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26 rows where experiment.library_selection = "cDNA", technology = "bulk" and tissue_curation = "Head"

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devstage_curation_coarse 2

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tissue_curation 1

  • Head · 26 ✖

technology 1

  • bulk · 26 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 26 ✖

experiment.library_layout 1

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
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
56512 56512 SRR10988549 SRX7649999 SRS6079496 SRP246053 PRJNA603897 Comparsion of transcriptome between slbp1 mutant and wildtype sibling GSE144517 Transcriptome Analysis The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.       head 2d rw440 sib3 GSM4289907   source name:head|tissue:Head|age:2dpf head 2d rw440 sib3 Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file head   Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Head|age:2dpf GSM4289907 GSM4289907: head 2d rw440 sib3; Danio rerio; RNA Seq GSM4289907   1 Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4289907 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP246053     2d_rw440_sib3_R2.fastq.gz 2d_rw440_sib3_R1.fastq.gz fastq fastq 3140682329.0 10457484.0 GSM4289907 r1 0:150.21 1:150.12 A:760684292;C:777389008;G:783922642;T:818121129;N:565258 150 150     760684292 777389008 783922642 818121129 565258 SRX7649999 SRS6079496 SRA1034453 GEO Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University 2 0.93527 0.95251 0.03293 0.02826 0.72032 0.73669 0.4787 0.47899 150 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   Japan 2020-01-30 Hatching Embryo Head Nervous System
56513 56513 SRR10988548 SRX7649998 SRS6079495 SRP246053 PRJNA603897 Comparsion of transcriptome between slbp1 mutant and wildtype sibling GSE144517 Transcriptome Analysis The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.       head 2d rw440 sib2 GSM4289906   source name:head|tissue:Head|age:2dpf head 2d rw440 sib2 Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file head   Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Head|age:2dpf GSM4289906 GSM4289906: head 2d rw440 sib2; Danio rerio; RNA Seq GSM4289906   1 Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4289906 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP246053     2d_rw440_sib2_R1.fastq.gz 2d_rw440_sib2_R2.fastq.gz fastq fastq 3194598681.0 10634398.0 GSM4289906 r1 0:150.24 1:150.17 A:771547062;C:789590364;G:796831526;T:835985747;N:643982 150 150     771547062 789590364 796831526 835985747 643982 SRX7649998 SRS6079495 SRA1034453 GEO Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University 2 0.93377 0.95416 0.02628 0.02182 0.72989 0.74805 0.46631 0.47654 149 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   Japan 2020-01-30 Hatching Embryo Head Nervous System
56514 56514 SRR10988547 SRX7649997 SRS6079494 SRP246053 PRJNA603897 Comparsion of transcriptome between slbp1 mutant and wildtype sibling GSE144517 Transcriptome Analysis The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.       head 2d rw440 sib1 GSM4289905   source name:head|tissue:Head|age:2dpf head 2d rw440 sib1 Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file head   Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Head|age:2dpf GSM4289905 GSM4289905: head 2d rw440 sib1; Danio rerio; RNA Seq GSM4289905   1 Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4289905 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP246053     2d_rw440_sib1_R1.fastq.gz 2d_rw440_sib1_R2.fastq.gz fastq fastq 2654979688.0 8840507.0 GSM4289905 r1 0:150.19 1:150.13 A:624000299;C:675145222;G:678635011;T:676731946;N:467210 150 150     624000299 675145222 678635011 676731946 467210 SRX7649997 SRS6079494 SRA1034453 GEO Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University 2 0.9317 0.94861 0.06364 0.05753 0.72811 0.75055 0.50771 0.52256 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   Japan 2020-01-30 Hatching Embryo Head Nervous System
56515 56515 SRR10988546 SRX7649996 SRS6079493 SRP246053 PRJNA603897 Comparsion of transcriptome between slbp1 mutant and wildtype sibling GSE144517 Transcriptome Analysis The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.       head 2d rw440 mut3 GSM4289904   source name:head|tissue:Head|age:2dpf / head 2d rw440 mut3 Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file head   Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Head|age:2dpf / GSM4289904 GSM4289904: head 2d rw440 mut3; Danio rerio; RNA Seq GSM4289904   1 Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4289904 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP246053     2d_rw440_mut3_R1.fastq.gz 2d_rw440_mut3_R2.fastq.gz fastq fastq 3282506507.0 10958106.0 GSM4289904 r1 0:149.81 1:149.74 A:781014809;C:816143245;G:824711112;T:858035111;N:2602230 149 149     781014809 816143245 824711112 858035111 2602230 SRX7649996 SRS6079493 SRA1034453 GEO Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University 2 0.93293 0.95901 0.02641 0.023 0.74408 0.76449 0.48032 0.475 151 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   Japan 2020-01-30 Hatching Embryo Head Nervous System
56516 56516 SRR10988545 SRX7649995 SRS6079492 SRP246053 PRJNA603897 Comparsion of transcriptome between slbp1 mutant and wildtype sibling GSE144517 Transcriptome Analysis The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.       head 2d rw440 mut2 GSM4289903   source name:head|tissue:Head|age:2dpf / head 2d rw440 mut2 Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file head   Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Head|age:2dpf / GSM4289903 GSM4289903: head 2d rw440 mut2; Danio rerio; RNA Seq GSM4289903   1 Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4289903 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP246053     2d_rw440_mut2_R2.fastq.gz 2d_rw440_mut2_R1.fastq.gz fastq fastq 2673347852.0 8908620.0 GSM4289903 r1 0:150.07 1:150.01 A:641733072;C:667262119;G:672992510;T:690242042;N:1118109 150 150     641733072 667262119 672992510 690242042 1118109 SRX7649995 SRS6079492 SRA1034453 GEO Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University 2 0.93754 0.95755 0.03962 0.0352 0.72234 0.73963 0.47668 0.49072 151 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   Japan 2020-01-30 Hatching Embryo Head Nervous System
56517 56517 SRR10988544 SRX7649994 SRS6079491 SRP246053 PRJNA603897 Comparsion of transcriptome between slbp1 mutant and wildtype sibling GSE144517 Transcriptome Analysis The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.       head 2d rw440 mut1 GSM4289902   source name:head|tissue:Head|age:2dpf / head 2d rw440 mut1 Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file head   Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Head|age:2dpf / GSM4289902 GSM4289902: head 2d rw440 mut1; Danio rerio; RNA Seq GSM4289902   1 Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM4289902 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP246053     2d_rw440_mut1_R1.fastq.gz 2d_rw440_mut1_R2.fastq.gz fastq fastq 2609801785.0 8695280.0 GSM4289902 r1 0:150.10 1:150.04 A:629026157;C:649393814;G:654616712;T:676204104;N:560998 150 150     629026157 649393814 654616712 676204104 560998 SRX7649994 SRS6079491 SRA1034453 GEO Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University 2 0.93478 0.95296 0.02959 0.0259 0.72458 0.74209 0.4765 0.47804 151 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   Japan 2020-01-30 Hatching Embryo Head Nervous System
71602 71602 SRR21782740 SRX17777236 SRS15303489 SRP400712 PRJNA886442 Tulp1 deficiency causes early onset retinal degeneration through affecting ciliogenesis and activating ferroptosis in zebrafish GSE214642 Transcriptome Analysis Mutations in TUB like protein 1 TULP1 are associated with severe early onset retinal degeneration in humans. However the pathogenesis remains largely unknown. There are two homologous genes of TULP1 in zebrafish namely tulp1a and tulp1b. Here we generated the single knockout tulp1a / and tulp1b / and double knockout tulp1 dKO models in zebrafish. Knockout of tulp1a results in the mislocalization of UV cone opsins and the degeneration of UV cones specifically while knockout of tulp1b results in mislocalization of rod opsins and rod cone degeneration. In the tulp1 dKO zebrafish mislocalization of opsins was present in all types of photoreceptors and severe degeneration was observed at a very early age mimicking the clinical manifestations of TULP1 patients. Photoreceptor cilium length was significantly reduced in the tulp1 dKO retinas. RNA seq analysis showed that the expression of tektin2 tekt2 a ciliary and flagellar microtubule structural component was downregulated in the tulp1 dKO zebrafish. Dual luciferase reporter assay suggested that Tulp1a and Tulp1b transcriptionally activate the promoter of tekt2. Additionally ferroptosis might be activated in the tulp1 dKO zebrafish as suggested by the up regulation of genes related to the ferroptosis pathway the shrinkage of mitochondria reduction or disappearance of mitochondria cristae and the iron and lipid droplet deposition in the retina of tulp1 dKO zebrafish. In conclusion our study establishes an appropriate zebrafish model for TULP1 associated retinal degeneration and proposes that loss of TULP1 causes defects in cilia structure and opsin trafficking through the downregulation of tekt2 which further increases the death of photoreceptors via ferroptosis. These findings offer insight into the pathogenesis and clinical treatment of early onset retinal degeneration. Overall design: Comparative gene expression profiling analysis of RNA seq data for wt and tulp1a&tulp1b zebrafish.   pubmed:36396940   T1a1b3 GSM6613557   source name:head|tissue:head|strain:AB|genotype:tulp1a&tulp1b knockout|developmental stage:4 dpf T1a1b3 Illumina Novaseq 6000 software used for basecalling. Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing poly N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Index of the reference genome was built using Hisat2 and paired end clean reads were aligned to the reference genome using Hisat2. TPM conversion was performed to obtain the standardized gene/transcript expression level. Assembly: GRCz11 Supplementary files format and content: * TPM.csv: Comma separated text files include TPM values. head   The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.   tissue:head|strain:AB|genotype:tulp1a&tulp1b knockout|developmental stage:4 dpf GSM6613557 GSM6613557: T1a1b3; Danio rerio; RNA Seq GSM6613557 r1 GSM6613557 1 The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP400712     L1EFA141680_T1a1b3.R1.raw.fastq.gz L1EFA141680_T1a1b3.R2.raw.fastq.gz fastq fastq 7320211824.0 24239112.0 GSM6613557 r1 0:151 1:151 A:1974398373;C:1670612801;G:1725496307;T:1949633870;N:70473 151 151     1974398373 1670612801 1725496307 1949633870 70473 SRX17777236 SRS15303489 SRA1511428 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.92785 0.92874 0.11839 0.11826 0.64346 0.64407 0.47262 0.47097 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   China 2022-10-02 Larval Larval Head Nervous System
71603 71603 SRR21782741 SRX17777235 SRS15303488 SRP400712 PRJNA886442 Tulp1 deficiency causes early onset retinal degeneration through affecting ciliogenesis and activating ferroptosis in zebrafish GSE214642 Transcriptome Analysis Mutations in TUB like protein 1 TULP1 are associated with severe early onset retinal degeneration in humans. However the pathogenesis remains largely unknown. There are two homologous genes of TULP1 in zebrafish namely tulp1a and tulp1b. Here we generated the single knockout tulp1a / and tulp1b / and double knockout tulp1 dKO models in zebrafish. Knockout of tulp1a results in the mislocalization of UV cone opsins and the degeneration of UV cones specifically while knockout of tulp1b results in mislocalization of rod opsins and rod cone degeneration. In the tulp1 dKO zebrafish mislocalization of opsins was present in all types of photoreceptors and severe degeneration was observed at a very early age mimicking the clinical manifestations of TULP1 patients. Photoreceptor cilium length was significantly reduced in the tulp1 dKO retinas. RNA seq analysis showed that the expression of tektin2 tekt2 a ciliary and flagellar microtubule structural component was downregulated in the tulp1 dKO zebrafish. Dual luciferase reporter assay suggested that Tulp1a and Tulp1b transcriptionally activate the promoter of tekt2. Additionally ferroptosis might be activated in the tulp1 dKO zebrafish as suggested by the up regulation of genes related to the ferroptosis pathway the shrinkage of mitochondria reduction or disappearance of mitochondria cristae and the iron and lipid droplet deposition in the retina of tulp1 dKO zebrafish. In conclusion our study establishes an appropriate zebrafish model for TULP1 associated retinal degeneration and proposes that loss of TULP1 causes defects in cilia structure and opsin trafficking through the downregulation of tekt2 which further increases the death of photoreceptors via ferroptosis. These findings offer insight into the pathogenesis and clinical treatment of early onset retinal degeneration. Overall design: Comparative gene expression profiling analysis of RNA seq data for wt and tulp1a&tulp1b zebrafish.   pubmed:36396940   T1a1b2 GSM6613556   source name:head|tissue:head|strain:AB|genotype:tulp1a&tulp1b knockout|developmental stage:4 dpf T1a1b2 Illumina Novaseq 6000 software used for basecalling. Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing poly N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Index of the reference genome was built using Hisat2 and paired end clean reads were aligned to the reference genome using Hisat2. TPM conversion was performed to obtain the standardized gene/transcript expression level. Assembly: GRCz11 Supplementary files format and content: * TPM.csv: Comma separated text files include TPM values. head   The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.   tissue:head|strain:AB|genotype:tulp1a&tulp1b knockout|developmental stage:4 dpf GSM6613556 GSM6613556: T1a1b2; Danio rerio; RNA Seq GSM6613556 r1 GSM6613556 1 The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP400712     L1EFA141679_T1a1b2.R1.raw.fastq.gz L1EFA141679_T1a1b2.R2.raw.fastq.gz fastq fastq 6606080578.0 21874439.0 GSM6613556 r1 0:151 1:151 A:1779483455;C:1510543058;G:1560971108;T:1755011649;N:71308 151 151     1779483455 1510543058 1560971108 1755011649 71308 SRX17777235 SRS15303488 SRA1511428 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.93096 0.93222 0.11127 0.11166 0.64731 0.64737 0.47921 0.47907 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   China 2022-10-02 Larval Larval Head Nervous System
71604 71604 SRR21782742 SRX17777234 SRS15303487 SRP400712 PRJNA886442 Tulp1 deficiency causes early onset retinal degeneration through affecting ciliogenesis and activating ferroptosis in zebrafish GSE214642 Transcriptome Analysis Mutations in TUB like protein 1 TULP1 are associated with severe early onset retinal degeneration in humans. However the pathogenesis remains largely unknown. There are two homologous genes of TULP1 in zebrafish namely tulp1a and tulp1b. Here we generated the single knockout tulp1a / and tulp1b / and double knockout tulp1 dKO models in zebrafish. Knockout of tulp1a results in the mislocalization of UV cone opsins and the degeneration of UV cones specifically while knockout of tulp1b results in mislocalization of rod opsins and rod cone degeneration. In the tulp1 dKO zebrafish mislocalization of opsins was present in all types of photoreceptors and severe degeneration was observed at a very early age mimicking the clinical manifestations of TULP1 patients. Photoreceptor cilium length was significantly reduced in the tulp1 dKO retinas. RNA seq analysis showed that the expression of tektin2 tekt2 a ciliary and flagellar microtubule structural component was downregulated in the tulp1 dKO zebrafish. Dual luciferase reporter assay suggested that Tulp1a and Tulp1b transcriptionally activate the promoter of tekt2. Additionally ferroptosis might be activated in the tulp1 dKO zebrafish as suggested by the up regulation of genes related to the ferroptosis pathway the shrinkage of mitochondria reduction or disappearance of mitochondria cristae and the iron and lipid droplet deposition in the retina of tulp1 dKO zebrafish. In conclusion our study establishes an appropriate zebrafish model for TULP1 associated retinal degeneration and proposes that loss of TULP1 causes defects in cilia structure and opsin trafficking through the downregulation of tekt2 which further increases the death of photoreceptors via ferroptosis. These findings offer insight into the pathogenesis and clinical treatment of early onset retinal degeneration. Overall design: Comparative gene expression profiling analysis of RNA seq data for wt and tulp1a&tulp1b zebrafish.   pubmed:36396940   T1a1b1 GSM6613555   source name:head|tissue:head|strain:AB|genotype:tulp1a&tulp1b knockout|developmental stage:4 dpf T1a1b1 Illumina Novaseq 6000 software used for basecalling. Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing poly N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Index of the reference genome was built using Hisat2 and paired end clean reads were aligned to the reference genome using Hisat2. TPM conversion was performed to obtain the standardized gene/transcript expression level. Assembly: GRCz11 Supplementary files format and content: * TPM.csv: Comma separated text files include TPM values. head   The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.   tissue:head|strain:AB|genotype:tulp1a&tulp1b knockout|developmental stage:4 dpf GSM6613555 GSM6613555: T1a1b1; Danio rerio; RNA Seq GSM6613555 r1 GSM6613555 1 The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP400712     L1EFA141678_T1a1b1.R1.raw.fastq.gz L1EFA141678_T1a1b1.R2.raw.fastq.gz fastq fastq 7890421044.0 26127222.0 GSM6613555 r1 0:151 1:151 A:2109953282;C:1817588024;G:1888600765;T:2074199840;N:79133 151 151     2109953282 1817588024 1888600765 2074199840 79133 SRX17777234 SRS15303487 SRA1511428 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.93144 0.93187 0.10756 0.1074 0.6546 0.65451 0.47652 0.47713 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   China 2022-10-02 Larval Larval Head Nervous System
71605 71605 SRR21782743 SRX17777233 SRS15303486 SRP400712 PRJNA886442 Tulp1 deficiency causes early onset retinal degeneration through affecting ciliogenesis and activating ferroptosis in zebrafish GSE214642 Transcriptome Analysis Mutations in TUB like protein 1 TULP1 are associated with severe early onset retinal degeneration in humans. However the pathogenesis remains largely unknown. There are two homologous genes of TULP1 in zebrafish namely tulp1a and tulp1b. Here we generated the single knockout tulp1a / and tulp1b / and double knockout tulp1 dKO models in zebrafish. Knockout of tulp1a results in the mislocalization of UV cone opsins and the degeneration of UV cones specifically while knockout of tulp1b results in mislocalization of rod opsins and rod cone degeneration. In the tulp1 dKO zebrafish mislocalization of opsins was present in all types of photoreceptors and severe degeneration was observed at a very early age mimicking the clinical manifestations of TULP1 patients. Photoreceptor cilium length was significantly reduced in the tulp1 dKO retinas. RNA seq analysis showed that the expression of tektin2 tekt2 a ciliary and flagellar microtubule structural component was downregulated in the tulp1 dKO zebrafish. Dual luciferase reporter assay suggested that Tulp1a and Tulp1b transcriptionally activate the promoter of tekt2. Additionally ferroptosis might be activated in the tulp1 dKO zebrafish as suggested by the up regulation of genes related to the ferroptosis pathway the shrinkage of mitochondria reduction or disappearance of mitochondria cristae and the iron and lipid droplet deposition in the retina of tulp1 dKO zebrafish. In conclusion our study establishes an appropriate zebrafish model for TULP1 associated retinal degeneration and proposes that loss of TULP1 causes defects in cilia structure and opsin trafficking through the downregulation of tekt2 which further increases the death of photoreceptors via ferroptosis. These findings offer insight into the pathogenesis and clinical treatment of early onset retinal degeneration. Overall design: Comparative gene expression profiling analysis of RNA seq data for wt and tulp1a&tulp1b zebrafish.   pubmed:36396940   WT3 GSM6613554   source name:head|tissue:head|strain:AB|genotype:wild type|developmental stage:4 dpf WT3 Illumina Novaseq 6000 software used for basecalling. Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing poly N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Index of the reference genome was built using Hisat2 and paired end clean reads were aligned to the reference genome using Hisat2. TPM conversion was performed to obtain the standardized gene/transcript expression level. Assembly: GRCz11 Supplementary files format and content: * TPM.csv: Comma separated text files include TPM values. head   The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.   tissue:head|strain:AB|genotype:wild type|developmental stage:4 dpf GSM6613554 GSM6613554: WT3; Danio rerio; RNA Seq GSM6613554 r1 GSM6613554 1 The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP400712     L1EFA141671_WT3.R1.raw.fastq.gz L1EFA141671_WT3.R2.raw.fastq.gz fastq fastq 6857606110.0 22707305.0 GSM6613554 r1 0:151 1:151 A:1855535051;C:1560967765;G:1614321395;T:1826715938;N:65961 151 151     1855535051 1560967765 1614321395 1826715938 65961 SRX17777233 SRS15303486 SRA1511428 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.92972 0.9306 0.11517 0.11512 0.65253 0.65242 0.47907 0.47833 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   China 2022-10-02 Larval Larval Head Nervous System
71606 71606 SRR21782744 SRX17777232 SRS15303484 SRP400712 PRJNA886442 Tulp1 deficiency causes early onset retinal degeneration through affecting ciliogenesis and activating ferroptosis in zebrafish GSE214642 Transcriptome Analysis Mutations in TUB like protein 1 TULP1 are associated with severe early onset retinal degeneration in humans. However the pathogenesis remains largely unknown. There are two homologous genes of TULP1 in zebrafish namely tulp1a and tulp1b. Here we generated the single knockout tulp1a / and tulp1b / and double knockout tulp1 dKO models in zebrafish. Knockout of tulp1a results in the mislocalization of UV cone opsins and the degeneration of UV cones specifically while knockout of tulp1b results in mislocalization of rod opsins and rod cone degeneration. In the tulp1 dKO zebrafish mislocalization of opsins was present in all types of photoreceptors and severe degeneration was observed at a very early age mimicking the clinical manifestations of TULP1 patients. Photoreceptor cilium length was significantly reduced in the tulp1 dKO retinas. RNA seq analysis showed that the expression of tektin2 tekt2 a ciliary and flagellar microtubule structural component was downregulated in the tulp1 dKO zebrafish. Dual luciferase reporter assay suggested that Tulp1a and Tulp1b transcriptionally activate the promoter of tekt2. Additionally ferroptosis might be activated in the tulp1 dKO zebrafish as suggested by the up regulation of genes related to the ferroptosis pathway the shrinkage of mitochondria reduction or disappearance of mitochondria cristae and the iron and lipid droplet deposition in the retina of tulp1 dKO zebrafish. In conclusion our study establishes an appropriate zebrafish model for TULP1 associated retinal degeneration and proposes that loss of TULP1 causes defects in cilia structure and opsin trafficking through the downregulation of tekt2 which further increases the death of photoreceptors via ferroptosis. These findings offer insight into the pathogenesis and clinical treatment of early onset retinal degeneration. Overall design: Comparative gene expression profiling analysis of RNA seq data for wt and tulp1a&tulp1b zebrafish.   pubmed:36396940   WT2 GSM6613553   source name:head|tissue:head|strain:AB|genotype:wild type|developmental stage:4 dpf WT2 Illumina Novaseq 6000 software used for basecalling. Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing poly N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Index of the reference genome was built using Hisat2 and paired end clean reads were aligned to the reference genome using Hisat2. TPM conversion was performed to obtain the standardized gene/transcript expression level. Assembly: GRCz11 Supplementary files format and content: * TPM.csv: Comma separated text files include TPM values. head   The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.   tissue:head|strain:AB|genotype:wild type|developmental stage:4 dpf GSM6613553 GSM6613553: WT2; Danio rerio; RNA Seq GSM6613553 r1 GSM6613553 1 The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP400712     L1EFA141670_WT2.R1.raw.fastq.gz L1EFA141670_WT2.R2.raw.fastq.gz fastq fastq 7061842972.0 23383586.0 GSM6613553 r1 0:151 1:151 A:1907854542;C:1612982080;G:1662929719;T:1878005269;N:71362 151 151     1907854542 1612982080 1662929719 1878005269 71362 SRX17777232 SRS15303484 SRA1511428 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.92374 0.92483 0.11424 0.11489 0.64709 0.6481 0.47529 0.47507 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   China 2022-10-02 Larval Larval Head Nervous System
71607 71607 SRR21782745 SRX17777231 SRS15303485 SRP400712 PRJNA886442 Tulp1 deficiency causes early onset retinal degeneration through affecting ciliogenesis and activating ferroptosis in zebrafish GSE214642 Transcriptome Analysis Mutations in TUB like protein 1 TULP1 are associated with severe early onset retinal degeneration in humans. However the pathogenesis remains largely unknown. There are two homologous genes of TULP1 in zebrafish namely tulp1a and tulp1b. Here we generated the single knockout tulp1a / and tulp1b / and double knockout tulp1 dKO models in zebrafish. Knockout of tulp1a results in the mislocalization of UV cone opsins and the degeneration of UV cones specifically while knockout of tulp1b results in mislocalization of rod opsins and rod cone degeneration. In the tulp1 dKO zebrafish mislocalization of opsins was present in all types of photoreceptors and severe degeneration was observed at a very early age mimicking the clinical manifestations of TULP1 patients. Photoreceptor cilium length was significantly reduced in the tulp1 dKO retinas. RNA seq analysis showed that the expression of tektin2 tekt2 a ciliary and flagellar microtubule structural component was downregulated in the tulp1 dKO zebrafish. Dual luciferase reporter assay suggested that Tulp1a and Tulp1b transcriptionally activate the promoter of tekt2. Additionally ferroptosis might be activated in the tulp1 dKO zebrafish as suggested by the up regulation of genes related to the ferroptosis pathway the shrinkage of mitochondria reduction or disappearance of mitochondria cristae and the iron and lipid droplet deposition in the retina of tulp1 dKO zebrafish. In conclusion our study establishes an appropriate zebrafish model for TULP1 associated retinal degeneration and proposes that loss of TULP1 causes defects in cilia structure and opsin trafficking through the downregulation of tekt2 which further increases the death of photoreceptors via ferroptosis. These findings offer insight into the pathogenesis and clinical treatment of early onset retinal degeneration. Overall design: Comparative gene expression profiling analysis of RNA seq data for wt and tulp1a&tulp1b zebrafish.   pubmed:36396940   WT1 GSM6613552   source name:head|tissue:head|strain:AB|genotype:wild type|developmental stage:4 dpf WT1 Illumina Novaseq 6000 software used for basecalling. Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing poly N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Index of the reference genome was built using Hisat2 and paired end clean reads were aligned to the reference genome using Hisat2. TPM conversion was performed to obtain the standardized gene/transcript expression level. Assembly: GRCz11 Supplementary files format and content: * TPM.csv: Comma separated text files include TPM values. head   The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.   tissue:head|strain:AB|genotype:wild type|developmental stage:4 dpf GSM6613552 GSM6613552: WT1; Danio rerio; RNA Seq GSM6613552 r1 GSM6613552 1 The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP400712     L1EFA141669_WT1.R1.raw.fastq.gz L1EFA141669_WT1.R2.raw.fastq.gz fastq fastq 7238862688.0 23969744.0 GSM6613552 r1 0:151 1:151 A:1972024445;C:1640211955;G:1685856317;T:1940696938;N:73033 151 151     1972024445 1640211955 1685856317 1940696938 73033 SRX17777231 SRS15303485 SRA1511428 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.9253 0.92638 0.11986 0.11995 0.6521 0.6519 0.47312 0.47348 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk bulk bulk   China 2022-10-02 Larval Larval Head Nervous System
75093 75093 SRR24239718 SRX20035841 SRS17374856 SRP433739 PRJNA958104 The secreted neuronal signal Spock1 regulates the blood brain barrier GSE230236 Transcriptome Analysis The blood brain barrier BBB is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally expressed Spock1 is cell non autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix ECM increased endothelial transcytosis and altered pericyte endothelial interactions. Furthermore a single dose of recombinant SPOCK1 into spock1 mutants quenches gelatinase activity restores vascular expression of BBB genes including mcamb and partially restores barrier function. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM thereby regulating pericyte endothelial interactions and downstream vascular gene expression. Overall design: Bulk RNAseq Libraries 66 71 of leaky mutant and wild type siblings to identify the genetic lesion responsible for the leaky phenotype. These analyses revealed linkage to chr14 and more specifically to the spock1 gene. scRNAseq Library scDRBrain of dissected spock1 mutant and wild type brains was then used to identify all cell type specific changes in gene expression in the mutant background.   pubmed:37437574   pooled hm41 mutant heads 5dpf [MUT 71] GSM7208219   tissue:mixed|cell type:mixed|genotype:hm41|time:5 dpf|geo loc name:missing|collection date:missing pooled hm41 mutant heads 5dpf [MUT 71] CLC Genomics Workbench v 11.0.1 Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter Quality limit: 0.05 Trimmed sequence reads were mapped to GRCz11 using tophat and bowtie2 with default parameters. Read counts were generated using rsem Assembly: GRCz11 Supplementary files format and content: The gene counts matrix is an output from rsem differential gene expression analysis and is a raw counts estimate not normalized for each gene. The first column is gene name and then post that each column represents an individual sample WT for the first 3 and then MUT for the last 3. Supplementary files format and content: The h5ad file contains the counts matrix for the demultiplexed single cell data. This file also holds relevant genotype and timepoint annotations as well as Multi seq barcode counts for each cell. mixed   RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.   cell type:mixed|genotype:hm41|time:5 dpf GSM7208219 GSM7208219: pooled hm41 mutant heads 5dpf [MUT 71]; Danio rerio; RNA Seq GSM7208219 r1 GSM7208219 1 RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP433739     MUT_71_1.fastq.gz MUT_71_2.fastq.gz fastq fastq 4611773700.0 30745158.0 GSM7208219 r1 0:75 1:75 A:1108714731;C:1198668257;G:1217612760;T:1086757260;N:20692 75 75     1108714731 1198668257 1217612760 1086757260 20692 SRX20035841 SRS17374856 SRA1728506 Megason Lab, Systems Biology, Harvard Medical School Megason Lab, Systems Biology, Harvard Medical School 2 0.99882 0.99887 0.2924 0.28775 0.91796 0.91717 0.75416 0.7594 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   United States 2023-04-21 Larval Larval Head Nervous System
75094 75094 SRR24239719 SRX20035840 SRS17374855 SRP433739 PRJNA958104 The secreted neuronal signal Spock1 regulates the blood brain barrier GSE230236 Transcriptome Analysis The blood brain barrier BBB is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally expressed Spock1 is cell non autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix ECM increased endothelial transcytosis and altered pericyte endothelial interactions. Furthermore a single dose of recombinant SPOCK1 into spock1 mutants quenches gelatinase activity restores vascular expression of BBB genes including mcamb and partially restores barrier function. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM thereby regulating pericyte endothelial interactions and downstream vascular gene expression. Overall design: Bulk RNAseq Libraries 66 71 of leaky mutant and wild type siblings to identify the genetic lesion responsible for the leaky phenotype. These analyses revealed linkage to chr14 and more specifically to the spock1 gene. scRNAseq Library scDRBrain of dissected spock1 mutant and wild type brains was then used to identify all cell type specific changes in gene expression in the mutant background.   pubmed:37437574   pooled hm41 mutant heads 5dpf [MUT 70] GSM7208218   tissue:mixed|cell type:mixed|genotype:hm41|time:5 dpf|geo loc name:missing|collection date:missing pooled hm41 mutant heads 5dpf [MUT 70] CLC Genomics Workbench v 11.0.1 Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter Quality limit: 0.05 Trimmed sequence reads were mapped to GRCz11 using tophat and bowtie2 with default parameters. Read counts were generated using rsem Assembly: GRCz11 Supplementary files format and content: The gene counts matrix is an output from rsem differential gene expression analysis and is a raw counts estimate not normalized for each gene. The first column is gene name and then post that each column represents an individual sample WT for the first 3 and then MUT for the last 3. Supplementary files format and content: The h5ad file contains the counts matrix for the demultiplexed single cell data. This file also holds relevant genotype and timepoint annotations as well as Multi seq barcode counts for each cell. mixed   RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.   cell type:mixed|genotype:hm41|time:5 dpf GSM7208218 GSM7208218: pooled hm41 mutant heads 5dpf [MUT 70]; Danio rerio; RNA Seq GSM7208218 r1 GSM7208218 1 RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP433739     MUT_70_2.fastq.gz MUT_70_1.fastq.gz fastq fastq 8194819050.0 54632127.0 GSM7208218 r1 0:75 1:75 A:1987080766;C:2124464685;G:2128760128;T:1954476175;N:37296 75 75     1987080766 2124464685 2128760128 1954476175 37296 SRX20035840 SRS17374855 SRA1728506 Megason Lab, Systems Biology, Harvard Medical School Megason Lab, Systems Biology, Harvard Medical School 2 0.99319 0.99856 0.28014 0.28098 0.90816 0.9083 0.75379 0.72377 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   United States 2023-04-21 Larval Larval Head Nervous System
75095 75095 SRR24239720 SRX20035839 SRS17374854 SRP433739 PRJNA958104 The secreted neuronal signal Spock1 regulates the blood brain barrier GSE230236 Transcriptome Analysis The blood brain barrier BBB is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally expressed Spock1 is cell non autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix ECM increased endothelial transcytosis and altered pericyte endothelial interactions. Furthermore a single dose of recombinant SPOCK1 into spock1 mutants quenches gelatinase activity restores vascular expression of BBB genes including mcamb and partially restores barrier function. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM thereby regulating pericyte endothelial interactions and downstream vascular gene expression. Overall design: Bulk RNAseq Libraries 66 71 of leaky mutant and wild type siblings to identify the genetic lesion responsible for the leaky phenotype. These analyses revealed linkage to chr14 and more specifically to the spock1 gene. scRNAseq Library scDRBrain of dissected spock1 mutant and wild type brains was then used to identify all cell type specific changes in gene expression in the mutant background.   pubmed:37437574   pooled hm41 mutant heads 5dpf [MUT 69] GSM7208217   tissue:mixed|cell type:mixed|genotype:hm41|time:5 dpf|geo loc name:missing|collection date:missing pooled hm41 mutant heads 5dpf [MUT 69] CLC Genomics Workbench v 11.0.1 Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter Quality limit: 0.05 Trimmed sequence reads were mapped to GRCz11 using tophat and bowtie2 with default parameters. Read counts were generated using rsem Assembly: GRCz11 Supplementary files format and content: The gene counts matrix is an output from rsem differential gene expression analysis and is a raw counts estimate not normalized for each gene. The first column is gene name and then post that each column represents an individual sample WT for the first 3 and then MUT for the last 3. Supplementary files format and content: The h5ad file contains the counts matrix for the demultiplexed single cell data. This file also holds relevant genotype and timepoint annotations as well as Multi seq barcode counts for each cell. mixed   RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.   cell type:mixed|genotype:hm41|time:5 dpf GSM7208217 GSM7208217: pooled hm41 mutant heads 5dpf [MUT 69]; Danio rerio; RNA Seq GSM7208217 r1 GSM7208217 1 RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP433739     MUT_69_1.fastq.gz MUT_69_2.fastq.gz fastq fastq 3704639250.0 24697595.0 GSM7208217 r1 0:75 1:75 A:905076115;C:952799802;G:967859063;T:878887138;N:17132 75 75     905076115 952799802 967859063 878887138 17132 SRX20035839 SRS17374854 SRA1728506 Megason Lab, Systems Biology, Harvard Medical School Megason Lab, Systems Biology, Harvard Medical School 2 0.99504 0.99872 0.28829 0.28591 0.90425 0.90563 0.71452 0.7524 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   United States 2023-04-21 Larval Larval Head Nervous System
75096 75096 SRR24239721 SRX20035838 SRS17374853 SRP433739 PRJNA958104 The secreted neuronal signal Spock1 regulates the blood brain barrier GSE230236 Transcriptome Analysis The blood brain barrier BBB is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally expressed Spock1 is cell non autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix ECM increased endothelial transcytosis and altered pericyte endothelial interactions. Furthermore a single dose of recombinant SPOCK1 into spock1 mutants quenches gelatinase activity restores vascular expression of BBB genes including mcamb and partially restores barrier function. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM thereby regulating pericyte endothelial interactions and downstream vascular gene expression. Overall design: Bulk RNAseq Libraries 66 71 of leaky mutant and wild type siblings to identify the genetic lesion responsible for the leaky phenotype. These analyses revealed linkage to chr14 and more specifically to the spock1 gene. scRNAseq Library scDRBrain of dissected spock1 mutant and wild type brains was then used to identify all cell type specific changes in gene expression in the mutant background.   pubmed:37437574   pooled wild type heads 5dpf [WT 68] GSM7208216   tissue:mixed|cell type:mixed|genotype:WT|time:5 dpf|geo loc name:missing|collection date:missing pooled wild type heads 5dpf [WT 68] CLC Genomics Workbench v 11.0.1 Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter Quality limit: 0.05 Trimmed sequence reads were mapped to GRCz11 using tophat and bowtie2 with default parameters. Read counts were generated using rsem Assembly: GRCz11 Supplementary files format and content: The gene counts matrix is an output from rsem differential gene expression analysis and is a raw counts estimate not normalized for each gene. The first column is gene name and then post that each column represents an individual sample WT for the first 3 and then MUT for the last 3. Supplementary files format and content: The h5ad file contains the counts matrix for the demultiplexed single cell data. This file also holds relevant genotype and timepoint annotations as well as Multi seq barcode counts for each cell. mixed   RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.   cell type:mixed|genotype:WT|time:5 dpf GSM7208216 GSM7208216: pooled wild type heads 5dpf [WT 68]; Danio rerio; RNA Seq GSM7208216 r1 GSM7208216 1 RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP433739     WT_68_1.fastq.gz WT_68_2.fastq.gz fastq fastq 9128261550.0 60855077.0 GSM7208216 r1 0:75 1:75 A:2191591927;C:2372873993;G:2387623448;T:2176133105;N:39077 75 75     2191591927 2372873993 2387623448 2176133105 39077 SRX20035838 SRS17374853 SRA1728506 Megason Lab, Systems Biology, Harvard Medical School Megason Lab, Systems Biology, Harvard Medical School 2 0.98004 0.99895 0.25842 0.26643 0.91547 0.91634 0.75544 0.69499 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   United States 2023-04-21 Larval Larval Head Nervous System
75097 75097 SRR24239722 SRX20035837 SRS17374852 SRP433739 PRJNA958104 The secreted neuronal signal Spock1 regulates the blood brain barrier GSE230236 Transcriptome Analysis The blood brain barrier BBB is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally expressed Spock1 is cell non autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix ECM increased endothelial transcytosis and altered pericyte endothelial interactions. Furthermore a single dose of recombinant SPOCK1 into spock1 mutants quenches gelatinase activity restores vascular expression of BBB genes including mcamb and partially restores barrier function. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM thereby regulating pericyte endothelial interactions and downstream vascular gene expression. Overall design: Bulk RNAseq Libraries 66 71 of leaky mutant and wild type siblings to identify the genetic lesion responsible for the leaky phenotype. These analyses revealed linkage to chr14 and more specifically to the spock1 gene. scRNAseq Library scDRBrain of dissected spock1 mutant and wild type brains was then used to identify all cell type specific changes in gene expression in the mutant background.   pubmed:37437574   pooled wild type heads 5dpf [WT 67] GSM7208215   tissue:mixed|cell type:mixed|genotype:WT|time:5 dpf|geo loc name:missing|collection date:missing pooled wild type heads 5dpf [WT 67] CLC Genomics Workbench v 11.0.1 Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter Quality limit: 0.05 Trimmed sequence reads were mapped to GRCz11 using tophat and bowtie2 with default parameters. Read counts were generated using rsem Assembly: GRCz11 Supplementary files format and content: The gene counts matrix is an output from rsem differential gene expression analysis and is a raw counts estimate not normalized for each gene. The first column is gene name and then post that each column represents an individual sample WT for the first 3 and then MUT for the last 3. Supplementary files format and content: The h5ad file contains the counts matrix for the demultiplexed single cell data. This file also holds relevant genotype and timepoint annotations as well as Multi seq barcode counts for each cell. mixed   RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.   cell type:mixed|genotype:WT|time:5 dpf GSM7208215 GSM7208215: pooled wild type heads 5dpf [WT 67]; Danio rerio; RNA Seq GSM7208215 r1 GSM7208215 1 RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP433739     WT_67_1.fastq.gz WT_67_2.fastq.gz fastq fastq 4212400800.0 28082672.0 GSM7208215 r1 0:75 1:75 A:1024709764;C:1090887683;G:1098819017;T:997964994;N:19342 75 75     1024709764 1090887683 1098819017 997964994 19342 SRX20035837 SRS17374852 SRA1728506 Megason Lab, Systems Biology, Harvard Medical School Megason Lab, Systems Biology, Harvard Medical School 2 0.99585 0.99873 0.27061 0.26987 0.9274 0.92801 0.66832 0.75671 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   United States 2023-04-21 Larval Larval Head Nervous System
75098 75098 SRR24239723 SRX20035836 SRS17374851 SRP433739 PRJNA958104 The secreted neuronal signal Spock1 regulates the blood brain barrier GSE230236 Transcriptome Analysis The blood brain barrier BBB is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally expressed Spock1 is cell non autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix ECM increased endothelial transcytosis and altered pericyte endothelial interactions. Furthermore a single dose of recombinant SPOCK1 into spock1 mutants quenches gelatinase activity restores vascular expression of BBB genes including mcamb and partially restores barrier function. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM thereby regulating pericyte endothelial interactions and downstream vascular gene expression. Overall design: Bulk RNAseq Libraries 66 71 of leaky mutant and wild type siblings to identify the genetic lesion responsible for the leaky phenotype. These analyses revealed linkage to chr14 and more specifically to the spock1 gene. scRNAseq Library scDRBrain of dissected spock1 mutant and wild type brains was then used to identify all cell type specific changes in gene expression in the mutant background.   pubmed:37437574   pooled wild type heads 5dpf [WT 66] GSM7208214   tissue:mixed|cell type:mixed|genotype:WT|time:5 dpf|geo loc name:missing|collection date:missing pooled wild type heads 5dpf [WT 66] CLC Genomics Workbench v 11.0.1 Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter Quality limit: 0.05 Trimmed sequence reads were mapped to GRCz11 using tophat and bowtie2 with default parameters. Read counts were generated using rsem Assembly: GRCz11 Supplementary files format and content: The gene counts matrix is an output from rsem differential gene expression analysis and is a raw counts estimate not normalized for each gene. The first column is gene name and then post that each column represents an individual sample WT for the first 3 and then MUT for the last 3. Supplementary files format and content: The h5ad file contains the counts matrix for the demultiplexed single cell data. This file also holds relevant genotype and timepoint annotations as well as Multi seq barcode counts for each cell. mixed   RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.   cell type:mixed|genotype:WT|time:5 dpf GSM7208214 GSM7208214: pooled wild type heads 5dpf [WT 66]; Danio rerio; RNA Seq GSM7208214 r1 GSM7208214 1 RNA was harvested using Rneasy mini plus kit Qiagen. 2 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using Wafergen Directional RNA Seq Library Prep Kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP433739     WT_66_1.fastq.gz WT_66_2.fastq.gz fastq fastq 13769803650.0 91798691.0 GSM7208214 r1 0:75 1:75 A:3330889453;C:3582492274;G:3570565492;T:3285794864;N:61567 75 75     3330889453 3582492274 3570565492 3285794864 61567 SRX20035836 SRS17374851 SRA1728506 Megason Lab, Systems Biology, Harvard Medical School Megason Lab, Systems Biology, Harvard Medical School 2 0.99425 0.99897 0.2711 0.27032 0.93214 0.93233 0.7136 0.76396 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   United States 2023-04-21 Larval Larval 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");;