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74 rows where devstage_curation = "Hatching" and tissue_curation = "Multi-tissue"

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technology 3

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Multi-tissue · 74 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_selection 1

devstage_curation_coarse 1

devstage_curation 1

  • Hatching · 74 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
29909 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.       deaf1 2 dpf rep11 GSM8020192   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       1106171674 1156870042 1092472583 1120212338 79563 SRX23261746 SRS20163710 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29910 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.       deaf1 2 dpf rep10 GSM8020191   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       1000059012 1020300240 981249122 999909425 68901 SRX23261745 SRS20163711 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29911 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.       deaf1 2 dpf rep9 GSM8020190   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       930732486 940157658 908687307 937097122 65727 SRX23261744 SRS20163709 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29912 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.       deaf1 2 dpf rep8 GSM8020189   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       929440558 958986044 914039968 938952561 65869 SRX23261743 SRS20163708 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29913 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.       deaf1 2 dpf rep7 GSM8020188   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       738636815 755836125 729168292 748297854 52314 SRX23261742 SRS20163707 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29914 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.       deaf1 2 dpf rep6 GSM8020187   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       1032735373 1051188374 1016197596 1034203095 73362 SRX23261741 SRS20163706 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29915 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.       deaf1 2 dpf rep5 GSM8020186   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       901094303 929956244 893844528 906664233 65192 SRX23261740 SRS20163705 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29916 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.       deaf1 2 dpf rep4 GSM8020185   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       835857971 854981364 824035698 834673793 60374 SRX23261739 SRS20163704 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29917 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.       deaf1 2 dpf rep3 GSM8020184   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       839050016 857965663 828869795 845766740 61086 SRX23261738 SRS20163703 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29918 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.       deaf1 2 dpf rep2 GSM8020183   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       938612608 949004833 927692516 941125085 66058 SRX23261737 SRS20163701 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29919 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.       deaf1 2 dpf rep1 GSM8020182   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       839320911 859028175 836373251 843291522 60241 SRX23261736 SRS20163702 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29920 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.       deaf1 t238p 2 dpf rep13 GSM8020181   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       655207900 616856238 613068980 637525231 223304 SRX23261735 SRS20163699 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29921 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.       deaf1 t238p 2 dpf rep12 GSM8020180   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       838706781 792017578 780975426 820709157 287360 SRX23261734 SRS20163698 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29922 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.       deaf1 t238p 2 dpf rep11 GSM8020179   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       797054679 770109006 759275000 778955169 277616 SRX23261733 SRS20163700 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29923 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.       deaf1 t238p 2 dpf rep10 GSM8020178   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       893360259 869418642 860403580 875711902 323481 SRX23261732 SRS20163697 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29924 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.       deaf1 t238p 2 dpf rep9 GSM8020177   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       847366551 800849702 791226044 829037606 291895 SRX23261731 SRS20163696 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29925 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.       deaf1 t238p 2 dpf rep8 GSM8020176   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       525317640 498055852 491357881 512263813 179139 SRX23261730 SRS20163695 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29926 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.       deaf1 t238p 2 dpf rep7 GSM8020175   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       722896986 681138747 674833627 708219281 251707 SRX23261729 SRS20163694 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29927 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.       deaf1 t238p 2 dpf rep6 GSM8020174   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       770250088 731344480 721594408 753713587 268981 SRX23261728 SRS20163693 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29928 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.       deaf1 t238p 2 dpf rep5 GSM8020173   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       665391714 618921995 614059292 647931593 225168 SRX23261727 SRS20163692 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29929 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.       deaf1 t238p 2 dpf rep4 GSM8020172   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       831927955 768758728 763547713 812339162 288180 SRX23261726 SRS20163691 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29930 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.       deaf1 t238p 2 dpf rep3 GSM8020171   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       297385645 276022399 273402666 289320311 101539 SRX23261725 SRS20163690 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29931 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.       deaf1 t238p 2 dpf rep2 GSM8020170   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       721197113 659588175 652875625 701848626 239480 SRX23261724 SRS20163689 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29932 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.       deaf1 t238p 2 dpf rep1 GSM8020169   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     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       883991145 814741172 809532162 861133903 301519 SRX23261723 SRS20163688 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29947 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.       deaf1 c207y 2 dpf rep13 GSM8020168   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       803333990 685431342 677569210 797384558 92267 SRX23261708 SRS20163673 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29948 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.       deaf1 c207y 2 dpf rep12 GSM8020167   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       847208990 751109498 736855605 848892893 98303 SRX23261707 SRS20163672 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29949 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.       deaf1 c207y 2 dpf rep11 GSM8020166   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       846133299 724401184 709966835 835240904 95961 SRX23261706 SRS20163671 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29950 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.       deaf1 c207y 2 dpf rep10 GSM8020165   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       753665483 638171516 626255827 749805524 85834 SRX23261705 SRS20163670 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29951 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.       deaf1 c207y 2 dpf rep9 GSM8020164   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       1459560082 1269220844 1235271759 1453256921 168794 SRX23261704 SRS20163669 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29952 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.       deaf1 c207y 2 dpf rep8 GSM8020163   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       657342317 558713775 547590726 654164599 74750 SRX23261703 SRS20163668 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29953 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.       deaf1 c207y 2 dpf rep7 GSM8020162   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       974139857 839029639 822572729 965450738 112325 SRX23261702 SRS20163667 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29954 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.       deaf1 c207y 2 dpf rep6 GSM8020161   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       689302325 596907356 578571204 680690103 78977 SRX23261701 SRS20163666 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29955 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.       deaf1 c207y 2 dpf rep5 GSM8020160   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       850838897 712670459 688515516 850736210 96076 SRX23261700 SRS20163665 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29956 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.       deaf1 c207y 2 dpf rep4 GSM8020159   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       933225760 786732356 770845968 924742081 105468 SRX23261699 SRS20163664 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29957 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.       deaf1 c207y 2 dpf rep3 GSM8020158   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       920850547 802940416 790735026 915103526 105457 SRX23261698 SRS20163663 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29958 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.       deaf1 c207y 2 dpf rep2 GSM8020157   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       742011214 673773327 656344142 738655690 86229 SRX23261697 SRS20163662 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29959 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.       deaf1 c207y 2 dpf rep1 GSM8020156   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       1104853000 1023572758 1001000314 1104961067 130680 SRX23261696 SRS20163661 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29993 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.       deaf1 2 dpf rep13 GSM8020194   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       1088757969 1142271720 1089301455 1097060536 79120 SRX23261662 SRS20163627 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29994 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.       deaf1 2 dpf rep12 GSM8020193   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   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       1040374012 1082175747 1042489373 1053094232 76136 SRX23261661 SRS20163626 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
33700 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.       ebf3a wt 2 dpf rep 2 GSM8504324   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   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP531514     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     6279354286 5013138453 5250498169 6092284847 294845 SRX26022472 SRS22594191 SRA1966071 UMass Chan Medical School UMass Chan Medical School                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-09-09 Hatching Embryo Multi-tissue Multi-system
33701 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.       ebf3a wt 2 dpf rep 1 GSM8504323   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   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP531514     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     5541464229 4291380685 4497372769 5380954703 253214 SRX26022471 SRS22594190 SRA1966071 UMass Chan Medical School UMass Chan Medical School                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-09-09 Hatching Embryo Multi-tissue Multi-system
33702 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.       ebf3a het 2 dpf rep 2 GSM8504322   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   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP531514     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     4240605272 3297282748 3449975456 4120084716 196108 SRX26022470 SRS22594189 SRA1966071 UMass Chan Medical School UMass Chan Medical School                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-09-09 Hatching Embryo Multi-tissue Multi-system
33703 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.       ebf3a het 2 dpf rep 1 GSM8504321   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   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP531514     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     4633062848 3617047326 3792365071 4495647394 217961 SRX26022469 SRS22594188 SRA1966071 UMass Chan Medical School UMass Chan Medical School                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-09-09 Hatching Embryo Multi-tissue Multi-system
33704 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.       ebf3a hom 2 dpf rep 2 GSM8504320   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   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP531514     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     4099529019 3162437766 3348146726 3976118566 189123 SRX26022468 SRS22594186 SRA1966071 UMass Chan Medical School UMass Chan Medical School                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-09-09 Hatching Embryo Multi-tissue Multi-system
33705 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.       ebf3a hom 2 dpf rep 1 GSM8504319   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   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   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP531514     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     3937137116 3134793115 3336004625 3827286589 183555 SRX26022467 SRS22594187 SRA1966071 UMass Chan Medical School UMass Chan Medical School                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-09-09 Hatching Embryo Multi-tissue Multi-system
65772 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.   pubmed:35996200   Zebrafish Metabolite treated ZM Rep3 GSM5535705   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   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina   strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Metabolite treated GSM5535705 GSM5535705: Zebrafish Metabolite treated ZM Rep3; Danio rerio; RNA Seq GSM5535705   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina GEO Accession:GSM5535705 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP334037   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     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   Canada 2021-08-25 Hatching Embryo Multi-tissue Multi-system
65773 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.   pubmed:35996200   Zebrafish Metabolite treated ZM Rep2 GSM5535704   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   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina   strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Metabolite treated GSM5535704 GSM5535704: Zebrafish Metabolite treated ZM Rep2; Danio rerio; RNA Seq GSM5535704   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina GEO Accession:GSM5535704 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP334037   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     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   Canada 2021-08-25 Hatching Embryo Multi-tissue Multi-system
65774 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.   pubmed:35996200   Zebrafish Metabolite treated ZM Rep1 GSM5535703   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   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina   strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Metabolite treated GSM5535703 GSM5535703: Zebrafish Metabolite treated ZM Rep1; Danio rerio; RNA Seq GSM5535703   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina GEO Accession:GSM5535703 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP334037   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     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   Canada 2021-08-25 Hatching Embryo Multi-tissue Multi-system
65775 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.   pubmed:35996200   Zebrafish Metabolite treated ZM Rep1 GSM5535703   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   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina   strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Metabolite treated GSM5535703 GSM5535703: Zebrafish Metabolite treated ZM Rep1; Danio rerio; RNA Seq GSM5535703   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina GEO Accession:GSM5535703 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP334037   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     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   Canada 2021-08-25 Hatching Embryo Multi-tissue Multi-system
65776 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.   pubmed:35996200   Germ free GF Rep3 GSM5535702   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   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina   strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Germ free GSM5535702 GSM5535702: Germ free GF Rep3; Danio rerio; RNA Seq GSM5535702   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina GEO Accession:GSM5535702 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP334037   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     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   Canada 2021-08-25 Hatching Embryo Multi-tissue Multi-system
65777 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.   pubmed:35996200   Germ free GF Rep2 GSM5535701   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   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina   strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Germ free GSM5535701 GSM5535701: Germ free GF Rep2; Danio rerio; RNA Seq GSM5535701   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina GEO Accession:GSM5535701 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP334037   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     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   Canada 2021-08-25 Hatching Embryo Multi-tissue Multi-system
65778 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.   pubmed:35996200   Germ free GF Rep1 GSM5535700   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   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina   strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Germ free GSM5535700 GSM5535700: Germ free GF Rep1; Danio rerio; RNA Seq GSM5535700   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina GEO Accession:GSM5535700 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP334037   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     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   Canada 2021-08-25 Hatching Embryo Multi-tissue Multi-system
65779 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.   pubmed:35996200   Conventionally raised CV Rep3 GSM5535699   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   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina   strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Conventionally raised GSM5535699 GSM5535699: Conventionally raised CV Rep3; Danio rerio; RNA Seq GSM5535699   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina GEO Accession:GSM5535699 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP334037   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     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   Canada 2021-08-25 Hatching Embryo Multi-tissue Multi-system
65780 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.   pubmed:35996200   Conventionally raised CV Rep2 GSM5535698   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   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina   strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Conventionally raised GSM5535698 GSM5535698: Conventionally raised CV Rep2; Danio rerio; RNA Seq GSM5535698   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina GEO Accession:GSM5535698 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP334037   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     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   Canada 2021-08-25 Hatching Embryo Multi-tissue Multi-system
65781 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.   pubmed:35996200   Conventionally raised CV Rep1 GSM5535697   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   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina   strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Conventionally raised GSM5535697 GSM5535697: Conventionally raised CV Rep1; Danio rerio; RNA Seq GSM5535697   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™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina GEO Accession:GSM5535697 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP334037   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     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   Canada 2021-08-25 Hatching Embryo Multi-tissue Multi-system
67934 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 repl…   pubmed:35286299   WT 3 GSM5782115   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       449912416 359801594 370071032 449082499 2219499 SRX13669342 SRS11554978 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.92746   0.13827   0.7205   0.49824   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67935 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 repl…   pubmed:35286299   WT 2 GSM5782114   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       380778577 335429272 346541394 382018742 2377299 SRX13669341 SRS11554977 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.92802   0.17848   0.75532   0.56527   74   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67936 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 repl…   pubmed:35286299   WT 1 GSM5782113   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       416561303 385113762 399863594 416577633 3233915 SRX13669340 SRS11554976 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.92305   0.23257   0.74014   0.56091   75   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67937 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 repl…   pubmed:35286299   neurod1delECD 3 GSM5782112   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       355745142 312936101 324744763 363430805 238599 SRX13669339 SRS11554974 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.92128   0.15319   0.73288   0.53288   75   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67938 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 repl…   pubmed:35286299   neurod1delECD 2 GSM5782111   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       604913044 434539299 447331142 610824543 4884218 SRX13669338 SRS11554975 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.91879   0.10797   0.76104   0.52877   62   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67939 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 repl…   pubmed:35286299   neurod1delECD 1 GSM5782110   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       538264168 438242103 449243134 538752938 3214175 SRX13669337 SRS11554973 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.93118   0.14524   0.7321   0.51618   74   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67940 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 repl…   pubmed:35286299   neurod1delUCE 3 GSM5782109   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       380743947 340934018 355401415 389502066 573194 SRX13669336 SRS11554972 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.91516   0.18328   0.75879   0.55356   75   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67941 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 repl…   pubmed:35286299   neurod1delUCE 2 GSM5782108   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       493321451 338009359 347924089 502447949 1110463 SRX13669335 SRS11554970 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.91603   0.1614   0.74438   0.46704   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67942 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 repl…   pubmed:35286299   neurod1delUCE 1 GSM5782107   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       397487731 403037604 415852572 395568466 2467664 SRX13669334 SRS11554971 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.94144   0.28263   0.75797   0.60121   75   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67943 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 repl…   pubmed:35286299   neurod1 4 GSM5782106   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       454322873 364604693 375789404 452598898 1169076 SRX13669333 SRS11554969 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.92394   0.14895   0.72679   0.50393   75   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67944 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 repl…   pubmed:35286299   neurod1 3 GSM5782105   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       492551901 368591027 378769440 497000610 3288698 SRX13669332 SRS11554968 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.92326   0.15045   0.73111   0.48416   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67945 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 repl…   pubmed:35286299   neurod1 2 GSM5782104   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       381296757 357576777 368515394 381354668 1848779 SRX13669331 SRS11554967 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.93947   0.22412   0.74627   0.53279   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67946 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 repl…   pubmed:35286299   neurod1 1 GSM5782103   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       465639733 424003340 441888689 466407058 5948558 SRX13669330 SRS11554966 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.86723   0.21618   0.75933   0.51887   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67947 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 repl…   pubmed:35286299   ascl1a 3 GSM5782102   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       292566345 247808465 257160518 298807697 330413 SRX13669329 SRS11554965 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.92008   0.13327   0.73476   0.51693   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67948 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 repl…   pubmed:35286299   ascl1a 2 GSM5782101   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       501002333 391986992 404213246 504382983 3290952 SRX13669328 SRS11554964 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.92048   0.13789   0.74036   0.52176   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
67949 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 repl…   pubmed:35286299   ascl1a 1 GSM5782100   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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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 neurod1ΔUCE/ΔUCE 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 µl of reaction buffer lysed by freezing in liquid nitrogen and stored at 80°C 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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP354077   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       370236340 362874334 379824149 370719450 3260743 SRX13669327 SRS11554963 SRA1353950 GIGA, University of Liège GIGA, University of Liège 1 0.90209   0.24217   0.78179   0.59143   76   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   Belgium 2022-01-08 Hatching Embryo Multi-tissue Multi-system
72204 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   pubmed:37024546   Foxc1b 48hpf GSM6734157   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   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°C. 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 3’ v2 protocol 10x Genomics.   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°C. 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP408138   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   5123945131 3326458224 3713701708 4435572452 573335 SRX18279945 SRS15772341 SRA1541630 Famulski, Biology, University of Kentucky Famulski, Biology, University of Kentucky 1 0.9134   0.07314   0.81379   0.49083   150   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-11-15 Hatching Embryo Multi-tissue Multi-system
72205 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   pubmed:37024546   Foxc1b 48hpf GSM6734157   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   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°C. 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 3’ v2 protocol 10x Genomics.   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°C. 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP408138   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   2795275569 2297425042 2482925319 2376906238 198982 SRX18279945 SRS15772341 SRA1541630 Famulski, Biology, University of Kentucky Famulski, Biology, University of Kentucky 1 0.95768   0.08708   0.81903   0.51103   150   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-11-15 Hatching Embryo Multi-tissue Multi-system
72206 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   pubmed:37024546   Foxc1b 48hpf GSM6734157   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   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°C. 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 3’ v2 protocol 10x Genomics.   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°C. 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP408138   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   2783844388 2288795302 2473127346 2367511149 238615 SRX18279945 SRS15772341 SRA1541630 Famulski, Biology, University of Kentucky Famulski, Biology, University of Kentucky 1 0.95903   0.08687   0.82085   0.53794   150   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2022-11-15 Hatching Embryo Multi-tissue Multi-system

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