, "SRX23261740", "SRS20163705", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29916, "SRR27592941", "SRX23261739", "SRS20163704", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep4", "GSM8020185", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep4", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i homozygous", "GSM8020185", "GSM8020185: deaf1  2 dpf  rep4; Danio rerio; RNA Seq", "GSM8020185 r1", "GSM8020185", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-hom_D21_S49_R1_001.fastq.gz", "fastq", 3349609200.0, 33496092.0, "GSM8020185 r1", "0:100", "A:835857971;C:854981364;G:824035698;T:834673793;N:60374", 100, null, null, null, 835857971, 854981364, 824035698, 834673793, 60374, "SRX23261739", "SRS20163704", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29917, "SRR27592942", "SRX23261738", "SRS20163703", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep3", "GSM8020184", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep3", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous", "GSM8020184", "GSM8020184: deaf1  2 dpf  rep3; Danio rerio; RNA Seq", "GSM8020184 r1", "GSM8020184", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-het_D20_S48_R1_001.fastq.gz", "fastq", 3371713300.0, 33717133.0, "GSM8020184 r1", "0:100", "A:839050016;C:857965663;G:828869795;T:845766740;N:61086", 100, null, null, null, 839050016, 857965663, 828869795, 845766740, 61086, "SRX23261738", "SRS20163703", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29918, "SRR27592943", "SRX23261737", "SRS20163701", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep2", "GSM8020183", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep2", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous", "GSM8020183", "GSM8020183: deaf1  2 dpf  rep2; Danio rerio; RNA Seq", "GSM8020183 r1", "GSM8020183", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-het_D18_S46_R1_001.fastq.gz", "fastq", 3756501100.0, 37565011.0, "GSM8020183 r1", "0:100", "A:938612608;C:949004833;G:927692516;T:941125085;N:66058", 100, null, null, null, 938612608, 949004833, 927692516, 941125085, 66058, "SRX23261737", "SRS20163701", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29919, "SRR27592944", "SRX23261736", "SRS20163702", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep1", "GSM8020182", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep1", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i heterozygous", "GSM8020182", "GSM8020182: deaf1  2 dpf  rep1; Danio rerio; RNA Seq", "GSM8020182 r1", "GSM8020182", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-het_D17_S45_R1_001.fastq.gz", "fastq", 3378074100.0, 33780741.0, "GSM8020182 r1", "0:100", "A:839320911;C:859028175;G:836373251;T:843291522;N:60241", 100, null, null, null, 839320911, 859028175, 836373251, 843291522, 60241, "SRX23261736", "SRS20163702", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29920, "SRR27592945", "SRX23261735", "SRS20163699", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep13", "GSM8020181", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep13", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types", "GSM8020181", "GSM8020181: deaf1 t238p  2 dpf  rep13; Danio rerio; RNA Seq", "GSM8020181 r1", "GSM8020181", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-wt_ST4.fastq.gz", "fastq", 2522881653.0, 33818740.0, "GSM8020181 r1", "0:74.60", "A:655207900;C:616856238;G:613068980;T:637525231;N:223304", 74, null, null, null, 655207900, 616856238, 613068980, 637525231, 223304, "SRX23261735", "SRS20163699", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29921, "SRR27592946", "SRX23261734", "SRS20163698", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep12", "GSM8020180", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep12", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types", "GSM8020180", "GSM8020180: deaf1 t238p  2 dpf  rep12; Danio rerio; RNA Seq", "GSM8020180 r1", "GSM8020180", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-wt_ST3.fastq.gz", "fastq", 3232696302.0, 43332777.0, "GSM8020180 r1", "0:74.60", "A:838706781;C:792017578;G:780975426;T:820709157;N:287360", 74, null, null, null, 838706781, 792017578, 780975426, 820709157, 287360, "SRX23261734", "SRS20163698", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29922, "SRR27592947", "SRX23261733", "SRS20163700", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep11", "GSM8020179", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep11", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types", "GSM8020179", "GSM8020179: deaf1 t238p  2 dpf  rep11; Danio rerio; RNA Seq", "GSM8020179 r1", "GSM8020179", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-wt_ST2.fastq.gz", "fastq", 3105671470.0, 41634840.0, "GSM8020179 r1", "0:74.59", "A:797054679;C:770109006;G:759275000;T:778955169;N:277616", 74, null, null, null, 797054679, 770109006, 759275000, 778955169, 277616, "SRX23261733", "SRS20163700", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29923, "SRR27592948", "SRX23261732", "SRS20163697", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep10", "GSM8020178", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep10", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p wild types", "GSM8020178", "GSM8020178: deaf1 t238p  2 dpf  rep10; Danio rerio; RNA Seq", "GSM8020178 r1", "GSM8020178", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-wt_ST1.fastq.gz", "fastq", 3499217864.0, 46905154.0, "GSM8020178 r1", "0:74.60", "A:893360259;C:869418642;G:860403580;T:875711902;N:323481", 74, null, null, null, 893360259, 869418642, 860403580, 875711902, 323481, "SRX23261732", "SRS20163697", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29924, "SRR27592949", "SRX23261731", "SRS20163696", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep9", "GSM8020177", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep9", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous", "GSM8020177", "GSM8020177: deaf1 t238p  2 dpf  rep9; Danio rerio; RNA Seq", "GSM8020177 r1", "GSM8020177", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-hom_ST8.fastq.gz", "fastq", 3268771798.0, 43820118.0, "GSM8020177 r1", "0:74.60", "A:847366551;C:800849702;G:791226044;T:829037606;N:291895", 74, null, null, null, 847366551, 800849702, 791226044, 829037606, 291895, "SRX23261731", "SRS20163696", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29925, "SRR27592950", "SRX23261730", "SRS20163695", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep8", "GSM8020176", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep8", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous", "GSM8020176", "GSM8020176: deaf1 t238p  2 dpf  rep8; Danio rerio; RNA Seq", "GSM8020176 r1", "GSM8020176", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-hom_ST7.fastq.gz", "fastq", 2027174325.0, 27178466.0, "GSM8020176 r1", "0:74.59", "A:525317640;C:498055852;G:491357881;T:512263813;N:179139", 74, null, null, null, 525317640, 498055852, 491357881, 512263813, 179139, "SRX23261730", "SRS20163695", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29926, "SRR27592951", "SRX23261729", "SRS20163694", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep7", "GSM8020175", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep7", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous", "GSM8020175", "GSM8020175: deaf1 t238p  2 dpf  rep7; Danio rerio; RNA Seq", "GSM8020175 r1", "GSM8020175", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-hom_ST6.fastq.gz", "fastq", 2787340348.0, 37363599.0, "GSM8020175 r1", "0:74.60", "A:722896986;C:681138747;G:674833627;T:708219281;N:251707", 74, null, null, null, 722896986, 681138747, 674833627, 708219281, 251707, "SRX23261729", "SRS20163694", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29927, "SRR27592952", "SRX23261728", "SRS20163693", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep6", "GSM8020174", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep6", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p homozygous", "GSM8020174", "GSM8020174: deaf1 t238p  2 dpf  rep6; Danio rerio; RNA Seq", "GSM8020174 r1", "GSM8020174", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-hom_ST5.fastq.gz", "fastq", 2977171544.0, 39908640.0, "GSM8020174 r1", "0:74.60", "A:770250088;C:731344480;G:721594408;T:753713587;N:268981", 74, null, null, null, 770250088, 731344480, 721594408, 753713587, 268981, "SRX23261728", "SRS20163693", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29928, "SRR27592953", "SRX23261727", "SRS20163692", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep5", "GSM8020173", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep5", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous", "GSM8020173", "GSM8020173: deaf1 t238p  2 dpf  rep5; Danio rerio; RNA Seq", "GSM8020173 r1", "GSM8020173", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-het_ST9.fastq.gz", "fastq", 2546529762.0, 34141024.0, "GSM8020173 r1", "0:74.59", "A:665391714;C:618921995;G:614059292;T:647931593;N:225168", 74, null, null, null, 665391714, 618921995, 614059292, 647931593, 225168, "SRX23261727", "SRS20163692", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29929, "SRR27592954", "SRX23261726", "SRS20163691", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep4", "GSM8020172", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep4", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous", "GSM8020172", "GSM8020172: deaf1 t238p  2 dpf  rep4; Danio rerio; RNA Seq", "GSM8020172 r1", "GSM8020172", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-het_ST13.fastq.gz", "fastq", 3176861738.0, 42588753.0, "GSM8020172 r1", "0:74.59", "A:831927955;C:768758728;G:763547713;T:812339162;N:288180", 74, null, null, null, 831927955, 768758728, 763547713, 812339162, 288180, "SRX23261726", "SRS20163691", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29930, "SRR27592955", "SRX23261725", "SRS20163690", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep3", "GSM8020171", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep3", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous", "GSM8020171", "GSM8020171: deaf1 t238p  2 dpf  rep3; Danio rerio; RNA Seq", "GSM8020171 r1", "GSM8020171", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-het_ST12.fastq.gz", "fastq", 1136232560.0, 15234548.0, "GSM8020171 r1", "0:74.58", "A:297385645;C:276022399;G:273402666;T:289320311;N:101539", 74, null, null, null, 297385645, 276022399, 273402666, 289320311, 101539, "SRX23261725", "SRS20163690", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29931, "SRR27592956", "SRX23261724", "SRS20163689", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep2", "GSM8020170", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep2", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous", "GSM8020170", "GSM8020170: deaf1 t238p  2 dpf  rep2; Danio rerio; RNA Seq", "GSM8020170 r1", "GSM8020170", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-het_ST11.fastq.gz", "fastq", 2735749019.0, 36680185.0, "GSM8020170 r1", "0:74.58", "A:721197113;C:659588175;G:652875625;T:701848626;N:239480", 74, null, null, null, 721197113, 659588175, 652875625, 701848626, 239480, "SRX23261724", "SRS20163689", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29932, "SRR27592957", "SRX23261723", "SRS20163688", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 t238p  2 dpf  rep1", "GSM8020169", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing", "deaf1 t238p  2 dpf  rep1", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 t238p heterozygous", "GSM8020169", "GSM8020169: deaf1 t238p  2 dpf  rep1; Danio rerio; RNA Seq", "GSM8020169 r1", "GSM8020169", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP484215", null, null, "deaf1-t238p-2dpf-het_ST10.fastq.gz", "fastq", 3369699901.0, 45178398.0, "GSM8020169 r1", "0:74.59", "A:883991145;C:814741172;G:809532162;T:861133903;N:301519", 74, null, null, null, 883991145, 814741172, 809532162, 861133903, 301519, "SRX23261723", "SRS20163688", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29947, "SRR27592972", "SRX23261708", "SRS20163673", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep13", "GSM8020168", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep13", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types", "GSM8020168", "GSM8020168: deaf1 c207y  2 dpf  rep13; Danio rerio; RNA Seq", "GSM8020168 r1", "GSM8020168", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-wt_B2_S14_R1_001.fastq.gz", "fastq", 2963811367.0, 29344667.0, "GSM8020168 r1", "0:101", "A:803333990;C:685431342;G:677569210;T:797384558;N:92267", 101, null, null, null, 803333990, 685431342, 677569210, 797384558, 92267, "SRX23261708", "SRS20163673", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29948, "SRR27592973", "SRX23261707", "SRS20163672", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep12", "GSM8020167", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep12", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types", "GSM8020167", "GSM8020167: deaf1 c207y  2 dpf  rep12; Danio rerio; RNA Seq", "GSM8020167 r1", "GSM8020167", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-wt_B1_S13_R1_001.fastq.gz", "fastq", 3184165289.0, 31526389.0, "GSM8020167 r1", "0:101", "A:847208990;C:751109498;G:736855605;T:848892893;N:98303", 101, null, null, null, 847208990, 751109498, 736855605, 848892893, 98303, "SRX23261707", "SRS20163672", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29949, "SRR27592974", "SRX23261706", "SRS20163671", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep11", "GSM8020166", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep11", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types", "GSM8020166", "GSM8020166: deaf1 c207y  2 dpf  rep11; Danio rerio; RNA Seq", "GSM8020166 r1", "GSM8020166", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-wt_A12_S12_R1_001.fastq.gz", "fastq", 3115838183.0, 30849883.0, "GSM8020166 r1", "0:101", "A:846133299;C:724401184;G:709966835;T:835240904;N:95961", 101, null, null, null, 846133299, 724401184, 709966835, 835240904, 95961, "SRX23261706", "SRS20163671", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29950, "SRR27592975", "SRX23261705", "SRS20163670", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep10", "GSM8020165", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep10", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types", "GSM8020165", "GSM8020165: deaf1 c207y  2 dpf  rep10; Danio rerio; RNA Seq", "GSM8020165 r1", "GSM8020165", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-wt_A11_S11_R1_001.fastq.gz", "fastq", 2767984184.0, 27405784.0, "GSM8020165 r1", "0:101", "A:753665483;C:638171516;G:626255827;T:749805524;N:85834", 101, null, null, null, 753665483, 638171516, 626255827, 749805524, 85834, "SRX23261705", "SRS20163670", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29951, "SRR27592976", "SRX23261704", "SRS20163669", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep9", "GSM8020164", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep9", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y wild types", "GSM8020164", "GSM8020164: deaf1 c207y  2 dpf  rep9; Danio rerio; RNA Seq", "GSM8020164 r1", "GSM8020164", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-wt_A10_S10_R1_001.fastq.gz", "fastq", 5417478400.0, 53638400.0, "GSM8020164 r1", "0:101", "A:1459560082;C:1269220844;G:1235271759;T:1453256921;N:168794", 101, null, null, null, 1459560082, 1269220844, 1235271759, 1453256921, 168794, "SRX23261704", "SRS20163669", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29952, "SRR27592977", "SRX23261703", "SRS20163668", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep8", "GSM8020163", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep8", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y homozygous", "GSM8020163", "GSM8020163: deaf1 c207y  2 dpf  rep8; Danio rerio; RNA Seq", "GSM8020163 r1", "GSM8020163", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-hom_A9_S9_R1_001.fastq.gz", "fastq", 2417886167.0, 23939467.0, "GSM8020163 r1", "0:101", "A:657342317;C:558713775;G:547590726;T:654164599;N:74750", 101, null, null, null, 657342317, 558713775, 547590726, 654164599, 74750, "SRX23261703", "SRS20163668", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29953, "SRR27592978", "SRX23261702", "SRS20163667", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep7", "GSM8020162", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep7", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y homozygous", "GSM8020162", "GSM8020162: deaf1 c207y  2 dpf  rep7; Danio rerio; RNA Seq", "GSM8020162 r1", "GSM8020162", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-hom_A8_S8_R1_001.fastq.gz", "fastq", 3601305288.0, 35656488.0, "GSM8020162 r1", "0:101", "A:974139857;C:839029639;G:822572729;T:965450738;N:112325", 101, null, null, null, 974139857, 839029639, 822572729, 965450738, 112325, "SRX23261702", "SRS20163667", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29954, "SRR27592979", "SRX23261701", "SRS20163666", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep6", "GSM8020161", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep6", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y homozygous", "GSM8020161", "GSM8020161: deaf1 c207y  2 dpf  rep6; Danio rerio; RNA Seq", "GSM8020161 r1", "GSM8020161", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-hom_A6_S6_R1_001.fastq.gz", "fastq", 2545549965.0, 25203465.0, "GSM8020161 r1", "0:101", "A:689302325;C:596907356;G:578571204;T:680690103;N:78977", 101, null, null, null, 689302325, 596907356, 578571204, 680690103, 78977, "SRX23261701", "SRS20163666", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29955, "SRR27592980", "SRX23261700", "SRS20163665", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep5", "GSM8020160", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep5", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous", "GSM8020160", "GSM8020160: deaf1 c207y  2 dpf  rep5; Danio rerio; RNA Seq", "GSM8020160 r1", "GSM8020160", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-het_A5_S5_R1_001.fastq.gz", "fastq", 3102857158.0, 30721358.0, "GSM8020160 r1", "0:101", "A:850838897;C:712670459;G:688515516;T:850736210;N:96076", 101, null, null, null, 850838897, 712670459, 688515516, 850736210, 96076, "SRX23261700", "SRS20163665", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29956, "SRR27592981", "SRX23261699", "SRS20163664", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep4", "GSM8020159", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep4", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous", "GSM8020159", "GSM8020159: deaf1 c207y  2 dpf  rep4; Danio rerio; RNA Seq", "GSM8020159 r1", "GSM8020159", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-het_A4_S4_R1_001.fastq.gz", "fastq", 3415651633.0, 33818333.0, "GSM8020159 r1", "0:101", "A:933225760;C:786732356;G:770845968;T:924742081;N:105468", 101, null, null, null, 933225760, 786732356, 770845968, 924742081, 105468, "SRX23261699", "SRS20163664", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29957, "SRR27592982", "SRX23261698", "SRS20163663", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep3", "GSM8020158", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep3", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous", "GSM8020158", "GSM8020158: deaf1 c207y  2 dpf  rep3; Danio rerio; RNA Seq", "GSM8020158 r1", "GSM8020158", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-het_A3_S3_R1_001.fastq.gz", "fastq", 3429734972.0, 33957772.0, "GSM8020158 r1", "0:101", "A:920850547;C:802940416;G:790735026;T:915103526;N:105457", 101, null, null, null, 920850547, 802940416, 790735026, 915103526, 105457, "SRX23261698", "SRS20163663", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29958, "SRR27592983", "SRX23261697", "SRS20163662", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep2", "GSM8020157", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep2", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous", "GSM8020157", "GSM8020157: deaf1 c207y  2 dpf  rep2; Danio rerio; RNA Seq", "GSM8020157 r1", "GSM8020157", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-het_A2_S2_R1_001.fastq.gz", "fastq", 2810870602.0, 27830402.0, "GSM8020157 r1", "0:101", "A:742011214;C:673773327;G:656344142;T:738655690;N:86229", 101, null, null, null, 742011214, 673773327, 656344142, 738655690, 86229, "SRX23261697", "SRS20163662", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29959, "SRR27592984", "SRX23261696", "SRS20163661", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1 c207y  2 dpf  rep1", "GSM8020156", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing", "deaf1 c207y  2 dpf  rep1", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 c207y heterozygous", "GSM8020156", "GSM8020156: deaf1 c207y  2 dpf  rep1; Danio rerio; RNA Seq", "GSM8020156 r1", "GSM8020156", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-c207y-2dpf-het_A1_S1_R1_001.fastq.gz", "fastq", 4234517819.0, 41925919.0, "GSM8020156 r1", "0:101", "A:1104853000;C:1023572758;G:1001000314;T:1104961067;N:130680", 101, null, null, null, 1104853000, 1023572758, 1001000314, 1104961067, 130680, "SRX23261696", "SRS20163661", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29993, "SRR27593018", "SRX23261662", "SRS20163627", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep13", "GSM8020194", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep13", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types", "GSM8020194", "GSM8020194: deaf1  2 dpf  rep13; Danio rerio; RNA Seq", "GSM8020194 r1", "GSM8020194", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-wt_D30_S58_R1_001.fastq.gz", "fastq", 4417470800.0, 44174708.0, "GSM8020194 r1", "0:100", "A:1088757969;C:1142271720;G:1089301455;T:1097060536;N:79120", 100, null, null, null, 1088757969, 1142271720, 1089301455, 1097060536, 79120, "SRX23261662", "SRS20163627", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [29994, "SRR27593019", "SRX23261661", "SRS20163626", "SRP484215", "PRJNA1065838", "Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations", "GSE253405", "Transcriptome Analysis", "Hundreds of human mutations are linked to autism and related disorders  yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages  as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa  defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing  we further defined molecular drivers of the observed phenotypes  identifying targetable disruptions in neuropeptide signaling  neuronal maturation  and cell proliferation. This multi modal screen has nominated brain regions  cell types  and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism  which were generated using CRISPR/Cas9 mutagenesis.", null, null, null, "deaf1  2 dpf  rep12", "GSM8020193", null, "source name:head with eyes  2 5 heads combined|tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing", "deaf1  2 dpf  rep12", "Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "head with eyes  2 5 heads combined", null, "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "tissue:head with eyes  2 5 heads combined|genotype:deaf1 23d46i wild types", "GSM8020193", "GSM8020193: deaf1  2 dpf  rep12; Danio rerio; RNA Seq", "GSM8020193 r1", "GSM8020193", "1", "RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02  with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2  followed by Nextera XT Library Preparation FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484215", null, "loader:fastq load.py", "deaf1-23d46i-2dpf-wt_D29_S57_R1_001.fastq.gz", "fastq", 4218209500.0, 42182095.0, "GSM8020193 r1", "0:100", "A:1040374012;C:1082175747;G:1042489373;T:1053094232;N:76136", 100, null, null, null, 1040374012, 1082175747, 1042489373, 1053094232, 76136, "SRX23261661", "SRS20163626", "SRA1787174", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-01-16", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [33700, "SRR30599779", "SRX26022472", "SRS22594191", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a wt  2 dpf  rep 2", "GSM8504324", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing", "ebf3a wt  2 dpf  rep 2", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types", "GSM8504324", "GSM8504324: ebf3a wt  2 dpf  rep 2; Danio rerio; RNA Seq", "GSM8504324 r1", "GSM8504324", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-WT-2-2dpf_R1_001.fastq.gz Ebf-WT-2-2dpf_R2_001.fastq.gz", "fastq fastq", 22635570600.0, 75451902.0, "GSM8504324 r1", "0:150 1:150", "A:6279354286;C:5013138453;G:5250498169;T:6092284847;N:294845", 150, 150, null, null, 6279354286, 5013138453, 5250498169, 6092284847, 294845, "SRX26022472", "SRS22594191", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [33701, "SRR30599780", "SRX26022471", "SRS22594190", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a wt  2 dpf  rep 1", "GSM8504323", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing", "ebf3a wt  2 dpf  rep 1", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types", "GSM8504323", "GSM8504323: ebf3a wt  2 dpf  rep 1; Danio rerio; RNA Seq", "GSM8504323 r1", "GSM8504323", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-WT-1-2dpf_R1_001.fastq.gz Ebf-WT-1-2dpf_R2_001.fastq.gz", "fastq fastq", 19711425600.0, 65704752.0, "GSM8504323 r1", "0:150 1:150", "A:5541464229;C:4291380685;G:4497372769;T:5380954703;N:253214", 150, 150, null, null, 5541464229, 4291380685, 4497372769, 5380954703, 253214, "SRX26022471", "SRS22594190", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [33702, "SRR30599781", "SRX26022470", "SRS22594189", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a het  2 dpf  rep 2", "GSM8504322", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous|geo loc name:missing|collection date:missing", "ebf3a het  2 dpf  rep 2", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous", "GSM8504322", "GSM8504322: ebf3a het  2 dpf  rep 2; Danio rerio; RNA Seq", "GSM8504322 r1", "GSM8504322", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-HET-2-2dpf_R1_001.fastq.gz Ebf-HET-2-2dpf_R2_001.fastq.gz", "fastq fastq", 15108144300.0, 50360481.0, "GSM8504322 r1", "0:150 1:150", "A:4240605272;C:3297282748;G:3449975456;T:4120084716;N:196108", 150, 150, null, null, 4240605272, 3297282748, 3449975456, 4120084716, 196108, "SRX26022470", "SRS22594189", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [33703, "SRR30599782", "SRX26022469", "SRS22594188", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a het  2 dpf  rep 1", "GSM8504321", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous|geo loc name:missing|collection date:missing", "ebf3a het  2 dpf  rep 1", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a heterozygous", "GSM8504321", "GSM8504321: ebf3a het  2 dpf  rep 1; Danio rerio; RNA Seq", "GSM8504321 r1", "GSM8504321", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-HET-1-2dpf_R1_001.fastq.gz Ebf-HET-1-2dpf_R2_001.fastq.gz", "fastq fastq", 16538340600.0, 55127802.0, "GSM8504321 r1", "0:150 1:150", "A:4633062848;C:3617047326;G:3792365071;T:4495647394;N:217961", 150, 150, null, null, 4633062848, 3617047326, 3792365071, 4495647394, 217961, "SRX26022469", "SRS22594188", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [33704, "SRR30599783", "SRX26022468", "SRS22594186", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a hom  2 dpf  rep 2", "GSM8504320", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous|geo loc name:missing|collection date:missing", "ebf3a hom  2 dpf  rep 2", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous", "GSM8504320", "GSM8504320: ebf3a hom  2 dpf  rep 2; Danio rerio; RNA Seq", "GSM8504320 r1", "GSM8504320", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-HOMO-2-2dpf_R1_001.fastq.gz Ebf-HOMO-2-2dpf_R2_001.fastq.gz", "fastq fastq", 14586421200.0, 48621404.0, "GSM8504320 r1", "0:150 1:150", "A:4099529019;C:3162437766;G:3348146726;T:3976118566;N:189123", 150, 150, null, null, 4099529019, 3162437766, 3348146726, 3976118566, 189123, "SRX26022468", "SRS22594186", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [33705, "SRR30599784", "SRX26022467", "SRS22594187", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a hom  2 dpf  rep 1", "GSM8504319", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous|geo loc name:missing|collection date:missing", "ebf3a hom  2 dpf  rep 1", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a homozygous", "GSM8504319", "GSM8504319: ebf3a hom  2 dpf  rep 1; Danio rerio; RNA Seq", "GSM8504319 r1", "GSM8504319", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-HOMO-1-2dpf_R1_001.fastq.gz Ebf-HOMO-1-2dpf_R2_001.fastq.gz", "fastq fastq", 14235405000.0, 47451350.0, "GSM8504319 r1", "0:150 1:150", "A:3937137116;C:3134793115;G:3336004625;T:3827286589;N:183555", 150, 150, null, null, 3937137116, 3134793115, 3336004625, 3827286589, 183555, "SRX26022467", "SRS22594187", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [65772, "SRR15606838", "SRX11904311", "SRS9915518", "SRP334037", "PRJNA757618", "RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", "GSE182725", "Transcriptome Analysis", "Here  we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long pec stage 2 dpf and sequenced at a depth of 80 100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA Seq analysis. Of these  42 were rescued with the treatment of zebrafish gut derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Overall design: RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", null, "pubmed:35996200", null, "Zebrafish Metabolite treated   ZM Rep3", "GSM5535705", null, "tissue:Zebrafish larvae|strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Metabolite treated", "Zebrafish Metabolite treated   ZM Rep3", "Demultiplexed read quality was checked for each sample using FastQC v0.11.8. Reads were aligned to GRCz11 using HISAT2 2.1.0 Expression estimates were calclulated using StringTie v1.3.4d and htseq count v0.11.0 Differential expression analysis was conducted using DESeq2 1.29.13 Genome build: GRCz11 Supplementary files format and content: abundance measurements in FPKM for all samples", "Zebrafish larvae", null, "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122\u00a0DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", null, "strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Metabolite treated", "GSM5535705", "GSM5535705: Zebrafish Metabolite treated   ZM Rep3; Danio rerio; RNA Seq", "GSM5535705", null, "1", "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122 DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", "GEO Accession:GSM5535705", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334037", null, "loader:fastq load.py", "ZM3_R1.fastq.gz ZM3_R2.fastq.gz", "fastq fastq", 12309886005.0, 40877552.0, "GSM5535705 r1", "0:150.51 1:150.63", "A:3334877731;C:2796328989;G:2982144702;T:3196312210;N:222373", 150, 150, null, null, 3334877731, 2796328989, 2982144702, 3196312210, 222373, "SRX11904311", "SRS9915518", "SRA1283476", "GEO", "Van Raay Lab, Molecular and Cellular Biology, University of Guelph", 2, 0.9492, 0.9511, 0.08506, 0.08391, 0.70546, 0.70449, 0.45419, 0.45526, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Canada", "2021-08-25", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [65773, "SRR15606837", "SRX11904310", "SRS9915517", "SRP334037", "PRJNA757618", "RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", "GSE182725", "Transcriptome Analysis", "Here  we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long pec stage 2 dpf and sequenced at a depth of 80 100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA Seq analysis. Of these  42 were rescued with the treatment of zebrafish gut derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Overall design: RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", null, "pubmed:35996200", null, "Zebrafish Metabolite treated   ZM Rep2", "GSM5535704", null, "tissue:Zebrafish larvae|strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Metabolite treated", "Zebrafish Metabolite treated   ZM Rep2", "Demultiplexed read quality was checked for each sample using FastQC v0.11.8. Reads were aligned to GRCz11 using HISAT2 2.1.0 Expression estimates were calclulated using StringTie v1.3.4d and htseq count v0.11.0 Differential expression analysis was conducted using DESeq2 1.29.13 Genome build: GRCz11 Supplementary files format and content: abundance measurements in FPKM for all samples", "Zebrafish larvae", null, "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122\u00a0DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", null, "strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Metabolite treated", "GSM5535704", "GSM5535704: Zebrafish Metabolite treated   ZM Rep2; Danio rerio; RNA Seq", "GSM5535704", null, "1", "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122 DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", "GEO Accession:GSM5535704", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334037", null, "loader:fastq load.py", "ZM2_R1.fastq.gz ZM2_R2.fastq.gz", "fastq fastq", 12010493063.0, 39885290.0, "GSM5535704 r1", "0:150.49 1:150.63", "A:3231967279;C:2771384606;G:2914941315;T:3091983923;N:215940", 150, 150, null, null, 3231967279, 2771384606, 2914941315, 3091983923, 215940, "SRX11904310", "SRS9915517", "SRA1283476", "GEO", "Van Raay Lab, Molecular and Cellular Biology, University of Guelph", 2, 0.95942, 0.96907, 0.06537, 0.06461, 0.70307, 0.70238, 0.46245, 0.4611, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Canada", "2021-08-25", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [65774, "SRR15606835", "SRX11904309", "SRS9915516", "SRP334037", "PRJNA757618", "RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", "GSE182725", "Transcriptome Analysis", "Here  we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long pec stage 2 dpf and sequenced at a depth of 80 100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA Seq analysis. Of these  42 were rescued with the treatment of zebrafish gut derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Overall design: RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", null, "pubmed:35996200", null, "Zebrafish Metabolite treated   ZM Rep1", "GSM5535703", null, "tissue:Zebrafish larvae|strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Metabolite treated", "Zebrafish Metabolite treated   ZM Rep1", "Demultiplexed read quality was checked for each sample using FastQC v0.11.8. Reads were aligned to GRCz11 using HISAT2 2.1.0 Expression estimates were calclulated using StringTie v1.3.4d and htseq count v0.11.0 Differential expression analysis was conducted using DESeq2 1.29.13 Genome build: GRCz11 Supplementary files format and content: abundance measurements in FPKM for all samples", "Zebrafish larvae", null, "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122\u00a0DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", null, "strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Metabolite treated", "GSM5535703", "GSM5535703: Zebrafish Metabolite treated   ZM Rep1; Danio rerio; RNA Seq", "GSM5535703", null, "1", "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122 DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", "GEO Accession:GSM5535703", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334037", null, "loader:fastq load.py", "ZM1_S7_L1_R1.fastq ZM1_S7_L1_R2.fastq", "fastq fastq", 4048843974.0, 20136659.0, "GSM5535703 r1", "0:100.51 1:100.55", "A:1080401747;C:941965495;G:965114058;T:1061305507;N:57167", 100, 100, null, null, 1080401747, 941965495, 965114058, 1061305507, 57167, "SRX11904309", "SRS9915516", "SRA1283476", "GEO", "Van Raay Lab, Molecular and Cellular Biology, University of Guelph", 2, 0.97446, 0.97623, 0.07143, 0.07008, 0.70567, 0.7052, 0.45986, 0.4601, 101, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Canada", "2021-08-25", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [65775, "SRR15606836", "SRX11904309", "SRS9915516", "SRP334037", "PRJNA757618", "RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", "GSE182725", "Transcriptome Analysis", "Here  we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long pec stage 2 dpf and sequenced at a depth of 80 100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA Seq analysis. Of these  42 were rescued with the treatment of zebrafish gut derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Overall design: RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", null, "pubmed:35996200", null, "Zebrafish Metabolite treated   ZM Rep1", "GSM5535703", null, "tissue:Zebrafish larvae|strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Metabolite treated", "Zebrafish Metabolite treated   ZM Rep1", "Demultiplexed read quality was checked for each sample using FastQC v0.11.8. Reads were aligned to GRCz11 using HISAT2 2.1.0 Expression estimates were calclulated using StringTie v1.3.4d and htseq count v0.11.0 Differential expression analysis was conducted using DESeq2 1.29.13 Genome build: GRCz11 Supplementary files format and content: abundance measurements in FPKM for all samples", "Zebrafish larvae", null, "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122\u00a0DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", null, "strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Metabolite treated", "GSM5535703", "GSM5535703: Zebrafish Metabolite treated   ZM Rep1; Danio rerio; RNA Seq", "GSM5535703", null, "1", "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122 DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", "GEO Accession:GSM5535703", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334037", null, "loader:fastq load.py", "ZM1_S7_L2_R1.fastq ZM1_S7_L2_R2.fastq", "fastq fastq", 4088576356.0, 20334286.0, "GSM5535703 r2", "0:100.51 1:100.55", "A:1090692847;C:951101617;G:974825114;T:1071765225;N:191553", 100, 100, null, null, 1090692847, 951101617, 974825114, 1071765225, 191553, "SRX11904309", "SRS9915516", "SRA1283476", "GEO", "Van Raay Lab, Molecular and Cellular Biology, University of Guelph", 2, 0.97491, 0.97653, 0.0713, 0.06927, 0.70181, 0.70136, 0.45972, 0.46481, 100, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Canada", "2021-08-25", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [65776, "SRR15606834", "SRX11904308", "SRS9915515", "SRP334037", "PRJNA757618", "RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", "GSE182725", "Transcriptome Analysis", "Here  we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long pec stage 2 dpf and sequenced at a depth of 80 100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA Seq analysis. Of these  42 were rescued with the treatment of zebrafish gut derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Overall design: RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", null, "pubmed:35996200", null, "Germ free   GF Rep3", "GSM5535702", null, "tissue:Zebrafish larvae|strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Germ free", "Germ free   GF Rep3", "Demultiplexed read quality was checked for each sample using FastQC v0.11.8. Reads were aligned to GRCz11 using HISAT2 2.1.0 Expression estimates were calclulated using StringTie v1.3.4d and htseq count v0.11.0 Differential expression analysis was conducted using DESeq2 1.29.13 Genome build: GRCz11 Supplementary files format and content: abundance measurements in FPKM for all samples", "Zebrafish larvae", null, "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122\u00a0DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", null, "strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Germ free", "GSM5535702", "GSM5535702: Germ free   GF Rep3; Danio rerio; RNA Seq", "GSM5535702", null, "1", "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122 DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", "GEO Accession:GSM5535702", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334037", null, "loader:fastq load.py", "GF3_R1.fastq.gz GF3_R2.fastq.gz", "fastq fastq", 14411259038.0, 47848646.0, "GSM5535702 r1", "0:150.53 1:150.66", "A:3916233501;C:3258779110;G:3470717572;T:3765263932;N:264923", 150, 150, null, null, 3916233501, 3258779110, 3470717572, 3765263932, 264923, "SRX11904308", "SRS9915515", "SRA1283476", "GEO", "Van Raay Lab, Molecular and Cellular Biology, University of Guelph", 2, 0.94451, 0.946, 0.08201, 0.08096, 0.70954, 0.7082, 0.45612, 0.45583, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Canada", "2021-08-25", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [65777, "SRR15606833", "SRX11904307", "SRS9915514", "SRP334037", "PRJNA757618", "RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", "GSE182725", "Transcriptome Analysis", "Here  we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long pec stage 2 dpf and sequenced at a depth of 80 100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA Seq analysis. Of these  42 were rescued with the treatment of zebrafish gut derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Overall design: RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", null, "pubmed:35996200", null, "Germ free   GF Rep2", "GSM5535701", null, "tissue:Zebrafish larvae|strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Germ free", "Germ free   GF Rep2", "Demultiplexed read quality was checked for each sample using FastQC v0.11.8. Reads were aligned to GRCz11 using HISAT2 2.1.0 Expression estimates were calclulated using StringTie v1.3.4d and htseq count v0.11.0 Differential expression analysis was conducted using DESeq2 1.29.13 Genome build: GRCz11 Supplementary files format and content: abundance measurements in FPKM for all samples", "Zebrafish larvae", null, "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122\u00a0DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", null, "strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Germ free", "GSM5535701", "GSM5535701: Germ free   GF Rep2; Danio rerio; RNA Seq", "GSM5535701", null, "1", "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122 DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", "GEO Accession:GSM5535701", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334037", null, "loader:fastq load.py", "GF2_R1.fastq.gz GF2_R2.fastq.gz", "fastq fastq", 10212016412.0, 33909177.0, "GSM5535701 r1", "0:150.52 1:150.64", "A:2772392259;C:2336154520;G:2457542539;T:2645743226;N:183868", 150, 150, null, null, 2772392259, 2336154520, 2457542539, 2645743226, 183868, "SRX11904307", "SRS9915514", "SRA1283476", "GEO", "Van Raay Lab, Molecular and Cellular Biology, University of Guelph", 2, 0.96146, 0.97171, 0.07117, 0.07096, 0.70772, 0.70546, 0.45041, 0.45036, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Canada", "2021-08-25", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [65778, "SRR15606832", "SRX11904306", "SRS9915513", "SRP334037", "PRJNA757618", "RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", "GSE182725", "Transcriptome Analysis", "Here  we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long pec stage 2 dpf and sequenced at a depth of 80 100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA Seq analysis. Of these  42 were rescued with the treatment of zebrafish gut derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Overall design: RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", null, "pubmed:35996200", null, "Germ free   GF Rep1", "GSM5535700", null, "tissue:Zebrafish larvae|strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Germ free", "Germ free   GF Rep1", "Demultiplexed read quality was checked for each sample using FastQC v0.11.8. Reads were aligned to GRCz11 using HISAT2 2.1.0 Expression estimates were calclulated using StringTie v1.3.4d and htseq count v0.11.0 Differential expression analysis was conducted using DESeq2 1.29.13 Genome build: GRCz11 Supplementary files format and content: abundance measurements in FPKM for all samples", "Zebrafish larvae", null, "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122\u00a0DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", null, "strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Germ free", "GSM5535700", "GSM5535700: Germ free   GF Rep1; Danio rerio; RNA Seq", "GSM5535700", null, "1", "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122 DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", "GEO Accession:GSM5535700", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334037", null, "loader:fastq load.py", "GF1_R1.fastq.gz GF1_R2.fastq.gz", "fastq fastq", 15494890731.0, 51452768.0, "GSM5535700 r1", "0:150.51 1:150.64", "A:4204554108;C:3538500955;G:3719345305;T:4032206656;N:283707", 150, 150, null, null, 4204554108, 3538500955, 3719345305, 4032206656, 283707, "SRX11904306", "SRS9915513", "SRA1283476", "GEO", "Van Raay Lab, Molecular and Cellular Biology, University of Guelph", 2, 0.96626, 0.97207, 0.0762, 0.07568, 0.69357, 0.69388, 0.45129, 0.45751, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Canada", "2021-08-25", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [65779, "SRR15606831", "SRX11904305", "SRS9915512", "SRP334037", "PRJNA757618", "RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", "GSE182725", "Transcriptome Analysis", "Here  we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long pec stage 2 dpf and sequenced at a depth of 80 100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA Seq analysis. Of these  42 were rescued with the treatment of zebrafish gut derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Overall design: RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", null, "pubmed:35996200", null, "Conventionally raised   CV Rep3", "GSM5535699", null, "tissue:Zebrafish larvae|strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Conventionally raised", "Conventionally raised   CV Rep3", "Demultiplexed read quality was checked for each sample using FastQC v0.11.8. Reads were aligned to GRCz11 using HISAT2 2.1.0 Expression estimates were calclulated using StringTie v1.3.4d and htseq count v0.11.0 Differential expression analysis was conducted using DESeq2 1.29.13 Genome build: GRCz11 Supplementary files format and content: abundance measurements in FPKM for all samples", "Zebrafish larvae", null, "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122\u00a0DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", null, "strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Conventionally raised", "GSM5535699", "GSM5535699: Conventionally raised   CV Rep3; Danio rerio; RNA Seq", "GSM5535699", null, "1", "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122 DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", "GEO Accession:GSM5535699", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334037", null, "loader:fastq load.py", "CV3_R1.fastq.gz CV3_R2.fastq.gz", "fastq fastq", 16180858567.0, 53734229.0, "GSM5535699 r1", "0:150.51 1:150.62", "A:4357714126;C:3723269650;G:3903764236;T:4195818077;N:292478", 150, 150, null, null, 4357714126, 3723269650, 3903764236, 4195818077, 292478, "SRX11904305", "SRS9915512", "SRA1283476", "GEO", "Van Raay Lab, Molecular and Cellular Biology, University of Guelph", 2, 0.95613, 0.95372, 0.08772, 0.08595, 0.68617, 0.68751, 0.4611, 0.46211, 151, 149, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Canada", "2021-08-25", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [65780, "SRR15606830", "SRX11904304", "SRS9915511", "SRP334037", "PRJNA757618", "RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", "GSE182725", "Transcriptome Analysis", "Here  we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long pec stage 2 dpf and sequenced at a depth of 80 100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA Seq analysis. Of these  42 were rescued with the treatment of zebrafish gut derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Overall design: RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", null, "pubmed:35996200", null, "Conventionally raised   CV Rep2", "GSM5535698", null, "tissue:Zebrafish larvae|strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Conventionally raised", "Conventionally raised   CV Rep2", "Demultiplexed read quality was checked for each sample using FastQC v0.11.8. Reads were aligned to GRCz11 using HISAT2 2.1.0 Expression estimates were calclulated using StringTie v1.3.4d and htseq count v0.11.0 Differential expression analysis was conducted using DESeq2 1.29.13 Genome build: GRCz11 Supplementary files format and content: abundance measurements in FPKM for all samples", "Zebrafish larvae", null, "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122\u00a0DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", null, "strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Conventionally raised", "GSM5535698", "GSM5535698: Conventionally raised   CV Rep2; Danio rerio; RNA Seq", "GSM5535698", null, "1", "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122 DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", "GEO Accession:GSM5535698", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334037", null, "loader:fastq load.py", "CV2_R1.fastq.gz CV2_R2.fastq.gz", "fastq fastq", 11808803713.0, 39214133.0, "GSM5535698 r1", "0:150.50 1:150.64", "A:3187132446;C:2696408684;G:2862457966;T:3062591535;N:213082", 150, 150, null, null, 3187132446, 2696408684, 2862457966, 3062591535, 213082, "SRX11904304", "SRS9915511", "SRA1283476", "GEO", "Van Raay Lab, Molecular and Cellular Biology, University of Guelph", 2, 0.9672, 0.97535, 0.07827, 0.07779, 0.68945, 0.68962, 0.4522, 0.45132, 149, 149, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Canada", "2021-08-25", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [65781, "SRR15606829", "SRX11904303", "SRS9915510", "SRP334037", "PRJNA757618", "RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", "GSE182725", "Transcriptome Analysis", "Here  we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long pec stage 2 dpf and sequenced at a depth of 80 100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA Seq analysis. Of these  42 were rescued with the treatment of zebrafish gut derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Overall design: RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites.", null, "pubmed:35996200", null, "Conventionally raised   CV Rep1", "GSM5535697", null, "tissue:Zebrafish larvae|strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Conventionally raised", "Conventionally raised   CV Rep1", "Demultiplexed read quality was checked for each sample using FastQC v0.11.8. Reads were aligned to GRCz11 using HISAT2 2.1.0 Expression estimates were calclulated using StringTie v1.3.4d and htseq count v0.11.0 Differential expression analysis was conducted using DESeq2 1.29.13 Genome build: GRCz11 Supplementary files format and content: abundance measurements in FPKM for all samples", "Zebrafish larvae", null, "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122\u00a0DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", null, "strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Conventionally raised", "GSM5535697", "GSM5535697: Conventionally raised   CV Rep1; Danio rerio; RNA Seq", "GSM5535697", null, "1", "Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol\u2122 TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen\u2122 DNA free\u2122 DNA Removal Kit PolyA mRNA was prepared using the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina", "GEO Accession:GSM5535697", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334037", null, "loader:fastq load.py", "CV1_R1.fastq.gz CV1_R2.fastq.gz", "fastq fastq", 11147171574.0, 37012120.0, "GSM5535697 r1", "0:150.52 1:150.66", "A:2990166316;C:2510615373;G:2775000662;T:2871190468;N:198755", 150, 150, null, null, 2990166316, 2510615373, 2775000662, 2871190468, 198755, "SRX11904303", "SRS9915510", "SRA1283476", "GEO", "Van Raay Lab, Molecular and Cellular Biology, University of Guelph", 2, 0.96613, 0.96585, 0.08675, 0.08563, 0.69796, 0.69765, 0.45882, 0.45647, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Canada", "2021-08-25", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67934, "SRR17499128", "SRX13669342", "SRS11554978", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "WT 3", "GSM5782115", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:n1|treatment:heat shock", "WT 3", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:n1|treatment:heat shock", "GSM5782115", "GSM5782115: WT 3; Danio rerio; RNA Seq", "GSM5782115 r1", "GSM5782115", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "WT_3.fastq.gz", "fastq", 1631087040.0, 22246950.0, "GSM5782115 r1", "0:73.32", "A:449912416;C:359801594;G:370071032;T:449082499;N:2219499", 73, null, null, null, 449912416, 359801594, 370071032, 449082499, 2219499, "SRX13669342", "SRS11554978", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.92746, null, 0.13827, null, 0.7205, null, 0.49824, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67935, "SRR17499129", "SRX13669341", "SRS11554977", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "WT 2", "GSM5782114", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:n1|treatment:heat shock", "WT 2", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:n1|treatment:heat shock", "GSM5782114", "GSM5782114: WT 2; Danio rerio; RNA Seq", "GSM5782114 r1", "GSM5782114", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "WT_2.fastq.gz", "fastq", 1447145284.0, 19935063.0, "GSM5782114 r1", "0:72.59", "A:380778577;C:335429272;G:346541394;T:382018742;N:2377299", 72, null, null, null, 380778577, 335429272, 346541394, 382018742, 2377299, "SRX13669341", "SRS11554977", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.92802, null, 0.17848, null, 0.75532, null, 0.56527, null, 74, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67936, "SRR17499130", "SRX13669340", "SRS11554976", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "WT 1", "GSM5782113", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:n1|treatment:heat shock", "WT 1", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:n1|treatment:heat shock", "GSM5782113", "GSM5782113: WT 1; Danio rerio; RNA Seq", "GSM5782113 r1", "GSM5782113", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "WT_1.fastq.gz", "fastq", 1621350207.0, 22195287.0, "GSM5782113 r1", "0:73.05", "A:416561303;C:385113762;G:399863594;T:416577633;N:3233915", 73, null, null, null, 416561303, 385113762, 399863594, 416577633, 3233915, "SRX13669340", "SRS11554976", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.92305, null, 0.23257, null, 0.74014, null, 0.56091, null, 75, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67937, "SRR17499131", "SRX13669339", "SRS11554974", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "neurod1delECD 3", "GSM5782112", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1delECD|treatment:heat shock", "neurod1delECD 3", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1delECD|treatment:heat shock", "GSM5782112", "GSM5782112: neurod1delECD 3; Danio rerio; RNA Seq", "GSM5782112 r1", "GSM5782112", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "neurod1delECD_3.fastq.gz", "fastq", 1357095410.0, 18184667.0, "GSM5782112 r1", "0:74.63", "A:355745142;C:312936101;G:324744763;T:363430805;N:238599", 74, null, null, null, 355745142, 312936101, 324744763, 363430805, 238599, "SRX13669339", "SRS11554974", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.92128, null, 0.15319, null, 0.73288, null, 0.53288, null, 75, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67938, "SRR17499132", "SRX13669338", "SRS11554975", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "neurod1delECD 2", "GSM5782111", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1delECD|treatment:heat shock", "neurod1delECD 2", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1delECD|treatment:heat shock", "GSM5782111", "GSM5782111: neurod1delECD 2; Danio rerio; RNA Seq", "GSM5782111 r1", "GSM5782111", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "neurod1delECD_2.fastq.gz", "fastq", 2102492246.0, 29517203.0, "GSM5782111 r1", "0:71.23", "A:604913044;C:434539299;G:447331142;T:610824543;N:4884218", 71, null, null, null, 604913044, 434539299, 447331142, 610824543, 4884218, "SRX13669338", "SRS11554975", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.91879, null, 0.10797, null, 0.76104, null, 0.52877, null, 62, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67939, "SRR17499133", "SRX13669337", "SRS11554973", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "neurod1delECD 1", "GSM5782110", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1delECD|treatment:heat shock", "neurod1delECD 1", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1delECD|treatment:heat shock", "GSM5782110", "GSM5782110: neurod1delECD 1; Danio rerio; RNA Seq", "GSM5782110 r1", "GSM5782110", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "neurod1delECD_1.fastq.gz", "fastq", 1967716518.0, 27124142.0, "GSM5782110 r1", "0:72.54", "A:538264168;C:438242103;G:449243134;T:538752938;N:3214175", 72, null, null, null, 538264168, 438242103, 449243134, 538752938, 3214175, "SRX13669337", "SRS11554973", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.93118, null, 0.14524, null, 0.7321, null, 0.51618, null, 74, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67940, "SRR17499134", "SRX13669336", "SRS11554972", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "neurod1delUCE 3", "GSM5782109", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1delUCE|treatment:heat shock", "neurod1delUCE 3", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1delUCE|treatment:heat shock", "GSM5782109", "GSM5782109: neurod1delUCE 3; Danio rerio; RNA Seq", "GSM5782109 r1", "GSM5782109", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "neurod1delUCE_3.fastq.gz", "fastq", 1467154640.0, 19780149.0, "GSM5782109 r1", "0:74.17", "A:380743947;C:340934018;G:355401415;T:389502066;N:573194", 74, null, null, null, 380743947, 340934018, 355401415, 389502066, 573194, "SRX13669336", "SRS11554972", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.91516, null, 0.18328, null, 0.75879, null, 0.55356, null, 75, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67941, "SRR17499135", "SRX13669335", "SRS11554970", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "neurod1delUCE 2", "GSM5782108", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1delUCE|treatment:heat shock", "neurod1delUCE 2", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1delUCE|treatment:heat shock", "GSM5782108", "GSM5782108: neurod1delUCE 2; Danio rerio; RNA Seq", "GSM5782108 r1", "GSM5782108", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "neurod1delUCE_2.fastq.gz", "fastq", 1682813311.0, 22675022.0, "GSM5782108 r1", "0:74.21", "A:493321451;C:338009359;G:347924089;T:502447949;N:1110463", 74, null, null, null, 493321451, 338009359, 347924089, 502447949, 1110463, "SRX13669335", "SRS11554970", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.91603, null, 0.1614, null, 0.74438, null, 0.46704, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67942, "SRR17499136", "SRX13669334", "SRS11554971", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "neurod1delUCE 1", "GSM5782107", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1delUCE|treatment:heat shock", "neurod1delUCE 1", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1delUCE|treatment:heat shock", "GSM5782107", "GSM5782107: neurod1delUCE 1; Danio rerio; RNA Seq", "GSM5782107 r1", "GSM5782107", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "neurod1delUCE_1.fastq.gz", "fastq", 1614414037.0, 22125782.0, "GSM5782107 r1", "0:72.97", "A:397487731;C:403037604;G:415852572;T:395568466;N:2467664", 72, null, null, null, 397487731, 403037604, 415852572, 395568466, 2467664, "SRX13669334", "SRS11554971", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.94144, null, 0.28263, null, 0.75797, null, 0.60121, null, 75, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67943, "SRR17499137", "SRX13669333", "SRS11554969", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "neurod1 4", "GSM5782106", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1|treatment:heat shock", "neurod1 4", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1|treatment:heat shock", "GSM5782106", "GSM5782106: neurod1 4; Danio rerio; RNA Seq", "GSM5782106 r1", "GSM5782106", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "neurod1_4.fastq.gz", "fastq", 1648484944.0, 22262329.0, "GSM5782106 r1", "0:74.05", "A:454322873;C:364604693;G:375789404;T:452598898;N:1169076", 74, null, null, null, 454322873, 364604693, 375789404, 452598898, 1169076, "SRX13669333", "SRS11554969", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.92394, null, 0.14895, null, 0.72679, null, 0.50393, null, 75, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67944, "SRR17499138", "SRX13669332", "SRS11554968", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "neurod1 3", "GSM5782105", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1|treatment:heat shock", "neurod1 3", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1|treatment:heat shock", "GSM5782105", "GSM5782105: neurod1 3; Danio rerio; RNA Seq", "GSM5782105 r1", "GSM5782105", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "neurod1_3.fastq.gz", "fastq", 1740201676.0, 23877235.0, "GSM5782105 r1", "0:72.88", "A:492551901;C:368591027;G:378769440;T:497000610;N:3288698", 72, null, null, null, 492551901, 368591027, 378769440, 497000610, 3288698, "SRX13669332", "SRS11554968", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.92326, null, 0.15045, null, 0.73111, null, 0.48416, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67945, "SRR17499139", "SRX13669331", "SRS11554967", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "neurod1 2", "GSM5782104", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1|treatment:heat shock", "neurod1 2", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1|treatment:heat shock", "GSM5782104", "GSM5782104: neurod1 2; Danio rerio; RNA Seq", "GSM5782104 r1", "GSM5782104", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "neurod1_2.fastq.gz", "fastq", 1490592375.0, 20401056.0, "GSM5782104 r1", "0:73.06", "A:381296757;C:357576777;G:368515394;T:381354668;N:1848779", 73, null, null, null, 381296757, 357576777, 368515394, 381354668, 1848779, "SRX13669331", "SRS11554967", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.93947, null, 0.22412, null, 0.74627, null, 0.53279, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67946, "SRR17499140", "SRX13669330", "SRS11554966", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "neurod1 1", "GSM5782103", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1|treatment:heat shock", "neurod1 1", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:neurod1|treatment:heat shock", "GSM5782103", "GSM5782103: neurod1 1; Danio rerio; RNA Seq", "GSM5782103 r1", "GSM5782103", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "neurod1_1.fastq.gz", "fastq", 1803887378.0, 25007301.0, "GSM5782103 r1", "0:72.13", "A:465639733;C:424003340;G:441888689;T:466407058;N:5948558", 72, null, null, null, 465639733, 424003340, 441888689, 466407058, 5948558, "SRX13669330", "SRS11554966", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.86723, null, 0.21618, null, 0.75933, null, 0.51887, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67947, "SRR17499141", "SRX13669329", "SRS11554965", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "ascl1a 3", "GSM5782102", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:ascl1a|treatment:heat shock", "ascl1a 3", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:ascl1a|treatment:heat shock", "GSM5782102", "GSM5782102: ascl1a 3; Danio rerio; RNA Seq", "GSM5782102 r1", "GSM5782102", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "ascl1a_3.fastq.gz", "fastq", 1096673438.0, 14758654.0, "GSM5782102 r1", "0:74.31", "A:292566345;C:247808465;G:257160518;T:298807697;N:330413", 74, null, null, null, 292566345, 247808465, 257160518, 298807697, 330413, "SRX13669329", "SRS11554965", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.92008, null, 0.13327, null, 0.73476, null, 0.51693, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67948, "SRR17499142", "SRX13669328", "SRS11554964", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "ascl1a 2", "GSM5782101", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:ascl1a|treatment:heat shock", "ascl1a 2", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:ascl1a|treatment:heat shock", "GSM5782101", "GSM5782101: ascl1a 2; Danio rerio; RNA Seq", "GSM5782101 r1", "GSM5782101", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "ascl1a_2.fastq.gz", "fastq", 1804876506.0, 24809874.0, "GSM5782101 r1", "0:72.75", "A:501002333;C:391986992;G:404213246;T:504382983;N:3290952", 72, null, null, null, 501002333, 391986992, 404213246, 504382983, 3290952, "SRX13669328", "SRS11554964", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.92048, null, 0.13789, null, 0.74036, null, 0.52176, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [67949, "SRR17499143", "SRX13669327", "SRS11554963", "SRP354077", "PRJNA795663", "Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation", "GSE193281", "Transcriptome Analysis", "ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues  coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors  recognizing highly similar DNA motifs  display specific activities  is not yet fully understood.     To address this issue  we overexpressed different ARP/ASCL factors in zebrafish ascl1a /  mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b  Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed  Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain of function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19 aa ultra conserved element UCE  present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression  known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes  validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly  the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed  we can envision a similar role of the UCE in other tissues  allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. Overall design: RNA sequencing of 23 samples. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4dpf wild type and neurod1 deleted from its conserved domain neurod1DelUCE /   zebrafish embryos were generated in in 3 replicates and 4 replicates  respectively.  Endodermal cells sox17:dsRed + transcriptomic profiles of 52hpf WT or transgenic hsp70:ascl1a  hsp70:neurod1  hsp70: neurod1DelUCE  hsp70: neurod1DelECD zebrafish embryos were generated in triplicates or in 4 replicates hsp70:neurod1 post 2 heat shocks inducing transgene expression.", null, "pubmed:35286299", null, "ascl1a 1", "GSM5782100", null, "source name:Endodermal cells|strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:ascl1a|treatment:heat shock", "ascl1a 1", "Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample", "Endodermal cells", "The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  Tgsox17:dsred Field et al  2003  neurod1 ulg052", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", "Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.", "strain:AB|tissue:Endoderm|age:52hpf|genotype:Wild type|transgene:hsp70:ascl1a|treatment:heat shock", "GSM5782100", "GSM5782100: ascl1a 1; Danio rerio; RNA Seq", "GSM5782100 r1", "GSM5782100", "1", "EECs were isolated by dissecting the gut from about 200 transgenic neurod1\u0394UCE/\u0394UCE or wild type Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and GFP expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17 dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tghsp70l:eGFP 2A ARP/Ascl or wild type Tgsox17:dsred larvae at 52 dpf  heat shocked at 38 and 48hpf  taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X Gibco for 8 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells. Each FACS sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 \u00b5l of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80\u00b0C according the Smart seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 20 million of reads 75 base single end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP354077", null, "loader:fastq load.py", "ascl1a_1.fastq.gz", "fastq", 1486915016.0, 20371110.0, "GSM5782100 r1", "0:72.99", "A:370236340;C:362874334;G:379824149;T:370719450;N:3260743", 72, null, null, null, 370236340, 362874334, 379824149, 370719450, 3260743, "SRX13669327", "SRS11554963", "SRA1353950", "GIGA, University of Li\u00e8ge", "GIGA, University of Li\u00e8ge", 1, 0.90209, null, 0.24217, null, 0.78179, null, 0.59143, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2022-01-08", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [72204, "SRR22306367", "SRX18279945", "SRS15772341", "SRP408138", "PRJNA902019", "Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament", "GSE218068", "Transcriptome Analysis", "Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing", null, "pubmed:37024546", null, "Foxc1b 48hpf", "GSM6734157", null, "source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf", "Foxc1b 48hpf", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files", "Anterior Segment Mesenchyme", null, "Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37\u00b0C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf", "GSM6734157", "GSM6734157: Foxc1b 48hpf; Danio rerio; RNA Seq", "GSM6734157 r1", "GSM6734157", "1", "Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37\u00b0C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP408138", null, "loader:fastq load.py", "48hpf_A_S1_L004_I1_001.fastq.gz 48hpf_A_S1_L004_R1_001.fastq.gz 48hpf_A_S1_L004_R2_001.fastq.gz", "fastq fastq fastq", 20362974376.0, 110668339.0, "GSM6734157 r1", "0:8 1:26 2:150", "A:5123945131;C:3326458224;G:3713701708;T:4435572452;N:573335", 8, 26, 150, null, 5123945131, 3326458224, 3713701708, 4435572452, 573335, "SRX18279945", "SRS15772341", "SRA1541630", "Famulski, Biology, University of Kentucky", "Famulski, Biology, University of Kentucky", 1, 0.9134, null, 0.07314, null, 0.81379, null, 0.49083, null, 150, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-11-15", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [72205, "SRR22306368", "SRX18279945", "SRS15772341", "SRP408138", "PRJNA902019", "Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament", "GSE218068", "Transcriptome Analysis", "Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing", null, "pubmed:37024546", null, "Foxc1b 48hpf", "GSM6734157", null, "source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf", "Foxc1b 48hpf", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files", "Anterior Segment Mesenchyme", null, "Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37\u00b0C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf", "GSM6734157", "GSM6734157: Foxc1b 48hpf; Danio rerio; RNA Seq", "GSM6734157 r1", "GSM6734157", "1", "Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37\u00b0C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP408138", null, "loader:fastq load.py", "48hpf_B_S3_L001_I1_001.fastq.gz 48hpf_B_S3_L001_R1_001.fastq.gz 48hpf_B_S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 12341386626.0, 66351541.0, "GSM6734157 r2", "0:8 1:28 2:150", "A:2795275569;C:2297425042;G:2482925319;T:2376906238;N:198982", 8, 28, 150, null, 2795275569, 2297425042, 2482925319, 2376906238, 198982, "SRX18279945", "SRS15772341", "SRA1541630", "Famulski, Biology, University of Kentucky", "Famulski, Biology, University of Kentucky", 1, 0.95768, null, 0.08708, null, 0.81903, null, 0.51103, null, 150, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-11-15", "Hatching", "Embryo", "Multi-tissue", "Multi-system"], [72206, "SRR22306369", "SRX18279945", "SRS15772341", "SRP408138", "PRJNA902019", "Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament", "GSE218068", "Transcriptome Analysis", "Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing", null, "pubmed:37024546", null, "Foxc1b 48hpf", "GSM6734157", null, "source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf", "Foxc1b 48hpf", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files", "Anterior Segment Mesenchyme", null, "Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37\u00b0C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics.", null, "tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf", "GSM6734157", "GSM6734157: Foxc1b 48hpf; Danio rerio; RNA Seq", "GSM6734157 r1", "GSM6734157", "1", "Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37\u00b0C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP408138", null, "loader:fastq load.py", "48hpf_B_S3_L002_I1_001.fastq.gz 48hpf_B_S3_L002_R1_001.fastq.gz 48hpf_B_S3_L002_R2_001.fastq.gz", "fastq fastq fastq", 12292760832.0, 66090112.0, "GSM6734157 r3", "0:8 1:28 2:150", "A:2783844388;C:2288795302;G:2473127346;T:2367511149;N:238615", 8, 28, 150, null, 2783844388, 2288795302, 2473127346, 2367511149, 238615, "SRX18279945", "SRS15772341", "SRA1541630", "Famulski, Biology, University of Kentucky", "Famulski, Biology, University of Kentucky", 1, 0.95903, null, 0.08687, null, 0.82085, null, 0.53794, null, 150, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-11-15", "Hatching", "Embryo", "Multi-tissue", "Multi-system"]], "truncated": false, "filtered_table_rows_count": 74, "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 \"devstage_curation\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Hatching", "p1": "Multi-tissue"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 74, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 71, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue", "results": [{"value": "cDNA", "label": "cDNA", "count": 74, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 55, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 74, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue", "results": [{"value": "Embryo", "label": "Embryo", "count": 74, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue", "results": [{"value": "Hatching", "label": "Hatching", "count": 74, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Multi-tissue", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue", "results": [{"value": "Multi-system", "label": "Multi-system", "count": 74, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue&tissue_curation_coarse=Multi-system", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue", "results": [{"value": "Multi-tissue", "label": "Multi-tissue", "count": 74, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue", "results": [{"value": "smartseq", "label": "smartseq", "count": 55, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue&technology=smartseq", "selected": false}, {"value": "unknown", "label": "unknown", "count": 16, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue&technology=unknown", "selected": false}, {"value": "10x", "label": "10x", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Multi-tissue&technology=10x", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 128.11904800037155}