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351 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Head"

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devstage_curation 8

technology 6

devstage_curation_coarse 5

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Head · 351 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 351 ✖

experiment.library_selection 1

  • cDNA · 351 ✖
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
32037 32037 SRR28992909 SRX24520261 SRS21267950 SRP506997 PRJNA1110229 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1110229 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Kcnd2 Wt1   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Wt1|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Kcnd2 Wt1 Kcnd2 Wt1 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP506997     Kcnd2_Wt1.fq.gz fastq 3386455050.0 22576367.0 Kcnd2 Wt1.fq.gz 0:150 A:967137430;C:730108913;G:738646978;T:950549427;N:12302 150       967137430 730108913 738646978 950549427 12302 SRX24520261 SRS21267950 SRA1863814 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-10 Larval Larval Head Nervous System
32038 32038 SRR28992910 SRX24520260 SRS21267949 SRP506997 PRJNA1110229 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1110229 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Hom3   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Hom3|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Hom3 Arfgef1 Hom3 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP506997     Arfgef1_Hom3.fq.gz fastq 3647365500.0 24315770.0 Arfgef1 Hom3.fq.gz 0:150 A:923919033;C:903440333;G:911845870;T:908147370;N:12894 150       923919033 903440333 911845870 908147370 12894 SRX24520260 SRS21267949 SRA1863814 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-10 Larval Larval Head Nervous System
32039 32039 SRR28992915 SRX24520258 SRS21267947 SRP506997 PRJNA1110229 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1110229 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Hom1   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Hom1|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Hom1 Arfgef1 Hom1 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP506997     Arfgef1_Hom1.fq.gz fastq 3388869300.0 22592462.0 Arfgef1 Hom1.fq.gz 0:150 A:869162615;C:827706442;G:835453288;T:856534517;N:12438 150       869162615 827706442 835453288 856534517 12438 SRX24520258 SRS21267947 SRA1863814 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-10 Larval Larval Head Nervous System
32040 32040 SRR28992912 SRX24520257 SRS21267946 SRP506997 PRJNA1110229 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1110229 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Het3   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Het3|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Het3 Arfgef1 Het3 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP506997     Arfgef1_Het3.fq.gz fastq 3369996750.0 22466645.0 Arfgef1 Het3.fq.gz 0:150 A:861941573;C:824864964;G:833793356;T:849388791;N:8066 150       861941573 824864964 833793356 849388791 8066 SRX24520257 SRS21267946 SRA1863814 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-10 Larval Larval Head Nervous System
32041 32041 SRR28992913 SRX24520256 SRS21267945 SRP506997 PRJNA1110229 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1110229 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Het2   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Het2|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Het2 Arfgef1 Het2 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP506997     Arfgef1_Het2.fq.gz fastq 4755406500.0 31702710.0 Arfgef1 Het2.fq.gz 0:150 A:1254995507;C:1127923454;G:1138127034;T:1234180808;N:179697 150       1254995507 1127923454 1138127034 1234180808 179697 SRX24520256 SRS21267945 SRA1863814 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-10 Larval Larval Head Nervous System
32042 32042 SRR28992916 SRX24520254 SRS21267943 SRP506997 PRJNA1110229 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1110229 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Wnt8b Hom3   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Hom3|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Wnt8b Hom3 Wnt8b Hom3 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP506997     Wnt8b_Hom3.fq.gz fastq 5283928950.0 35226193.0 Wnt8b Hom3.fq.gz 0:150 A:1389228037;C:1262004726;G:1265392219;T:1367105548;N:198420 150       1389228037 1262004726 1265392219 1367105548 198420 SRX24520254 SRS21267943 SRA1863814 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-10 Larval Larval Head Nervous System
32043 32043 SRR28992919 SRX24520251 SRS21267940 SRP506997 PRJNA1110229 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1110229 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Wnt8b Het3   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Het3|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Wnt8b Het3 Wnt8b Het3 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP506997     Wnt8b_Het3.fq.gz fastq 4357330950.0 29048873.0 Wnt8b Het3.fq.gz 0:150 A:1179652667;C:1002955689;G:1008147493;T:1166494534;N:80567 150       1179652667 1002955689 1008147493 1166494534 80567 SRX24520251 SRS21267940 SRA1863814 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-10 Larval Larval Head Nervous System
32068 32068 SRR29007557 SRX24534635 SRS21280318 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Kcnd2 Wt 1   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Wt1|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Kcnd2 Wt 1 Kcnd2 Wt 1 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Kcnd2_Wt_1_1.fq.gz Kcnd2_Wt_1_2.fq.gz fastq fastq 6772910100.0 22576367.0 Kcnd2 Wt 1 1.fq.gz 0:150 1:150 A:1933789152;C:1464135438;G:1474439143;T:1900463092;N:83275 150 150     1933789152 1464135438 1474439143 1900463092 83275 SRX24534635 SRS21280318 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32069 32069 SRR29007558 SRX24534634 SRS21280317 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Hom 3   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Hom3|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Hom 3 Arfgef1 Hom 3 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Arfgef1_Hom_3_1.fq.gz Arfgef1_Hom_3_2.fq.gz fastq fastq 7294731000.0 24315770.0 Arfgef1 Hom 3 1.fq.gz 0:150 1:150 A:1847018467;C:1809604703;G:1818278888;T:1819707786;N:121156 150 150     1847018467 1809604703 1818278888 1819707786 121156 SRX24534634 SRS21280317 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32070 32070 SRR29007559 SRX24534633 SRS21280316 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Hom 2   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Hom2|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Hom 2 Arfgef1 Hom 2 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Arfgef1_Hom_2_1.fq.gz Arfgef1_Hom_2_2.fq.gz fastq fastq 6607825200.0 22026084.0 Arfgef1 Hom 2 1.fq.gz 0:150 1:150 A:1694417387;C:1616938849;G:1625276704;T:1671046414;N:145846 150 150     1694417387 1616938849 1625276704 1671046414 145846 SRX24534633 SRS21280316 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32071 32071 SRR29007560 SRX24534632 SRS21280315 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Hom 1   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Hom1|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Hom 1 Arfgef1 Hom 1 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Arfgef1_Hom_1_1.fq.gz Arfgef1_Hom_1_2.fq.gz fastq fastq 6777738600.0 22592462.0 Arfgef1 Hom 1 1.fq.gz 0:150 1:150 A:1739306802;C:1658195023;G:1665806667;T:1714318423;N:111685 150 150     1739306802 1658195023 1665806667 1714318423 111685 SRX24534632 SRS21280315 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32072 32072 SRR29007561 SRX24534631 SRS21280314 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Het 3   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Het3|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Het 3 Arfgef1 Het 3 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Arfgef1_Het_3_1.fq.gz Arfgef1_Het_3_2.fq.gz fastq fastq 6739993500.0 22466645.0 Arfgef1 Het 3 1.fq.gz 0:150 1:150 A:1725253563;C:1652471358;G:1662793828;T:1699392429;N:82322 150 150     1725253563 1652471358 1662793828 1699392429 82322 SRX24534631 SRS21280314 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32073 32073 SRR29007562 SRX24534630 SRS21280313 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Het 2   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Het2|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Het 2 Arfgef1 Het 2 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Arfgef1_Het_2_1.fq.gz Arfgef1_Het_2_2.fq.gz fastq fastq 9510813000.0 31702710.0 Arfgef1 Het 2 1.fq.gz 0:150 1:150 A:2509621883;C:2259671963;G:2271899998;T:2469380560;N:238596 150 150     2509621883 2259671963 2271899998 2469380560 238596 SRX24534630 SRS21280313 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32074 32074 SRR29007563 SRX24534629 SRS21280312 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Het 1   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Het1|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Het 1 Arfgef1 Het 1 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Arfgef1_Het_1_1.fq.gz Arfgef1_Het_1_2.fq.gz fastq fastq 6887369100.0 22957897.0 Arfgef1 Het 1 1.fq.gz 0:150 1:150 A:1766549896;C:1685533018;G:1694949682;T:1740214059;N:122445 150 150     1766549896 1685533018 1694949682 1740214059 122445 SRX24534629 SRS21280312 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32075 32075 SRR29007564 SRX24534628 SRS21280311 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Wnt8b Hom 3   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Hom3|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Wnt8b Hom 3 Wnt8b Hom 3 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Wnt8b_Hom_3_1.fq.gz Wnt8b_Hom_3_2.fq.gz fastq fastq 10567857900.0 35226193.0 Wnt8b Hom 3 1.fq.gz 0:150 1:150 A:2775044850;C:2525957688;G:2527072827;T:2739479844;N:302691 150 150     2775044850 2525957688 2527072827 2739479844 302691 SRX24534628 SRS21280311 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32076 32076 SRR29007565 SRX24534627 SRS21280310 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Wnt8b Hom 2   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Hom2|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Wnt8b Hom 2 Wnt8b Hom 2 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Wnt8b_Hom_2_1.fq.gz Wnt8b_Hom_2_2.fq.gz fastq fastq 7666806600.0 25556022.0 Wnt8b Hom 2 1.fq.gz 0:150 1:150 A:2029345938;C:1820579149;G:1819606043;T:1996786660;N:488810 150 150     2029345938 1820579149 1819606043 1996786660 488810 SRX24534627 SRS21280310 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32077 32077 SRR29007566 SRX24534626 SRS21280309 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Wnt8b Hom 1   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Hom1|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Wnt8b Hom 1 Wnt8b Hom 1 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Wnt8b_Hom_1_1.fq.gz Wnt8b_Hom_1_2.fq.gz fastq fastq 6514544400.0 21715148.0 Wnt8b Hom 1 1.fq.gz 0:150 1:150 A:1711943699;C:1556010812;G:1555687818;T:1690731439;N:170632 150 150     1711943699 1556010812 1555687818 1690731439 170632 SRX24534626 SRS21280309 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32078 32078 SRR29007567 SRX24534625 SRS21280308 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Wnt8b Het 3   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Het3|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Wnt8b Het 3 Wnt8b Het 3 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Wnt8b_Het_3_1.fq.gz Wnt8b_Het_3_2.fq.gz fastq fastq 8714661900.0 29048873.0 Wnt8b Het 3 1.fq.gz 0:150 1:150 A:2360994905;C:2008091028;G:2013456743;T:2332006781;N:112443 150 150     2360994905 2008091028 2013456743 2332006781 112443 SRX24534625 SRS21280308 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32079 32079 SRR29007568 SRX24534624 SRS21280307 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Wnt8b Het 2   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Het2|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Wnt8b Het 2 Wnt8b Het 2 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Wnt8b_Het_2_1.fq.gz Wnt8b_Het_2_2.fq.gz fastq fastq 8370112800.0 27900376.0 Wnt8b Het 2 1.fq.gz 0:150 1:150 A:2275496039;C:1920819728;G:1927597917;T:2246091711;N:107405 150 150     2275496039 1920819728 1927597917 2246091711 107405 SRX24534624 SRS21280307 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32080 32080 SRR29007569 SRX24534623 SRS21280306 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Wnt8b Het 1   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Het1|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Wnt8b Het 1 Wnt8b Het 1 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Wnt8b_Het_1_1.fq.gz Wnt8b_Het_1_2.fq.gz fastq fastq 7614189000.0 25380630.0 Wnt8b Het 1 1.fq.gz 0:150 1:150 A:2059784093;C:1755740426;G:1761242316;T:2037325656;N:96509 150 150     2059784093 1755740426 1761242316 2037325656 96509 SRX24534623 SRS21280306 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32081 32081 SRR29007570 SRX24534622 SRS21280305 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Wnt8b Wt 3   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Wt3|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Wnt8b Wt 3 Wnt8b Wt 3 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Wnt8b_Wt_3_1.fq.gz Wnt8b_Wt_3_2.fq.gz fastq fastq 6809737500.0 22699125.0 Wnt8b Wt 3 1.fq.gz 0:150 1:150 A:1869159615;C:1548130956;G:1547169482;T:1845192460;N:84987 150 150     1869159615 1548130956 1547169482 1845192460 84987 SRX24534622 SRS21280305 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32082 32082 SRR29007571 SRX24534621 SRS21280304 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Wt 3   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Wt3|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Wt 3 Arfgef1 Wt 3 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Arfgef1_Wt_3_1.fq.gz Arfgef1_Wt_3_2.fq.gz fastq fastq 6162364200.0 20541214.0 Arfgef1 Wt 3 1.fq.gz 0:150 1:150 A:1606427072;C:1484826935;G:1488745137;T:1582299135;N:65921 150 150     1606427072 1484826935 1488745137 1582299135 65921 SRX24534621 SRS21280304 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32083 32083 SRR29007572 SRX24534620 SRS21280303 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Wnt8b Wt 2   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Wt2|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Wnt8b Wt 2 Wnt8b Wt 2 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Wnt8b_Wt_2_1.fq.gz Wnt8b_Wt_2_2.fq.gz fastq fastq 6743670600.0 22478902.0 Wnt8b Wt 2 1.fq.gz 0:150 1:150 A:1852520280;C:1531023930;G:1536795067;T:1823243896;N:87427 150 150     1852520280 1531023930 1536795067 1823243896 87427 SRX24534620 SRS21280303 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32084 32084 SRR29007573 SRX24534619 SRS21280302 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Wnt8b Wt 1   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Wt1|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Wnt8b Wt 1 Wnt8b Wt 1 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Wnt8b_Wt_1_1.fq.gz Wnt8b_Wt_1_2.fq.gz fastq fastq 6534620400.0 21782068.0 Wnt8b Wt 1 1.fq.gz 0:150 1:150 A:1783250074;C:1493088330;G:1497228073;T:1760957638;N:96285 150 150     1783250074 1493088330 1497228073 1760957638 96285 SRX24534619 SRS21280302 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32085 32085 SRR29007574 SRX24534618 SRS21280301 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Kcnd2 Hom 4   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Hom4|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Kcnd2 Hom 4 Kcnd2 Hom 4 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Kcnd2_Hom_4_1.fq.gz Kcnd2_Hom_4_2.fq.gz fastq fastq 7596974100.0 25323247.0 Kcnd2 Hom 4 1.fq.gz 0:150 1:150 A:2007694949;C:1807188755;G:1800403701;T:1981369650;N:317045 150 150     2007694949 1807188755 1800403701 1981369650 317045 SRX24534618 SRS21280301 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32086 32086 SRR29007575 SRX24534617 SRS21280300 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Kcnd2 Hom 2   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Hom2|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Kcnd2 Hom 2 Kcnd2 Hom 2 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Kcnd2_Hom_2_1.fq.gz Kcnd2_Hom_2_2.fq.gz fastq fastq 7289261100.0 24297537.0 Kcnd2 Hom 2 1.fq.gz 0:150 1:150 A:2078143741;C:1581832453;G:1587225393;T:2041970189;N:89324 150 150     2078143741 1581832453 1587225393 2041970189 89324 SRX24534617 SRS21280300 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32087 32087 SRR29007576 SRX24534616 SRS21280299 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Kcnd2 Hom 1   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Hom1|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Kcnd2 Hom 1 Kcnd2 Hom 1 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Kcnd2_Hom_1_1.fq.gz Kcnd2_Hom_1_2.fq.gz fastq fastq 8331212400.0 27770708.0 Kcnd2 Hom 1 1.fq.gz 0:150 1:150 A:2185320924;C:1987553985;G:1999101969;T:2159195984;N:39538 150 150     2185320924 1987553985 1999101969 2159195984 39538 SRX24534616 SRS21280299 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32088 32088 SRR29007577 SRX24534615 SRS21280298 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Kcnd2 Het 4   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Het4|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Kcnd2 Het 4 Kcnd2 Het 4 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Kcnd2_Het_4_1.fq.gz Kcnd2_Het_4_2.fq.gz fastq fastq 10195958700.0 33986529.0 Kcnd2 Het 4 1.fq.gz 0:150 1:150 A:2675050868;C:2442920285;G:2439165482;T:2638402351;N:419714 150 150     2675050868 2442920285 2439165482 2638402351 419714 SRX24534615 SRS21280298 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32089 32089 SRR29007578 SRX24534614 SRS21280297 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Kcnd2 Het 2   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Het2|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Kcnd2 Het 2 Kcnd2 Het 2 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Kcnd2_Het_2_1.fq.gz Kcnd2_Het_2_2.fq.gz fastq fastq 7549108800.0 25163696.0 Kcnd2 Het 2 1.fq.gz 0:150 1:150 A:1994641167;C:1795831385;G:1796069017;T:1962477823;N:89408 150 150     1994641167 1795831385 1796069017 1962477823 89408 SRX24534614 SRS21280297 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32090 32090 SRR29007579 SRX24534613 SRS21280296 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Kcnd2 Het 1   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Het1|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Kcnd2 Het 1 Kcnd2 Het 1 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Kcnd2_Het_1_1.fq.gz Kcnd2_Het_1_2.fq.gz fastq fastq 7081857600.0 23606192.0 Kcnd2 Het 1 1.fq.gz 0:150 1:150 A:1860484446;C:1694088253;G:1695161253;T:1832038793;N:84855 150 150     1860484446 1694088253 1695161253 1832038793 84855 SRX24534613 SRS21280296 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32091 32091 SRR29007580 SRX24534612 SRS21280295 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Kcnd2 Wt 4   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Wt4|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Kcnd2 Wt 4 Kcnd2 Wt 4 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Kcnd2_Wt_4_1.fq.gz Kcnd2_Wt_4_2.fq.gz fastq fastq 8142446700.0 27141489.0 Kcnd2 Wt 4 1.fq.gz 0:150 1:150 A:2136890254;C:1951822302;G:1947544318;T:2105854363;N:335463 150 150     2136890254 1951822302 1947544318 2105854363 335463 SRX24534612 SRS21280295 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32092 32092 SRR29007581 SRX24534611 SRS21280294 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Kcnd2 Wt 2   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Wt2|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Kcnd2 Wt 2 Kcnd2 Wt 2 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Kcnd2_Wt_2_1.fq.gz Kcnd2_Wt_2_2.fq.gz fastq fastq 6688680600.0 22295602.0 Kcnd2 Wt 2 1.fq.gz 0:150 1:150 A:1902466623;C:1451301657;G:1460696794;T:1874184765;N:30761 150 150     1902466623 1451301657 1460696794 1874184765 30761 SRX24534611 SRS21280294 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32093 32093 SRR29007582 SRX24534610 SRS21280293 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Wt 2   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Wt2|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Wt 2 Arfgef1 Wt 2 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Arfgef1_Wt_2_1.fq.gz Arfgef1_Wt_2_2.fq.gz fastq fastq 7399981500.0 24666605.0 Arfgef1 Wt 2 1.fq.gz 0:150 1:150 A:1904125951;C:1807905407;G:1812898141;T:1874904149;N:147852 150 150     1904125951 1807905407 1812898141 1874904149 147852 SRX24534610 SRS21280293 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32094 32094 SRR29007583 SRX24534609 SRS21280292 SRP507312 PRJNA1111077 Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability PRJNA1111077 Other Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 48 were developed into stable loss of function zebrafish models. Of those 48 evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further RNA Seq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.         Arfgef1 Wt 1   strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Wt1|BioSampleModel:Model organism or animal                 RNA Seq of Danio Rerio: pools of isolated larval head Arfgef1 Wt 1 Arfgef1 Wt 1 Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     Arfgef1_Wt_1_1.fq.gz Arfgef1_Wt_1_2.fq.gz fastq fastq 7542057300.0 25140191.0 Arfgef1 Wt 1 1.fq.gz 0:150 1:150 A:1927852618;C:1855757148;G:1860100302;T:1898222485;N:124747 150 150     1927852618 1855757148 1860100302 1898222485 124747 SRX24534609 SRS21280292 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32098 32098 SRR29008446 SRX24535482 SRS21281082 SRP507332 PRJNA1111082 Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA] GSE267333 Transcriptome Analysis Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation and notochord sheath cells which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research the genetic regulation of bone formation as well as mechanisms of transcriptional control of entpd5a remain largely unknown. Here using a newly generated transgenic line we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually to establish open chromatin regions and gene expression profiles respectively. We then integrated the data to enable us to produce a list of candidate transcription fa…       Chondrocyte head biolRep3 GSM8264152   source name:head|tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing Chondrocyte head biolRep3 QC of sequences adapter trimming and duplicate removal using fastp package with dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column head   RNA was isolated using the RNeasy Plus Micro Kit QIAGEN 74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample 15M reads were sequenced.   tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf GSM8264152 GSM8264152: Chondrocyte head biolRep3; Danio rerio; RNA Seq GSM8264152 r1 GSM8264152 1 RNA was isolated using the RNeasy Plus Micro Kit QIAGEN 74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample 15M reads were sequenced.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507332   loader:fastq load.py cartilRep3_R1.fastq.gz cartilRep3_R2.fastq.gz fastq fastq 6819648393.0 25781563.0 GSM8264152 r1 0:132.28 1:132.24 A:1843991471;C:1548648708;G:1568393744;T:1858508350;N:106120 132 132     1843991471 1548648708 1568393744 1858508350 106120 SRX24535482 SRS21281082 SRA1865629 Institute for Cardiovascular Organogenesis and Regeneration Institute for Cardiovascular Organogenesis and Regeneration                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2024-05-13 Larval Larval Head Nervous System
32099 32099 SRR29008447 SRX24535481 SRS21281081 SRP507332 PRJNA1111082 Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA] GSE267333 Transcriptome Analysis Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation and notochord sheath cells which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research the genetic regulation of bone formation as well as mechanisms of transcriptional control of entpd5a remain largely unknown. Here using a newly generated transgenic line we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually to establish open chromatin regions and gene expression profiles respectively. We then integrated the data to enable us to produce a list of candidate transcription fa…       Chondrocyte head biolRep2 GSM8264151   source name:head|tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing Chondrocyte head biolRep2 QC of sequences adapter trimming and duplicate removal using fastp package with dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column head   RNA was isolated using the RNeasy Plus Micro Kit QIAGEN 74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample 15M reads were sequenced.   tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf GSM8264151 GSM8264151: Chondrocyte head biolRep2; Danio rerio; RNA Seq GSM8264151 r1 GSM8264151 1 RNA was isolated using the RNeasy Plus Micro Kit QIAGEN 74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample 15M reads were sequenced.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507332   loader:fastq load.py cartilRep2_R1.fastq.gz cartilRep2_R2.fastq.gz fastq fastq 6328377834.0 23616303.0 GSM8264151 r1 0:134.02 1:133.95 A:1697207927;C:1464700434;G:1476121489;T:1690068467;N:279517 134 133     1697207927 1464700434 1476121489 1690068467 279517 SRX24535481 SRS21281081 SRA1865629 Institute for Cardiovascular Organogenesis and Regeneration Institute for Cardiovascular Organogenesis and Regeneration                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2024-05-13 Larval Larval Head Nervous System
32100 32100 SRR29008448 SRX24535480 SRS21281080 SRP507332 PRJNA1111082 Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA] GSE267333 Transcriptome Analysis Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation and notochord sheath cells which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research the genetic regulation of bone formation as well as mechanisms of transcriptional control of entpd5a remain largely unknown. Here using a newly generated transgenic line we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually to establish open chromatin regions and gene expression profiles respectively. We then integrated the data to enable us to produce a list of candidate transcription fa…       Chondrocyte head biolRep1 GSM8264150   source name:head|tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing Chondrocyte head biolRep1 QC of sequences adapter trimming and duplicate removal using fastp package with dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column head   RNA was isolated using the RNeasy Plus Micro Kit QIAGEN 74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample 15M reads were sequenced.   tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf GSM8264150 GSM8264150: Chondrocyte head biolRep1; Danio rerio; RNA Seq GSM8264150 r1 GSM8264150 1 RNA was isolated using the RNeasy Plus Micro Kit QIAGEN 74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample 15M reads were sequenced.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507332   loader:fastq load.py cartilRep1_R1.fastq.gz cartilRep1_R2.fastq.gz fastq fastq 3594349367.0 13391209.0 GSM8264150 r1 0:134.24 1:134.17 A:956150712;C:837180050;G:846748291;T:954113728;N:156586 134 134     956150712 837180050 846748291 954113728 156586 SRX24535480 SRS21281080 SRA1865629 Institute for Cardiovascular Organogenesis and Regeneration Institute for Cardiovascular Organogenesis and Regeneration                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2024-05-13 Larval Larval Head Nervous System
32104 32104 SRR29008452 SRX24535476 SRS21281076 SRP507332 PRJNA1111082 Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA] GSE267333 Transcriptome Analysis Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation and notochord sheath cells which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research the genetic regulation of bone formation as well as mechanisms of transcriptional control of entpd5a remain largely unknown. Here using a newly generated transgenic line we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually to establish open chromatin regions and gene expression profiles respectively. We then integrated the data to enable us to produce a list of candidate transcription fa…       Osteoblast head biolRep3 GSM8264146   source name:head|tissue:head|cell type:osteoblast classical|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing Osteoblast head biolRep3 QC of sequences adapter trimming and duplicate removal using fastp package with dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column head   RNA was isolated using the RNeasy Plus Micro Kit QIAGEN 74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample 15M reads were sequenced.   tissue:head|cell type:osteoblast classical|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf GSM8264146 GSM8264146: Osteoblast head biolRep3; Danio rerio; RNA Seq GSM8264146 r1 GSM8264146 1 RNA was isolated using the RNeasy Plus Micro Kit QIAGEN 74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample 15M reads were sequenced.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507332   loader:fastq load.py osteobRep3_R1.fastq.gz osteobRep3_R2.fastq.gz fastq fastq 4016101824.0 15220140.0 GSM8264146 r1 0:131.95 1:131.92 A:1091466642;C:915105554;G:923772050;T:1085593417;N:164161 131 131     1091466642 915105554 923772050 1085593417 164161 SRX24535476 SRS21281076 SRA1865629 Institute for Cardiovascular Organogenesis and Regeneration Institute for Cardiovascular Organogenesis and Regeneration                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2024-05-13 Larval Larval Head Nervous System
32105 32105 SRR29008453 SRX24535475 SRS21281075 SRP507332 PRJNA1111082 Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA] GSE267333 Transcriptome Analysis Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation and notochord sheath cells which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research the genetic regulation of bone formation as well as mechanisms of transcriptional control of entpd5a remain largely unknown. Here using a newly generated transgenic line we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually to establish open chromatin regions and gene expression profiles respectively. We then integrated the data to enable us to produce a list of candidate transcription fa…       Osteoblast head biolRep2 GSM8264145   source name:head|tissue:head|cell type:osteoblast classical|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing Osteoblast head biolRep2 QC of sequences adapter trimming and duplicate removal using fastp package with dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column head   RNA was isolated using the RNeasy Plus Micro Kit QIAGEN 74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample 15M reads were sequenced.   tissue:head|cell type:osteoblast classical|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf GSM8264145 GSM8264145: Osteoblast head biolRep2; Danio rerio; RNA Seq GSM8264145 r1 GSM8264145 1 RNA was isolated using the RNeasy Plus Micro Kit QIAGEN 74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample 15M reads were sequenced.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507332   loader:fastq load.py osteobRep2_R1.fastq.gz osteobRep2_R2.fastq.gz fastq fastq 3692172504.0 14317610.0 GSM8264145 r1 0:128.95 1:128.93 A:1007186967;C:837532125;G:846083342;T:1001209204;N:160866 128 128     1007186967 837532125 846083342 1001209204 160866 SRX24535475 SRS21281075 SRA1865629 Institute for Cardiovascular Organogenesis and Regeneration Institute for Cardiovascular Organogenesis and Regeneration                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2024-05-13 Larval Larval Head Nervous System
32106 32106 SRR29008454 SRX24535474 SRS21281074 SRP507332 PRJNA1111082 Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA] GSE267333 Transcriptome Analysis Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation and notochord sheath cells which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research the genetic regulation of bone formation as well as mechanisms of transcriptional control of entpd5a remain largely unknown. Here using a newly generated transgenic line we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually to establish open chromatin regions and gene expression profiles respectively. We then integrated the data to enable us to produce a list of candidate transcription fa…       Osteoblast head biolRep1 GSM8264144   source name:head|tissue:head|cell type:osteoblast classical|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing Osteoblast head biolRep1 QC of sequences adapter trimming and duplicate removal using fastp package with dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column head   RNA was isolated using the RNeasy Plus Micro Kit QIAGEN 74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample 15M reads were sequenced.   tissue:head|cell type:osteoblast classical|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf GSM8264144 GSM8264144: Osteoblast head biolRep1; Danio rerio; RNA Seq GSM8264144 r1 GSM8264144 1 RNA was isolated using the RNeasy Plus Micro Kit QIAGEN 74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample 15M reads were sequenced.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507332   loader:fastq load.py osteobRep1_R1.fastq.gz osteobRep1_R2.fastq.gz fastq fastq 8569394356.0 28375478.0 GSM8264144 r1 0:151 1:151 A:2308551585;C:1841082082;G:2161425693;T:2253505108;N:4829888 151 151     2308551585 1841082082 2161425693 2253505108 4829888 SRX24535474 SRS21281074 SRA1865629 Institute for Cardiovascular Organogenesis and Regeneration Institute for Cardiovascular Organogenesis and Regeneration                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2024-05-13 Larval Larval Head Nervous System
32806 32806 SRR29478752 SRX24989905 SRS21691708 SRP515053 PRJNA1126173 Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity GSE270309 Transcriptome Analysis The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to sever…   pubmed:39289367   head scarb2a mut rep 3 GSM8339369   source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing head scarb2a mut rep 3 done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset txt file contaning normalized UMI counts table for all samples. head   For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.   tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut GSM8339369 GSM8339369: head scarb2a mut rep 3; Danio rerio; RNA Seq GSM8339369 r1 GSM8339369 1 For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP515053     scarb2_mut3_R2.fastq.gz scarb2_mut3_R1.fastq.gz fastq fastq 590803877.0 7118119.0 GSM8339369 r1 0:75 1:8 A:171152826;C:118382558;G:138973475;T:162287717;N:7301 75 8     171152826 118382558 138973475 162287717 7301 SRX24989905 SRS21691708 SRA1904886 Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science 2 0.86187 0.0 0.06751 0.0 0.80081 1.0 0.47421   75 8 B T sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate marsseq   Israel 2024-06-20 Hatching Embryo Head Nervous System
32807 32807 SRR29478753 SRX24989904 SRS21691707 SRP515053 PRJNA1126173 Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity GSE270309 Transcriptome Analysis The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to sever…   pubmed:39289367   head scarb2a mut rep 2 GSM8339368   source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing head scarb2a mut rep 2 done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset txt file contaning normalized UMI counts table for all samples. head   For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.   tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut GSM8339368 GSM8339368: head scarb2a mut rep 2; Danio rerio; RNA Seq GSM8339368 r1 GSM8339368 1 For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP515053     scarb2_mut2_R2.fastq.gz scarb2_mut2_R1.fastq.gz fastq fastq 560228337.0 6749739.0 GSM8339368 r1 0:75 1:8 A:161395198;C:113034644;G:131199008;T:154592664;N:6823 75 8     161395198 113034644 131199008 154592664 6823 SRX24989904 SRS21691707 SRA1904886 Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science 2 0.85633 0.0 0.06116 0.0 0.80438 1.0 0.47226   75 8 B T sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate marsseq   Israel 2024-06-20 Hatching Embryo Head Nervous System
32808 32808 SRR29478754 SRX24989903 SRS21691706 SRP515053 PRJNA1126173 Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity GSE270309 Transcriptome Analysis The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to sever…   pubmed:39289367   head scarb2a mut rep 1 GSM8339367   source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing head scarb2a mut rep 1 done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset txt file contaning normalized UMI counts table for all samples. head   For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.   tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut GSM8339367 GSM8339367: head scarb2a mut rep 1; Danio rerio; RNA Seq GSM8339367 r1 GSM8339367 1 For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP515053     scarb2_mut1_R1.fastq.gz scarb2_mut1_R2.fastq.gz fastq fastq 536045042.0 6458374.0 GSM8339367 r1 0:75 1:8 A:152863781;C:109210501;G:126922310;T:147041910;N:6540 75 8     152863781 109210501 126922310 147041910 6540 SRX24989903 SRS21691706 SRA1904886 Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science 2 0.86464 0.0 0.06577 0.0 0.80359 1.0 0.48395   75 8 B T sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate marsseq   Israel 2024-06-20 Hatching Embryo Head Nervous System
32809 32809 SRR29478755 SRX24989902 SRS21691705 SRP515053 PRJNA1126173 Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity GSE270309 Transcriptome Analysis The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to sever…   pubmed:39289367   head wt rep 4 GSM8339366   source name:head|tissue:head|cell type:scarb2a+ cells|genotype:wt|geo loc name:missing|collection date:missing head wt rep 4 done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset txt file contaning normalized UMI counts table for all samples. head   For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.   tissue:head|cell type:scarb2a+ cells|genotype:wt GSM8339366 GSM8339366: head wt rep 4; Danio rerio; RNA Seq GSM8339366 r1 GSM8339366 1 For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP515053     scarb2_wt4_R1.fastq.gz scarb2_wt4_R2.fastq.gz fastq fastq 723943430.0 8722210.0 GSM8339366 r1 0:75 1:8 A:206155698;C:145344454;G:172171717;T:200262536;N:9025 75 8     206155698 145344454 172171717 200262536 9025 SRX24989902 SRS21691705 SRA1904886 Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science 2 0.86958 0.0 0.0737 0.0 0.79928 1.0 0.47906   75 8 B T sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate marsseq   Israel 2024-06-20 Hatching Embryo Head Nervous System
32810 32810 SRR29478756 SRX24989901 SRS21691704 SRP515053 PRJNA1126173 Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity GSE270309 Transcriptome Analysis The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to sever…   pubmed:39289367   head wt rep 3 GSM8339365   source name:head|tissue:head|cell type:scarb2a+ cells|genotype:wt|geo loc name:missing|collection date:missing head wt rep 3 done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset txt file contaning normalized UMI counts table for all samples. head   For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.   tissue:head|cell type:scarb2a+ cells|genotype:wt GSM8339365 GSM8339365: head wt rep 3; Danio rerio; RNA Seq GSM8339365 r1 GSM8339365 1 For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP515053     scarb2_wt3_R1.fastq.gz scarb2_wt3_R2.fastq.gz fastq fastq 560881132.0 6757604.0 GSM8339365 r1 0:75 1:8 A:158992539;C:112696361;G:133852695;T:155332822;N:6715 75 8     158992539 112696361 133852695 155332822 6715 SRX24989901 SRS21691704 SRA1904886 Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science 2 0.8706 0.0 0.07425 0.0 0.80038 1.0 0.47161   75 8 B T sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate marsseq   Israel 2024-06-20 Hatching Embryo Head Nervous System
32811 32811 SRR29478757 SRX24989900 SRS21691703 SRP515053 PRJNA1126173 Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity GSE270309 Transcriptome Analysis The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to sever…   pubmed:39289367   head wt rep 1 GSM8339364   source name:head|tissue:head|cell type:scarb2a+ cells|genotype:wt|geo loc name:missing|collection date:missing head wt rep 1 done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset txt file contaning normalized UMI counts table for all samples. head   For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.   tissue:head|cell type:scarb2a+ cells|genotype:wt GSM8339364 GSM8339364: head wt rep 1; Danio rerio; RNA Seq GSM8339364 r1 GSM8339364 1 For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP515053     scarb2_wt1_R1.fastq.gz scarb2_wt1_R2.fastq.gz fastq fastq 539653799.0 6501853.0 GSM8339364 r1 0:75 1:8 A:153571518;C:110489477;G:128477853;T:147108152;N:6799 75 8     153571518 110489477 128477853 147108152 6799 SRX24989900 SRS21691703 SRA1904886 Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science 2 0.87359 0.0 0.07353 0.0 0.80184 1.0 0.47111   75 8 B T sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate marsseq   Israel 2024-06-20 Hatching Embryo Head Nervous System
33619 33619 SRR30310487 SRX25770932 SRS22407035 SRP527479 PRJNA1150074 Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling GSE275235 Transcriptome Analysis SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …   pubmed:40208862   DM biol rep 3 GSM8473259   source name:heads|tissue:heads|genotype:5a / ;5b / |treatment:untreated|geo loc name:missing|collection date:missing DM biol rep 3 Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample heads untreated Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning. tissue:heads|genotype:5a / ;5b / |treatment:untreated GSM8473259 GSM8473259: DM biol rep 3; Danio rerio; RNA Seq GSM8473259 r1 GSM8473259 1 Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     Li47814-DM3_S6_R2_001.fastq.gz Li47814-DM3_S6_R1_001.fastq.gz fastq fastq 4759652497.0 39356384.0 GSM8473259 r1 0:60.49 1:60.44 A:1221224093;C:1133209753;G:1144876807;T:1252303477;N:8038367 60 60     1221224093 1133209753 1144876807 1252303477 8038367 SRX25770932 SRS22407035 SRA1951631 Kurrasch Lab, Department of Medical Genetics, University of Calgary Kurrasch Lab, Department of Medical Genetics, University of Calgary 2 0.94992 0.95405 0.07666 0.07486 0.64969 0.648 0.47911 0.48137 61 61 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Canada 2024-08-20 Adult Adult Head Nervous System
33620 33620 SRR30310488 SRX25770931 SRS22407034 SRP527479 PRJNA1150074 Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling GSE275235 Transcriptome Analysis SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …   pubmed:40208862   DM biol rep 2 GSM8473258   source name:heads|tissue:heads|genotype:5a / ;5b / |treatment:untreated|geo loc name:missing|collection date:missing DM biol rep 2 Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample heads untreated Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning. tissue:heads|genotype:5a / ;5b / |treatment:untreated GSM8473258 GSM8473258: DM biol rep 2; Danio rerio; RNA Seq GSM8473258 r1 GSM8473258 1 Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     Li47813-DM2_S5_R2_001.fastq.gz Li47813-DM2_S5_R1_001.fastq.gz fastq fastq 5030260806.0 41607672.0 GSM8473258 r1 0:60.47 1:60.43 A:1291665135;C:1198581962;G:1206075180;T:1323425262;N:10513267 60 60     1291665135 1198581962 1206075180 1323425262 10513267 SRX25770931 SRS22407034 SRA1951631 Kurrasch Lab, Department of Medical Genetics, University of Calgary Kurrasch Lab, Department of Medical Genetics, University of Calgary 2 0.94958 0.95221 0.08402 0.0824 0.64628 0.64553 0.47628 0.47968 61 60 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Canada 2024-08-20 Adult Adult Head Nervous System
33621 33621 SRR30310489 SRX25770930 SRS22407033 SRP527479 PRJNA1150074 Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling GSE275235 Transcriptome Analysis SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …   pubmed:40208862   DM biol rep 1 GSM8473257   source name:heads|tissue:heads|genotype:5a / ;5b / |treatment:untreated|geo loc name:missing|collection date:missing DM biol rep 1 Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample heads untreated Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning. tissue:heads|genotype:5a / ;5b / |treatment:untreated GSM8473257 GSM8473257: DM biol rep 1; Danio rerio; RNA Seq GSM8473257 r1 GSM8473257 1 Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     Li47812-DM1_S4_R2_001.fastq.gz Li47812-DM1_S4_R1_001.fastq.gz fastq fastq 5442095245.0 45006091.0 GSM8473257 r1 0:60.48 1:60.44 A:1406768036;C:1288396960;G:1297715980;T:1439122995;N:10091274 60 60     1406768036 1288396960 1297715980 1439122995 10091274 SRX25770930 SRS22407033 SRA1951631 Kurrasch Lab, Department of Medical Genetics, University of Calgary Kurrasch Lab, Department of Medical Genetics, University of Calgary 2 0.94722 0.95046 0.09788 0.09612 0.63984 0.6411 0.46913 0.4759 61 61 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Canada 2024-08-20 Adult Adult Head Nervous System
33622 33622 SRR30310490 SRX25770929 SRS22407032 SRP527479 PRJNA1150074 Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling GSE275235 Transcriptome Analysis SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …   pubmed:40208862   5b biol rep 3 GSM8473256   source name:heads|tissue:heads|genotype:5b / |treatment:untreated|geo loc name:missing|collection date:missing 5b biol rep 3 Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample heads untreated Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning. tissue:heads|genotype:5b / |treatment:untreated GSM8473256 GSM8473256: 5b biol rep 3; Danio rerio; RNA Seq GSM8473256 r1 GSM8473256 1 Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     Li47820-5b3_S12_R2_001.fastq.gz Li47820-5b3_S12_R1_001.fastq.gz fastq fastq 5532330845.0 45739498.0 GSM8473256 r1 0:60.50 1:60.46 A:1435251569;C:1304605813;G:1312598084;T:1471267089;N:8608290 60 60     1435251569 1304605813 1312598084 1471267089 8608290 SRX25770929 SRS22407032 SRA1951631 Kurrasch Lab, Department of Medical Genetics, University of Calgary Kurrasch Lab, Department of Medical Genetics, University of Calgary 2 0.94396 0.94717 0.11216 0.11051 0.64717 0.64768 0.47525 0.47841 60 61 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Canada 2024-08-20 Adult Adult Head Nervous System
33623 33623 SRR30310491 SRX25770928 SRS22407031 SRP527479 PRJNA1150074 Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling GSE275235 Transcriptome Analysis SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …   pubmed:40208862   5b biol rep 2 GSM8473255   source name:heads|tissue:heads|genotype:5b / |treatment:untreated|geo loc name:missing|collection date:missing 5b biol rep 2 Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample heads untreated Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning. tissue:heads|genotype:5b / |treatment:untreated GSM8473255 GSM8473255: 5b biol rep 2; Danio rerio; RNA Seq GSM8473255 r1 GSM8473255 1 Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     Li47819-5b2_S11_R2_001.fastq.gz Li47819-5b2_S11_R1_001.fastq.gz fastq fastq 5530076725.0 45717614.0 GSM8473255 r1 0:60.50 1:60.46 A:1432780615;C:1306496067;G:1314858379;T:1467817877;N:8123787 60 60     1432780615 1306496067 1314858379 1467817877 8123787 SRX25770928 SRS22407031 SRA1951631 Kurrasch Lab, Department of Medical Genetics, University of Calgary Kurrasch Lab, Department of Medical Genetics, University of Calgary 2 0.94205 0.94641 0.11508 0.11379 0.64788 0.64672 0.47602 0.47695 61 59 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Canada 2024-08-20 Adult Adult Head Nervous System
33624 33624 SRR30310492 SRX25770927 SRS22407030 SRP527479 PRJNA1150074 Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling GSE275235 Transcriptome Analysis SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …   pubmed:40208862   5b biol rep 1 GSM8473254   source name:heads|tissue:heads|genotype:5b / |treatment:untreated|geo loc name:missing|collection date:missing 5b biol rep 1 Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample heads untreated Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning. tissue:heads|genotype:5b / |treatment:untreated GSM8473254 GSM8473254: 5b biol rep 1; Danio rerio; RNA Seq GSM8473254 r1 GSM8473254 1 Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     Li47818-5b1_S10_R2_001.fastq.gz Li47818-5b1_S10_R1_001.fastq.gz fastq fastq 4784996431.0 39556747.0 GSM8473254 r1 0:60.50 1:60.46 A:1241886071;C:1129207908;G:1136918789;T:1270031996;N:6951667 60 60     1241886071 1129207908 1136918789 1270031996 6951667 SRX25770927 SRS22407030 SRA1951631 Kurrasch Lab, Department of Medical Genetics, University of Calgary Kurrasch Lab, Department of Medical Genetics, University of Calgary 2 0.94373 0.94771 0.11067 0.10905 0.64729 0.64583 0.47752 0.47625 59 60 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Canada 2024-08-20 Adult Adult Head Nervous System
33625 33625 SRR30310493 SRX25770926 SRS22407029 SRP527479 PRJNA1150074 Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling GSE275235 Transcriptome Analysis SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …   pubmed:40208862   5a biol rep 3 GSM8473253   source name:heads|tissue:heads|genotype:5a / |treatment:untreated|geo loc name:missing|collection date:missing 5a biol rep 3 Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample heads untreated Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning. tissue:heads|genotype:5a / |treatment:untreated GSM8473253 GSM8473253: 5a biol rep 3; Danio rerio; RNA Seq GSM8473253 r1 GSM8473253 1 Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     Li47817-5a3_S9_R2_001.fastq.gz Li47817-5a3_S9_R1_001.fastq.gz fastq fastq 5455669007.0 45101219.0 GSM8473253 r1 0:60.51 1:60.46 A:1408981430;C:1292361893;G:1307301180;T:1439131814;N:7892690 60 60     1408981430 1292361893 1307301180 1439131814 7892690 SRX25770926 SRS22407029 SRA1951631 Kurrasch Lab, Department of Medical Genetics, University of Calgary Kurrasch Lab, Department of Medical Genetics, University of Calgary 2 0.95182 0.95421 0.081 0.07901 0.6524 0.65115 0.48336 0.48307 61 59 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Canada 2024-08-20 Adult Adult Head Nervous System
33626 33626 SRR30310494 SRX25770925 SRS22407028 SRP527479 PRJNA1150074 Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling GSE275235 Transcriptome Analysis SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …   pubmed:40208862   5a biol rep 2 GSM8473252   source name:heads|tissue:heads|genotype:5a / |treatment:untreated|geo loc name:missing|collection date:missing 5a biol rep 2 Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample heads untreated Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning. tissue:heads|genotype:5a / |treatment:untreated GSM8473252 GSM8473252: 5a biol rep 2; Danio rerio; RNA Seq GSM8473252 r1 GSM8473252 1 Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     Li47816-5a2_S8_R2_001.fastq.gz Li47816-5a2_S8_R1_001.fastq.gz fastq fastq 5585703633.0 46182982.0 GSM8473252 r1 0:60.50 1:60.45 A:1439568272;C:1324867892;G:1340137608;T:1471972622;N:9157239 60 60     1439568272 1324867892 1340137608 1471972622 9157239 SRX25770925 SRS22407028 SRA1951631 Kurrasch Lab, Department of Medical Genetics, University of Calgary Kurrasch Lab, Department of Medical Genetics, University of Calgary 2 0.95103 0.95419 0.0813 0.07916 0.6565 0.65563 0.47441 0.47598 61 61 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Canada 2024-08-20 Adult Adult Head Nervous System
33627 33627 SRR30310495 SRX25770924 SRS22407027 SRP527479 PRJNA1150074 Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling GSE275235 Transcriptome Analysis SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …   pubmed:40208862   5a biol rep 1 GSM8473251   source name:heads|tissue:heads|genotype:5a / |treatment:untreated|geo loc name:missing|collection date:missing 5a biol rep 1 Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample heads untreated Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning. tissue:heads|genotype:5a / |treatment:untreated GSM8473251 GSM8473251: 5a biol rep 1; Danio rerio; RNA Seq GSM8473251 r1 GSM8473251 1 Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     Li47815-5a1_S7_R2_001.fastq.gz Li47815-5a1_S7_R1_001.fastq.gz fastq fastq 5421245773.0 44832660.0 GSM8473251 r1 0:60.48 1:60.44 A:1406624107;C:1276257498;G:1288190603;T:1440236606;N:9936959 60 60     1406624107 1276257498 1288190603 1440236606 9936959 SRX25770924 SRS22407027 SRA1951631 Kurrasch Lab, Department of Medical Genetics, University of Calgary Kurrasch Lab, Department of Medical Genetics, University of Calgary 2 0.9497 0.95318 0.08896 0.08766 0.64983 0.65009 0.46836 0.46856 60 61 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Canada 2024-08-20 Adult Adult Head Nervous System
33628 33628 SRR30310496 SRX25770923 SRS22407026 SRP527479 PRJNA1150074 Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling GSE275235 Transcriptome Analysis SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …   pubmed:40208862   WT biol rep 3 GSM8473250   source name:heads|tissue:heads|genotype:WT|treatment:untreated|geo loc name:missing|collection date:missing WT biol rep 3 Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample heads untreated Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning. tissue:heads|genotype:WT|treatment:untreated GSM8473250 GSM8473250: WT biol rep 3; Danio rerio; RNA Seq GSM8473250 r1 GSM8473250 1 Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     Li47811-WT3_S3_R2_001.fastq.gz Li47811-WT3_S3_R1_001.fastq.gz fastq fastq 5445129556.0 45027951.0 GSM8473250 r1 0:60.48 1:60.45 A:1410861744;C:1282813821;G:1294884711;T:1446863056;N:9706224 60 60     1410861744 1282813821 1294884711 1446863056 9706224 SRX25770923 SRS22407026 SRA1951631 Kurrasch Lab, Department of Medical Genetics, University of Calgary Kurrasch Lab, Department of Medical Genetics, University of Calgary 2 0.94943 0.95269 0.11544 0.11414 0.64644 0.64699 0.46439 0.47415 61 61 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Canada 2024-08-20 Adult Adult Head Nervous System
33629 33629 SRR30310497 SRX25770922 SRS22407025 SRP527479 PRJNA1150074 Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling GSE275235 Transcriptome Analysis SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …   pubmed:40208862   WT biol rep 2 GSM8473249   source name:heads|tissue:heads|genotype:WT|treatment:untreated|geo loc name:missing|collection date:missing WT biol rep 2 Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample heads untreated Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning. tissue:heads|genotype:WT|treatment:untreated GSM8473249 GSM8473249: WT biol rep 2; Danio rerio; RNA Seq GSM8473249 r1 GSM8473249 1 Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     Li47810-WT2_S2_R2_001.fastq.gz Li47810-WT2_S2_R1_001.fastq.gz fastq fastq 4788359140.0 39599012.0 GSM8473249 r1 0:60.48 1:60.44 A:1237189996;C:1129331953;G:1143753687;T:1268980159;N:9103345 60 60     1237189996 1129331953 1143753687 1268980159 9103345 SRX25770922 SRS22407025 SRA1951631 Kurrasch Lab, Department of Medical Genetics, University of Calgary Kurrasch Lab, Department of Medical Genetics, University of Calgary 2 0.94746 0.95043 0.1121 0.11092 0.64411 0.64342 0.46922 0.47301 59 61 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Canada 2024-08-20 Adult Adult Head Nervous System
33630 33630 SRR30310498 SRX25770921 SRS22407024 SRP527479 PRJNA1150074 Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling GSE275235 Transcriptome Analysis SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures developmental delays behavioral deficits poor motor progression and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression disrupted neurometabolism and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics hyperexcitable calcium events and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls 5a mutants 5b …   pubmed:40208862   WT biol rep 1 GSM8473248   source name:heads|tissue:heads|genotype:WT|treatment:untreated|geo loc name:missing|collection date:missing WT biol rep 1 Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample heads untreated Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle Adult zebrafish TL and AB strains were maintained at 28°C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions and fertilized eggs were collected via natural spawning. tissue:heads|genotype:WT|treatment:untreated GSM8473248 GSM8473248: WT biol rep 1; Danio rerio; RNA Seq GSM8473248 r1 GSM8473248 1 Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     Li47809-WT1_S1_R2_001.fastq.gz Li47809-WT1_S1_R1_001.fastq.gz fastq fastq 5047587318.0 41741097.0 GSM8473248 r1 0:60.48 1:60.44 A:1311031310;C:1185882586;G:1198272234;T:1343072853;N:9328335 60 60     1311031310 1185882586 1198272234 1343072853 9328335 SRX25770921 SRS22407024 SRA1951631 Kurrasch Lab, Department of Medical Genetics, University of Calgary Kurrasch Lab, Department of Medical Genetics, University of Calgary 2 0.94688 0.95005 0.12622 0.12476 0.6463 0.64528 0.47305 0.47428 61 61 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified unknown bulk unknown unknown   Canada 2024-08-20 Adult Adult Head Nervous System
34945 34945 SRR32472665 SRX27787001 SRS24165038 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched mtmr5 knockout biol rep4 GSM8811137   source name:head|tissue:head|genotype:mtmr5 knockout|geo loc name:missing|collection date:missing Brain enriched mtmr5 knockout biol rep4 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:mtmr5 knockout GSM8811137 GSM8811137: Brain enriched mtmr5 knockout biol rep4; Danio rerio; RNA Seq GSM8811137 r1 GSM8811137 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_KO_4_S45_L002_R1_001.fastq.gz mtmr5_KO_4_S45_L002_R2_001.fastq.gz fastq fastq 10453259182.0 34613441.0 GSM8811137 r1 0:151 1:151 A:3266219433;C:1966251945;G:2032163425;T:3188611188;N:13191 151 151     3266219433 1966251945 2032163425 3188611188 13191 SRX27787001 SRS24165038 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34946 34946 SRR32472666 SRX27787000 SRS24165036 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched mtmr5 knockout biol rep3 GSM8811136   source name:head|tissue:head|genotype:mtmr5 knockout|geo loc name:missing|collection date:missing Brain enriched mtmr5 knockout biol rep3 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:mtmr5 knockout GSM8811136 GSM8811136: Brain enriched mtmr5 knockout biol rep3; Danio rerio; RNA Seq GSM8811136 r1 GSM8811136 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_KO_3_S43_L002_R1_001.fastq.gz mtmr5_KO_3_S43_L002_R2_001.fastq.gz fastq fastq 12084666202.0 40015451.0 GSM8811136 r1 0:151 1:151 A:3753711310;C:2294198185;G:2375272418;T:3661468451;N:15838 151 151     3753711310 2294198185 2375272418 3661468451 15838 SRX27787000 SRS24165036 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34947 34947 SRR32472667 SRX27786999 SRS24165037 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched mtmr5 knockout biol rep2 GSM8811135   source name:head|tissue:head|genotype:mtmr5 knockout|geo loc name:missing|collection date:missing Brain enriched mtmr5 knockout biol rep2 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:mtmr5 knockout GSM8811135 GSM8811135: Brain enriched mtmr5 knockout biol rep2; Danio rerio; RNA Seq GSM8811135 r1 GSM8811135 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_KO_2_S41_L002_R1_001.fastq.gz mtmr5_KO_2_S41_L002_R2_001.fastq.gz fastq fastq 11376848568.0 37671684.0 GSM8811135 r1 0:151 1:151 A:3528535891;C:2164674917;G:2231865046;T:3451757695;N:15019 151 151     3528535891 2164674917 2231865046 3451757695 15019 SRX27786999 SRS24165037 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34948 34948 SRR32472668 SRX27786998 SRS24165034 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched mtmr5 knockout biol rep1 GSM8811134   source name:head|tissue:head|genotype:mtmr5 knockout|geo loc name:missing|collection date:missing Brain enriched mtmr5 knockout biol rep1 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:mtmr5 knockout GSM8811134 GSM8811134: Brain enriched mtmr5 knockout biol rep1; Danio rerio; RNA Seq GSM8811134 r1 GSM8811134 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_KO_1_S39_L002_R1_001.fastq.gz mtmr5_KO_1_S39_L002_R2_001.fastq.gz fastq fastq 10620109350.0 35165925.0 GSM8811134 r1 0:151 1:151 A:3306163050;C:2008249825;G:2075153541;T:3230528981;N:13953 151 151     3306163050 2008249825 2075153541 3230528981 13953 SRX27786998 SRS24165034 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34949 34949 SRR32472669 SRX27786997 SRS24165033 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched wild type biol rep4 GSM8811133   source name:head|tissue:head|genotype:wild type|geo loc name:missing|collection date:missing Brain enriched wild type biol rep4 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:wild type GSM8811133 GSM8811133: Brain enriched wild type biol rep4; Danio rerio; RNA Seq GSM8811133 r1 GSM8811133 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_WT_4_S44_L002_R1_001.fastq.gz mtmr5_WT_4_S44_L002_R2_001.fastq.gz fastq fastq 12990872770.0 43016135.0 GSM8811133 r1 0:151 1:151 A:3923529419;C:2571621367;G:2649969483;T:3845735356;N:17145 151 151     3923529419 2571621367 2649969483 3845735356 17145 SRX27786997 SRS24165033 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning 2 0.89808 0.89653 0.27845 0.2761 0.74479 0.74412 0.52081 0.52503 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34950 34950 SRR32472670 SRX27786996 SRS24165032 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched wild type biol rep3 GSM8811132   source name:head|tissue:head|genotype:wild type|geo loc name:missing|collection date:missing Brain enriched wild type biol rep3 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:wild type GSM8811132 GSM8811132: Brain enriched wild type biol rep3; Danio rerio; RNA Seq GSM8811132 r1 GSM8811132 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_WT_3_S42_L002_R1_001.fastq.gz mtmr5_WT_3_S42_L002_R2_001.fastq.gz fastq fastq 11980025618.0 39668959.0 GSM8811132 r1 0:151 1:151 A:3620876130;C:2376508941;G:2435934723;T:3546690015;N:15809 151 151     3620876130 2376508941 2435934723 3546690015 15809 SRX27786996 SRS24165032 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34951 34951 SRR32472671 SRX27786995 SRS24165035 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched wild type biol rep2 GSM8811131   source name:head|tissue:head|genotype:wild type|geo loc name:missing|collection date:missing Brain enriched wild type biol rep2 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:wild type GSM8811131 GSM8811131: Brain enriched wild type biol rep2; Danio rerio; RNA Seq GSM8811131 r1 GSM8811131 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_WT_2_S40_L002_R1_001.fastq.gz mtmr5_WT_2_S40_L002_R2_001.fastq.gz fastq fastq 12148102812.0 40225506.0 GSM8811131 r1 0:151 1:151 A:3574846721;C:2501278590;G:2563116243;T:3508845082;N:16176 151 151     3574846721 2501278590 2563116243 3508845082 16176 SRX27786995 SRS24165035 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
34952 34952 SRR32472672 SRX27786994 SRS24165031 SRP565999 PRJNA1227535 Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3 GSE290354 Transcriptome Analysis Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.   pubmed:40066109   Brain enriched wild type biol rep1 GSM8811130   source name:head|tissue:head|genotype:wild type|geo loc name:missing|collection date:missing Brain enriched wild type biol rep1 Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples head   Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto. Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care. tissue:head|genotype:wild type GSM8811130 GSM8811130: Brain enriched wild type biol rep1; Danio rerio; RNA Seq GSM8811130 r1 GSM8811130 1 Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP565999     mtmr5_WT_1_S38_L002_R1_001.fastq.gz mtmr5_WT_1_S38_L002_R2_001.fastq.gz fastq fastq 12280050236.0 40662418.0 GSM8811130 r1 0:151 1:151 A:3666524090;C:2479893988;G:2540363922;T:3593251867;N:16369 151 151     3666524090 2479893988 2540363922 3593251867 16369 SRX27786994 SRS24165031 SRA2083091 Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning 2 0.91363 0.9138 0.2442 0.24267 0.72232 0.72123 0.47864 0.53039 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   Canada 2025-02-24 Larval Larval Head Nervous System
36479 36479 SRR527834 SRX171221 SRS352107 SRP014596 PRJNA171539 Transcriptomic analysis of zebrafish during development and homeostasis GSE39703 Transcriptome Analysis Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end 16 hpf 36 hpf 5 day larvae adult head and adult tail or paired end 24 hpf libraries Illumina. Single end reads of 36 nucleotides and paired end reads 2 x 76 nucleotides were obtained with a GAIIx Illumina. Gene expression at the different stages/tissu was assessed by cufflinks and HTseq. Overall design: RNAseq on 5 differents samples: 24hpf embryos pool of 16 hour to 36 hour embryos 5 dpf larvea adult head and adult tail   pubmed:23684812   head GSM977959   tissue:entire adult head|genotype:Wild type|strain:AB|Stage:adult head head Basecalls performed using CASAVA version 1.4 Reads aligned to zebrafish genome Zv9 Ensembl with Tophat v 1.4.1 and Bowtie v 0.12.7 options: butterfly search coverage search microexon search min anchor length 5 G GTF Determination of raw reads aligned to ZV9 with HTSeq v0.5.3p3 and gtf file ensembl zv9 release 60 Determination of RPKM/FPKM with cufflinks v 1.3.0 with the options u b M rRNA/Mtgenes mask G gtf Genome build: Zv9 v 60 Supplementary files format and content: *.count file are the output of Htseq reads quantification. *.fpkm files are the output of cufflinks quantification entire adult head   Extraction of total RNA with Trizol following manufacturer's instruction. Generation of mRNA libraries with Trueseq RNA kit following Illumina's instructions   genotype:Wild type|strain:AB|Stage:adult head GSM977959 GSM977959: head; Danio rerio; RNA Seq GSM977959 1 GSM977959: head 1   GEO Accession:GSM977959 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP014596         516054600.0 14334850.0 GSM977959 r1 0:36 A:144148482;C:115800670;G:121205261;T:134746787;N:153400 36       144148482 115800670 121205261 134746787 153400 SRX171221 SRS352107 SRA056408 GEO ITG 1 0.89668   0.12577   0.66803   0.45871   36   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2012-07-27 Adult Adult Head Nervous System
37210 37210 SRR1028004 SRX376581 SRS501207 SRP032838 PRJNA227277 Danio rerio Transcriptome or Gene expression PRJNA227277 Other transcriptome analysis of zebrafish whole head.     wild type zebrafish sample 3 Wt 3 iiina   label:3|age:6 days|tissue type:whole head                 Transcriptome analysis of zebrafish's whole head. ZF na iiina 1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP032838     iiina_1.fastq.tar.gz iiina_2.fastq.tar.gz fastq fastq 4316715356.0 21369878.0 iiina 0:101 1:101 A:1146719253;C:995646710;G:1009198100;T:1125396496;N:39754797 101 101     1146719253 995646710 1009198100 1125396496 39754797 SRX376581 SRS501207 SRA110728 BIU|Levanon BIU 2 0.92916 0.92726 0.08723 0.0948 0.65514 0.68923 0.47003 0.47006 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Israel 2014-11-11 Larval Larval Head Nervous System
37211 37211 SRR1028003 SRX376580 SRS501206 SRP032838 PRJNA227277 Danio rerio Transcriptome or Gene expression PRJNA227277 Other transcriptome analysis of zebrafish whole head.     wild type zebrafish sample 2 Wt 2 iina   label:2|age:6 days|tissue type:whole head                 Transcriptome analysis of zebrafish's whole head. ZF na iina 1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP032838     iina_1.fastq.tar.gz iina_2.fastq.tar.gz fastq fastq 4955839518.0 24533859.0 iina 0:101 1:101 A:1280850150;C:1179933762;G:1174869989;T:1275240888;N:44944729 101 101     1280850150 1179933762 1174869989 1275240888 44944729 SRX376580 SRS501206 SRA110728 BIU|Levanon BIU 2 0.93499 0.9343 0.07143 0.07615 0.65427 0.67233 0.47221 0.47326 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Israel 2014-11-11 Larval Larval Head Nervous System
37212 37212 SRR1028002 SRX375515 SRS501219 SRP032838 PRJNA227277 Danio rerio Transcriptome or Gene expression PRJNA227277 Other transcriptome analysis of zebrafish whole head.     wild type zebrafish sample 1 Wt 1 ina   label:1|age:6 days|tissue type:whole head                 Transcriptome analysis of zebrafish's whole head. ZF na ina 1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP032838     ina_2.fastq.tar.gz ina_1.fastq.tar.gz fastq fastq 5519994006.0 27326703.0 ina 1 0:101 1:101 A:1456361266;C:1288156090;G:1276246591;T:1448748282;N:50481777 101 101     1456361266 1288156090 1276246591 1448748282 50481777 SRX375515 SRS501219 SRA110728 BIU|Levanon BIU 2 0.92874 0.9272 0.08523 0.09251 0.65445 0.67681 0.47526 0.47863 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Israel 2014-11-11 Larval Larval Head Nervous System
38299 38299 SRR1648856 SRX757983 SRS743130 SRP049716 PRJNA266970 RNA sequencing of the developing zebrafish head GSE63191 Transcriptome Analysis We sequenced strand specific mRNA from the heads of 3 groups of wild type zebrafish Danio rerio 5 dpf Overall design: Examination of the relative expression of genes in the developing zebrafish brain   pubmed:25561519   Wildtype Replicate 3 GSM1543674   source name:whole head|develolpmental stage:5 dpf embryo|tissue:whole head Wildtype Replicate 3 Basecalls performed using CASAVA version 1.5 Alignment was performed with Gsnap v2012 07 20 using default parameters and the zv9 genome/transcriptome from Ensembl Accurate dose response was verified with custom analysis tools and the included ERCC RNA spike ins Aligned reads were quantified with Cufflinks v2.1.0 using default parameters and the zv9 transcriptome from Ensembl Genome build: zv9 Supplementary files format and content: Cufflinks v2.1.0 genes.fpkm tracking whole head   TRIzol Invitrogen extraction per manufactor's instructions Strand specific polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection. Zebrafish embryos from natural matings were maintained at 28C in 6 or 10cm dishes. 5 dpf the heads of 80 100 embryos per replicate were obtained for RNA extraction. develolpmental stage:5 dpf embryo|tissue:whole head GSM1543674 GSM1543674: Wildtype Replicate 3; Danio rerio; RNA Seq GSM1543674   1 TRIzol Invitrogen extraction per manufactor's instructions Strand specific polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection. GEO Accession:GSM1543674 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP049716     uninjected_rep3_zebrafish_121230_AC1BMGACXX_Illumina8_1.fastq.gz uninjected_rep3_zebrafish_121230_AC1BMGACXX_Illumina8_2.fastq.gz fastq fastq 7947025900.0 79470259.0 GSM1543674 r1 0:50 1:50 A:2171440033;C:1752204345;G:1782154451;T:2240911661;N:315410 50 50     2171440033 1752204345 1782154451 2240911661 315410 SRX757983 SRS743130 SRA200859 GEO Center for Human Genetic Research, Massachusetts General Hospital 2 0.92472 0.92889 0.15282 0.15037 0.72015 0.71969 0.47465 0.48174 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2014-11-12 Larval Larval Head Nervous System
38300 38300 SRR1648855 SRX757982 SRS743129 SRP049716 PRJNA266970 RNA sequencing of the developing zebrafish head GSE63191 Transcriptome Analysis We sequenced strand specific mRNA from the heads of 3 groups of wild type zebrafish Danio rerio 5 dpf Overall design: Examination of the relative expression of genes in the developing zebrafish brain   pubmed:25561519   Wildtype Replicate 2 GSM1543673   source name:whole head|develolpmental stage:5 dpf embryo|tissue:whole head Wildtype Replicate 2 Basecalls performed using CASAVA version 1.5 Alignment was performed with Gsnap v2012 07 20 using default parameters and the zv9 genome/transcriptome from Ensembl Accurate dose response was verified with custom analysis tools and the included ERCC RNA spike ins Aligned reads were quantified with Cufflinks v2.1.0 using default parameters and the zv9 transcriptome from Ensembl Genome build: zv9 Supplementary files format and content: Cufflinks v2.1.0 genes.fpkm tracking whole head   TRIzol Invitrogen extraction per manufactor's instructions Strand specific polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection. Zebrafish embryos from natural matings were maintained at 28C in 6 or 10cm dishes. 5 dpf the heads of 80 100 embryos per replicate were obtained for RNA extraction. develolpmental stage:5 dpf embryo|tissue:whole head GSM1543673 GSM1543673: Wildtype Replicate 2; Danio rerio; RNA Seq GSM1543673   1 TRIzol Invitrogen extraction per manufactor's instructions Strand specific polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection. GEO Accession:GSM1543673 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP049716     uninjected_rep2_zebrafish_121230_AC1BMGACXX_Illumina5_2.fastq.gz uninjected_rep2_zebrafish_121230_AC1BMGACXX_Illumina5_1.fastq.gz fastq fastq 7400831800.0 74008318.0 GSM1543673 r1 0:50 1:50 A:1997686488;C:1645601571;G:1723353684;T:2033898648;N:291409 50 50     1997686488 1645601571 1723353684 2033898648 291409 SRX757982 SRS743129 SRA200859 GEO Center for Human Genetic Research, Massachusetts General Hospital 2 0.90663 0.91107 0.33386 0.33587 0.7153 0.71553 0.48819 0.49079 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2014-11-12 Larval Larval Head Nervous System
38301 38301 SRR1648854 SRX757981 SRS743128 SRP049716 PRJNA266970 RNA sequencing of the developing zebrafish head GSE63191 Transcriptome Analysis We sequenced strand specific mRNA from the heads of 3 groups of wild type zebrafish Danio rerio 5 dpf Overall design: Examination of the relative expression of genes in the developing zebrafish brain   pubmed:25561519   Wildtype Replicate 1 GSM1543672   source name:whole head|develolpmental stage:5 dpf embryo|tissue:whole head Wildtype Replicate 1 Basecalls performed using CASAVA version 1.5 Alignment was performed with Gsnap v2012 07 20 using default parameters and the zv9 genome/transcriptome from Ensembl Accurate dose response was verified with custom analysis tools and the included ERCC RNA spike ins Aligned reads were quantified with Cufflinks v2.1.0 using default parameters and the zv9 transcriptome from Ensembl Genome build: zv9 Supplementary files format and content: Cufflinks v2.1.0 genes.fpkm tracking whole head   TRIzol Invitrogen extraction per manufactor's instructions Strand specific polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection. Zebrafish embryos from natural matings were maintained at 28C in 6 or 10cm dishes. 5 dpf the heads of 80 100 embryos per replicate were obtained for RNA extraction. develolpmental stage:5 dpf embryo|tissue:whole head GSM1543672 GSM1543672: Wildtype Replicate 1; Danio rerio; RNA Seq GSM1543672   1 TRIzol Invitrogen extraction per manufactor's instructions Strand specific polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection. GEO Accession:GSM1543672 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP049716     uninjected_rep1_zebrafish_121230_AC1BMGACXX_Illumina2_1.fastq.gz uninjected_rep1_zebrafish_121230_AC1BMGACXX_Illumina2_2.fastq.gz fastq fastq 5994627800.0 59946278.0 GSM1543672 r1 0:50 1:50 A:1649718236;C:1309696705;G:1340401079;T:1694576298;N:235482 50 50     1649718236 1309696705 1340401079 1694576298 235482 SRX757981 SRS743128 SRA200859 GEO Center for Human Genetic Research, Massachusetts General Hospital 2 0.9191 0.92223 0.18431 0.18241 0.68889 0.68793 0.48942 0.48534 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2014-11-12 Larval Larval Head Nervous System
39887 39887 SRR2239197 SRX1181673 SRS1053962 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   mutant 5 hr treatment replicate 3 GSM1868446   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:metronidazole|time:5 hr|tissue:head mutant 5 hr treatment replicate 3 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:metronidazole|time:5 hr|tissue:head GSM1868446 GSM1868446: mutant 5 hr treatment replicate 3; Danio rerio; RNA Seq GSM1868446   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868446 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1349_s_3_withindex_sequence.txt_AGGCGAA.fq.gz fastq 1486758800.0 29735176.0 GSM1868446 r1 0:50 A:407157206;C:348516474;G:333581236;T:397373823;N:130061 50       407157206 348516474 333581236 397373823 130061 SRX1181673 SRS1053962 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89356   0.24716   0.66348   0.55072   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39888 39888 SRR2239196 SRX1181672 SRS1053963 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   mutant 5 hr treatment replicate 2 GSM1868445   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:metronidazole|time:5 hr|tissue:head mutant 5 hr treatment replicate 2 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:metronidazole|time:5 hr|tissue:head GSM1868445 GSM1868445: mutant 5 hr treatment replicate 2; Danio rerio; RNA Seq GSM1868445   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868445 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1349_s_3_withindex_sequence.txt_AATTCAT.fq.gz fastq 1324305100.0 26486102.0 GSM1868445 r1 0:50 A:346866338;C:322967018;G:303987755;T:350367920;N:116069 50       346866338 322967018 303987755 350367920 116069 SRX1181672 SRS1053963 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.86992   0.2794   0.67087   0.45   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39889 39889 SRR2239195 SRX1181671 SRS1053965 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   mutant 5 hr treatment replicate 1 GSM1868444   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:metronidazole|time:5 hr|tissue:head mutant 5 hr treatment replicate 1 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:metronidazole|time:5 hr|tissue:head GSM1868444 GSM1868444: mutant 5 hr treatment replicate 1; Danio rerio; RNA Seq GSM1868444   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868444 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1349_s_3_withindex_sequence.txt_CTGCAAT.fq.gz fastq 1996223000.0 39924460.0 GSM1868444 r1 0:50 A:548376523;C:462971670;G:439194387;T:545504649;N:175771 50       548376523 462971670 439194387 545504649 175771 SRX1181671 SRS1053965 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.90072   0.27661   0.66809   0.54999   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39890 39890 SRR2239194 SRX1181670 SRS1053966 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   mutant control replicate 3 GSM1868443   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:control|tissue:head mutant control replicate 3 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:control|tissue:head GSM1868443 GSM1868443: mutant control replicate 3; Danio rerio; RNA Seq GSM1868443   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868443 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1349_s_3_withindex_sequence.txt_GTAAAAA.fq.gz fastq 1689695100.0 33793902.0 GSM1868443 r1 0:50 A:469281850;C:387188418;G:368970934;T:464103273;N:150625 50       469281850 387188418 368970934 464103273 150625 SRX1181670 SRS1053966 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.88353   0.30543   0.66785   0.53952   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39891 39891 SRR2239193 SRX1181669 SRS1053964 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   mutant control replicate 2 GSM1868442   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:control|tissue:head mutant control replicate 2 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:control|tissue:head GSM1868442 GSM1868442: mutant control replicate 2; Danio rerio; RNA Seq GSM1868442   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868442 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1349_s_3_withindex_sequence.txt_TGGCATA.fq.gz fastq 1744754500.0 34895090.0 GSM1868442 r1 0:50 A:475432211;C:407457752;G:387941759;T:473768506;N:154272 50       475432211 407457752 387941759 473768506 154272 SRX1181669 SRS1053964 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.8967   0.27571   0.66342   0.5413   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39892 39892 SRR2239192 SRX1181668 SRS1053967 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   mutant control replicate 1 GSM1868441   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:control|tissue:head mutant control replicate 1 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:control|tissue:head GSM1868441 GSM1868441: mutant control replicate 1; Danio rerio; RNA Seq GSM1868441   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868441 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1349_s_3_withindex_sequence.txt_GGAGTCC.fq.gz fastq 1300091300.0 26001826.0 GSM1868441 r1 0:50 A:356312292;C:301731841;G:287159447;T:354773803;N:113917 50       356312292 301731841 287159447 354773803 113917 SRX1181668 SRS1053967 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89407   0.27485   0.66263   0.54402   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39893 39893 SRR2239190 SRX1181667 SRS1053968 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type 5 hr treatment replicate 3 GSM1868440   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head wild type 5 hr treatment replicate 3 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head GSM1868440 GSM1868440: wild type 5 hr treatment replicate 3; Danio rerio; RNA Seq GSM1868440   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868440 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_6_withindex_sequence.txt_GGTCCTC.fq.gz fastq 788127550.0 15762551.0 GSM1868440 r1 0:50 A:219123307;C:174342061;G:168810140;T:225814483;N:37559 50       219123307 174342061 168810140 225814483 37559 SRX1181667 SRS1053968 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89391   0.27826   0.67034   0.55775   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39894 39894 SRR2239191 SRX1181667 SRS1053968 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type 5 hr treatment replicate 3 GSM1868440   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head wild type 5 hr treatment replicate 3 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head GSM1868440 GSM1868440: wild type 5 hr treatment replicate 3; Danio rerio; RNA Seq GSM1868440   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868440 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_7_withindex_sequence.txt_GGTCCTC.fq.gz fastq 779058950.0 15581179.0 GSM1868440 r2 0:50 A:216843690;C:172197112;G:166801096;T:223172377;N:44675 50       216843690 172197112 166801096 223172377 44675 SRX1181667 SRS1053968 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89268   0.27974   0.67067   0.55617   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39895 39895 SRR2239188 SRX1181666 SRS1053969 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type 5 hr treatment replicate 2 GSM1868439   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head wild type 5 hr treatment replicate 2 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head GSM1868439 GSM1868439: wild type 5 hr treatment replicate 2; Danio rerio; RNA Seq GSM1868439   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868439 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_6_withindex_sequence.txt_GCTTAGA.fq.gz fastq 884810450.0 17696209.0 GSM1868439 r1 0:50 A:244801024;C:196884736;G:189692109;T:253390454;N:42127 50       244801024 196884736 189692109 253390454 42127 SRX1181666 SRS1053969 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89625   0.26571   0.66247   0.52896   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39896 39896 SRR2239189 SRX1181666 SRS1053969 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type 5 hr treatment replicate 2 GSM1868439   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head wild type 5 hr treatment replicate 2 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head GSM1868439 GSM1868439: wild type 5 hr treatment replicate 2; Danio rerio; RNA Seq GSM1868439   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868439 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_7_withindex_sequence.txt_GCTTAGA.fq.gz fastq 875476350.0 17509527.0 GSM1868439 r2 0:50 A:242411986;C:194719083;G:187698234;T:250595738;N:51309 50       242411986 194719083 187698234 250595738 51309 SRX1181666 SRS1053969 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89632   0.26574   0.66332   0.53633   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39897 39897 SRR2239186 SRX1181665 SRS1053970 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type 5 hr treatment replicate 1 GSM1868438   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head wild type 5 hr treatment replicate 1 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head GSM1868438 GSM1868438: wild type 5 hr treatment replicate 1; Danio rerio; RNA Seq GSM1868438   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868438 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_6_withindex_sequence.txt_GTCGATA.fq.gz fastq 981479900.0 19629598.0 GSM1868438 r1 0:50 A:272447863;C:217586061;G:210457740;T:280941539;N:46697 50       272447863 217586061 210457740 280941539 46697 SRX1181665 SRS1053970 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89259   0.28519   0.66413   0.54434   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39898 39898 SRR2239187 SRX1181665 SRS1053970 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type 5 hr treatment replicate 1 GSM1868438   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head wild type 5 hr treatment replicate 1 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head GSM1868438 GSM1868438: wild type 5 hr treatment replicate 1; Danio rerio; RNA Seq GSM1868438   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868438 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_7_withindex_sequence.txt_GTCGATA.fq.gz fastq 970627300.0 19412546.0 GSM1868438 r2 0:50 A:269587370;C:215107358;G:208077535;T:277799059;N:55978 50       269587370 215107358 208077535 277799059 55978 SRX1181665 SRS1053970 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.8924   0.2863   0.66486   0.54277   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39899 39899 SRR2239184 SRX1181664 SRS1053971 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type 2 hr treatment replicate 3 GSM1868437   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head wild type 2 hr treatment replicate 3 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head GSM1868437 GSM1868437: wild type 2 hr treatment replicate 3; Danio rerio; RNA Seq GSM1868437   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868437 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_6_withindex_sequence.txt_AGATACT.fq.gz fastq 1034107450.0 20682149.0 GSM1868437 r1 0:50 A:263807622;C:250451504;G:242163638;T:277636652;N:48034 50       263807622 250451504 242163638 277636652 48034 SRX1181664 SRS1053971 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.90878   0.23218   0.65916   0.49411   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39900 39900 SRR2239185 SRX1181664 SRS1053971 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type 2 hr treatment replicate 3 GSM1868437   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head wild type 2 hr treatment replicate 3 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head GSM1868437 GSM1868437: wild type 2 hr treatment replicate 3; Danio rerio; RNA Seq GSM1868437   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868437 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_7_withindex_sequence.txt_AGATACT.fq.gz fastq 1021705150.0 20434103.0 GSM1868437 r2 0:50 A:260838269;C:247381617;G:239188036;T:274238961;N:58267 50       260838269 247381617 239188036 274238961 58267 SRX1181664 SRS1053971 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.91116   0.23255   0.65918   0.49596   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39901 39901 SRR2239182 SRX1181663 SRS1053972 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type 2 hr treatment replicate 2 GSM1868436   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head wild type 2 hr treatment replicate 2 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head GSM1868436 GSM1868436: wild type 2 hr treatment replicate 2; Danio rerio; RNA Seq GSM1868436   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868436 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_6_withindex_sequence.txt_GGGTCAA.fq.gz fastq 756008650.0 15120173.0 GSM1868436 r1 0:50 A:209261412;C:168123618;G:163450516;T:215134424;N:38680 50       209261412 168123618 163450516 215134424 38680 SRX1181663 SRS1053972 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.8978   0.26699   0.66172   0.53653   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39902 39902 SRR2239183 SRX1181663 SRS1053972 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type 2 hr treatment replicate 2 GSM1868436   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head wild type 2 hr treatment replicate 2 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head GSM1868436 GSM1868436: wild type 2 hr treatment replicate 2; Danio rerio; RNA Seq GSM1868436   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868436 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_7_withindex_sequence.txt_GGGTCAA.fq.gz fastq 747959000.0 14959180.0 GSM1868436 r2 0:50 A:207110574;C:166254650;G:161670187;T:212878047;N:45542 50       207110574 166254650 161670187 212878047 45542 SRX1181663 SRS1053972 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89508   0.26657   0.66373   0.53734   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39903 39903 SRR2239180 SRX1181662 SRS1053973 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type 2 hr treatment replicate 1 GSM1868435   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head wild type 2 hr treatment replicate 1 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head GSM1868435 GSM1868435: wild type 2 hr treatment replicate 1; Danio rerio; RNA Seq GSM1868435   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868435 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_6_withindex_sequence.txt_CAATATC.fq.gz fastq 843938700.0 16878774.0 GSM1868435 r1 0:50 A:235353785;C:185755129;G:180220044;T:242567413;N:42329 50       235353785 185755129 180220044 242567413 42329 SRX1181662 SRS1053973 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.8819   0.31587   0.6719   0.53852   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39904 39904 SRR2239181 SRX1181662 SRS1053973 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type 2 hr treatment replicate 1 GSM1868435   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head wild type 2 hr treatment replicate 1 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head GSM1868435 GSM1868435: wild type 2 hr treatment replicate 1; Danio rerio; RNA Seq GSM1868435   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868435 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_7_withindex_sequence.txt_CAATATC.fq.gz fastq 837375500.0 16747510.0 GSM1868435 r2 0:50 A:233691274;C:184249473;G:178762050;T:240622009;N:50694 50       233691274 184249473 178762050 240622009 50694 SRX1181662 SRS1053973 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.88228   0.31306   0.67042   0.53933   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39905 39905 SRR2239178 SRX1181661 SRS1053976 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type control replicate 3 GSM1868434   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head wild type control replicate 3 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head GSM1868434 GSM1868434: wild type control replicate 3; Danio rerio; RNA Seq GSM1868434   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868434 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_6_withindex_sequence.txt_ACCCACT.fq.gz fastq 946427500.0 18928550.0 GSM1868434 r1 0:50 A:260851494;C:211313068;G:205344403;T:268874280;N:44255 50       260851494 211313068 205344403 268874280 44255 SRX1181661 SRS1053976 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89626   0.27082   0.66058   0.53343   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39906 39906 SRR2239179 SRX1181661 SRS1053976 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type control replicate 3 GSM1868434   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head wild type control replicate 3 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head GSM1868434 GSM1868434: wild type control replicate 3; Danio rerio; RNA Seq GSM1868434   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868434 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_7_withindex_sequence.txt_ACCCACT.fq.gz fastq 935318450.0 18706369.0 GSM1868434 r2 0:50 A:258004973;C:208706255;G:202911059;T:265642847;N:53316 50       258004973 208706255 202911059 265642847 53316 SRX1181661 SRS1053976 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89576   0.27216   0.663   0.53587   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39907 39907 SRR2239176 SRX1181660 SRS1053974 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type control replicate 2 GSM1868433   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head wild type control replicate 2 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head GSM1868433 GSM1868433: wild type control replicate 2; Danio rerio; RNA Seq GSM1868433   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868433 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_6_withindex_sequence.txt_TCAACTG.fq.gz fastq 914021500.0 18280430.0 GSM1868433 r1 0:50 A:252009242;C:204125475;G:197760562;T:260083313;N:42908 50       252009242 204125475 197760562 260083313 42908 SRX1181660 SRS1053974 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89646   0.26998   0.65979   0.53202   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39908 39908 SRR2239177 SRX1181660 SRS1053974 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type control replicate 2 GSM1868433   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head wild type control replicate 2 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head GSM1868433 GSM1868433: wild type control replicate 2; Danio rerio; RNA Seq GSM1868433   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868433 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_7_withindex_sequence.txt_TCAACTG.fq.gz fastq 904836300.0 18096726.0 GSM1868433 r2 0:50 A:249726925;C:201939252;G:195727802;T:257389594;N:52727 50       249726925 201939252 195727802 257389594 52727 SRX1181660 SRS1053974 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89504   0.27105   0.6607   0.5314   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39909 39909 SRR2239174 SRX1181659 SRS1053975 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type control replicate 1 GSM1868432   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head wild type control replicate 1 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head GSM1868432 GSM1868432: wild type control replicate 1; Danio rerio; RNA Seq GSM1868432   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868432 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_6_withindex_sequence.txt_TTTAACT.fq.gz fastq 919147800.0 18382956.0 GSM1868432 r1 0:50 A:255238211;C:203629686;G:197780664;T:262454873;N:44366 50       255238211 203629686 197780664 262454873 44366 SRX1181659 SRS1053975 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89498   0.2793   0.6636   0.54563   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
39910 39910 SRR2239175 SRX1181659 SRS1053975 SRP063290 PRJNA294660 Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish GSE72682 Transcriptome Analysis Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.   pubmed:26863206   wild type control replicate 1 GSM1868432   source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head wild type control replicate 1 Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs head For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs. Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.   age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head GSM1868432 GSM1868432: wild type control replicate 1; Danio rerio; RNA Seq GSM1868432   1 Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 μg total RNA was used for each wild type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags. GEO Accession:GSM1868432 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP063290     run_1266_s_7_withindex_sequence.txt_TTTAACT.fq.gz fastq 908786950.0 18175739.0 GSM1868432 r2 0:50 A:252518589;C:201251252;G:195514386;T:259449857;N:52866 50       252518589 201251252 195514386 259449857 52866 SRX1181659 SRS1053975 SRA294351 GEO Voigt, Pharmacology and Physiology, Saint Louis University 1 0.89351   0.27857   0.66492   0.54418   50   B   usable mapping rate illumina hiseq_era unknown poly_a ribozero bulk unknown unknown   United States 2015-09-03 Larval Larval Head Nervous System
40494 40494 SRR3204724 SRX1614066 SRS1323928 SRP070923 PRJNA313387 Transcriptomic of ß diketone antibiotics on zebrafish post a 3 month DKAs exposure. PRJNA313387 Other RNA libraries were constructed from control 6.25 and 12.5 mg/L treatment groups respectively. post DKAs exposure to 3 mpf zebrafish the whole transcriptome was determined.     12.5 mg/L with equal weight concentrations and volumes for each of the six DKA species ofloxacin ciprofloxacin enrofloxacin doxycycline chlortetracycline and oxytetracycline was exposure to zebrafish from embryo to 90 dpf dpf 12.5mg/L DKAs T21   strain:AB strain|isolate:Oregon State University|breed:Danio rerio|cultivar:not applicable|ecotype:Wild type|age:3 mpf|dev stage:3 mpf|sex:pooled male and female|tissue:we performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems.|treatment:12.5 mg/L DKAs exposure|BioSampleModel:Model organism or animal                 12.5mg/L DKAs T21 1 Zebrafish in 12.5 mg/L β diketone antibiotics treatment groupwith equal weight concentrations and volumes for ofloxacin ciprofloxacin enrofloxacin doxycycline chlortetracycline and oxytetracycline with purity of 99% except for 95% for chlortetracycline were randomly selected post DKAs exposure at 90 dpf and rinsed with phosphorous buffer solution. We performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems. The retained tissues were used to extract total RNA using Trizol Invitrogen Carlsbad CA USA according to the manufacturer's procedures. The quantity and purity of total RNA were analyzed by employing a Bioanalyzer 2100 and RNA 6000 Nano LabChipKit Agilent Santa Clara CA USA with RIN number >7.0. Poly A mRNA was isolated by poly T oligo attached magnetic beads Invitrogen. The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature. Then the final cDNA library was produced by the reverse transcription of the cleaved RNA fragments on the basis of the mRNA Seq sample preparation kit Illumina San Diego USA and the average 300±50 bp insert size was used for the paired end libraries. Finally the paired end sequencing was performed on an Illumina Hiseq2000/2500. Prior to assembly the low quality reads 1 reads containing sequencing adaptors; 2 reads containing sequencing primer; 3 nucleotide with q scores lower than 20 were removed. Next the cleaned and paired end reads were produced.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070923     T21_Clean_Data1.fq.gz T21_Clean_Data2.fq.gz fastq fastq 10502615500.0 42010462.0 T21 0:125 1:125 A:2848309151;C:2371408734;G:2356749579;T:2925931092;N:216944 125 125     2848309151 2371408734 2356749579 2925931092 216944 SRX1614066 SRS1323928 SRA359545 School of Life Sciences School of Life Sciences 2 0.87768 0.88612 0.29688 0.29743 0.68738 0.68363 0.52932 0.52507 125 125 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown bulk unknown unknown   Unknown 2016-03-16 Adult Adult Head Nervous System
40495 40495 SRR3203073 SRX1612569 SRS1321766 SRP070923 PRJNA313387 Transcriptomic of ß diketone antibiotics on zebrafish post a 3 month DKAs exposure. PRJNA313387 Other RNA libraries were constructed from control 6.25 and 12.5 mg/L treatment groups respectively. post DKAs exposure to 3 mpf zebrafish the whole transcriptome was determined.     6.25 mg/L with equal weight concentrations and volumes for each of the six DKA species ofloxacin ciprofloxacin enrofloxacin doxycycline chlortetracycline and oxytetracycline was exposure to zebrafish from embryo to 90 dpf dpf 6.25mg/L DKAs T11   strain:AB strain|isolate:Oregon State University|breed:Danio rerio|cultivar:not applicable|ecotype:Wild type|age:3 mpf|dev stage:3 mpf|sex:pooled male and female|tissue:we performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems.|treatment:6.25 mg/L DKAs exposure|BioSampleModel:Model organism or animal                 6.25 mg/L DKAs T11 1 Zebrafish in 6.25 mg/L β diketone antibiotics treatment groupwith equal weight concentrations and volumes for ofloxacin ciprofloxacin enrofloxacin doxycycline chlortetracycline and oxytetracycline with purity of 99% except for 95% for chlortetracycline were randomly selected post DKAs exposure at 90 dpf and rinsed with phosphorous buffer solution. We performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems. The retained tissues were used to extract total RNA using Trizol Invitrogen Carlsbad CA USA according to the manufacturer's procedures. The quantity and purity of total RNA were analyzed by employing a Bioanalyzer 2100 and RNA 6000 Nano LabChipKit Agilent Santa Clara CA USA with RIN number >7.0. Poly A mRNA was isolated by poly T oligo attached magnetic beads Invitrogen. The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature. Then the final cDNA library was produced by the reverse transcription of the cleaved RNA fragments on the basis of the mRNA Seq sample preparation kit Illumina San Diego USA and the average 300±50 bp insert size was used for the paired end libraries. Finally the paired end sequencing was performed on an Illumina Hiseq2000/2500. Prior to assembly the low quality reads 1 reads containing sequencing adaptors; 2 reads containing sequencing primer; 3 nucleotide with q scores lower than 20 were removed. Next the cleaned and paired end reads were produced.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070923     T11_Clean_Data1.fq.gz T11_Clean_Data2.fq.gz fastq fastq 8178356500.0 32713426.0 T11 0:125 1:125 A:2135090304;C:1929011381;G:1912585084;T:2201518295;N:151436 125 125     2135090304 1929011381 1912585084 2201518295 151436 SRX1612569 SRS1321766 SRA359545 School of Life Sciences School of Life Sciences 2 0.84003 0.84827 0.32283 0.32402 0.71031 0.70502 0.58398 0.58631 125 125 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown bulk unknown unknown   Unknown 2016-03-15 Adult Adult Head Nervous System
40496 40496 SRR3195594 SRX1604653 SRS1314385 SRP070923 PRJNA313387 Transcriptomic of ß diketone antibiotics on zebrafish post a 3 month DKAs exposure. PRJNA313387 Other RNA libraries were constructed from control 6.25 and 12.5 mg/L treatment groups respectively. post DKAs exposure to 3 mpf zebrafish the whole transcriptome was determined.         zebrafish   strain:AB strain|isolate:Oregon State University|breed:Danio rerio|cultivar:not applicable|ecotype:Wild type|age:3 mpf|dev stage:3 mpf|sex:pooled male and female|tissue:we performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems.|BioSampleModel:Model organism or animal                 control CON 01 1 Zebrafish in control group were randomly selected post DKAs exposure at 90 dpf and rinsed with phosphorous buffer solution. We performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems. The retained tissues were used to extract total RNA according to the manufacturer's procedures. The quantity and purity of total RNA were analyzed by employing a Bioanalyzer 2100 and RNA 6000 Nano LabChipKit Agilent Santa Clara CA USA with RIN number >7.0. Poly A mRNA was isolated by poly T oligo attached magnetic beads Invitrogen. The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature. Then the final cDNA library was produced by the reverse transcription of the cleaved RNA fragments on the basis of the mRNA Seq sample preparation kit Illumina San Diego USA and the average 300±50 bp insert size was used for the paired end libraries. Finally the paired end sequencing was performed on an Illumina Hiseq2000/2500. Prior to assembly the low quality reads 1 reads containing sequencing adaptors; 2 reads containing sequencing primer; 3 nucleotide with q scores lower than 20 were removed. Next the cleaned and paired end reads were produced.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP070923     CON_01_Clean_Data2.fq.gz CON_01_Clean_Data1.fq.gz fastq fastq 8941582750.0 35766331.0 control 0:125 1:125 A:2282842470;C:2172817074;G:2169521320;T:2316254609;N:147277 125 125     2282842470 2172817074 2169521320 2316254609 147277 SRX1604653 SRS1314385 SRA359545 School of Life Sciences School of Life Sciences 2 0.62865 0.62758 0.22408 0.21961 0.7525 0.75024 0.5332 0.519 125 125 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown bulk unknown unknown   Unknown 2016-03-15 Adult Adult Head Nervous 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");;