{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", technology = \"bulk\" and tissue_curation = \"Head\"", "rows": [[34192, "SRR31443228", "SRX26812023", "SRS23296672", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. 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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.", null, "pubmed:40066109", null, "Brain enriched  mtmr5 knockout  biol rep4", "GSM8811137", null, "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! 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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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", "Zebrafish AB strain were raised and maintained at 28.5\u00b0C 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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565999", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2025-02-24", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:40066109", null, "Brain enriched  mtmr5 knockout  biol rep3", "GSM8811136", null, "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", null, "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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", "Zebrafish AB strain were raised and maintained at 28.5\u00b0C 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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565999", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2025-02-24", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:40066109", null, "Brain enriched  mtmr5 knockout  biol rep2", "GSM8811135", null, "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", null, "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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", "Zebrafish AB strain were raised and maintained at 28.5\u00b0C 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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565999", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2025-02-24", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:40066109", null, "Brain enriched  mtmr5 knockout  biol rep1", "GSM8811134", null, "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", null, "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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", "Zebrafish AB strain were raised and maintained at 28.5\u00b0C 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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565999", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2025-02-24", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:40066109", null, "Brain enriched  wild type  biol rep4", "GSM8811133", null, "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", null, "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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", "Zebrafish AB strain were raised and maintained at 28.5\u00b0C 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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565999", null, null, "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, null, null, 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", null, "Canada", "2025-02-24", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:40066109", null, "Brain enriched  wild type  biol rep3", "GSM8811132", null, "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", null, "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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", "Zebrafish AB strain were raised and maintained at 28.5\u00b0C 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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565999", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2025-02-24", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:40066109", null, "Brain enriched  wild type  biol rep2", "GSM8811131", null, "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", null, "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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", "Zebrafish AB strain were raised and maintained at 28.5\u00b0C 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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565999", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Canada", "2025-02-24", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:40066109", null, "Brain enriched  wild type  biol rep1", "GSM8811130", null, "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", null, "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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", "Zebrafish AB strain were raised and maintained at 28.5\u00b0C 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\u2014Next Generation Sequencing Facility PGCRL  The Hospital for Sick Children  Toronto.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP565999", null, null, "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, null, null, 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", null, "Canada", "2025-02-24", "Larval", "Larval", "Head", "Nervous System"], [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.", null, null, null, "head  2d rw440 sib3", "GSM4289907", null, "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", null, "Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Head|age:2dpf", "GSM4289907", "GSM4289907: head  2d rw440 sib3; Danio rerio; RNA Seq", "GSM4289907", null, "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", null, "SRP246053", null, null, "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, null, null, 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", null, "Japan", "2020-01-30", "Hatching", "Embryo", "Head", "Nervous System"], [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.", null, null, null, "head  2d rw440 sib2", "GSM4289906", null, "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", null, "Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Head|age:2dpf", "GSM4289906", "GSM4289906: head  2d rw440 sib2; Danio rerio; RNA Seq", "GSM4289906", null, "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", null, "SRP246053", null, null, "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, null, null, 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", null, "Japan", "2020-01-30", "Hatching", "Embryo", "Head", "Nervous System"], [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.", null, null, null, "head  2d rw440 sib1", "GSM4289905", null, "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", null, "Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Head|age:2dpf", "GSM4289905", "GSM4289905: head  2d rw440 sib1; Danio rerio; RNA Seq", "GSM4289905", null, "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", null, "SRP246053", null, null, "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, null, null, 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", null, "Japan", "2020-01-30", "Hatching", "Embryo", "Head", "Nervous System"], [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.", null, null, null, "head  2d rw440 mut3", "GSM4289904", null, "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", null, "Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Head|age:2dpf / ", "GSM4289904", "GSM4289904: head  2d rw440 mut3; Danio rerio; RNA Seq", "GSM4289904", null, "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", null, "SRP246053", null, null, "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, null, null, 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", null, "Japan", "2020-01-30", "Hatching", "Embryo", "Head", "Nervous System"], [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.", null, null, null, "head  2d rw440 mut2", "GSM4289903", null, "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", null, "Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Head|age:2dpf / ", "GSM4289903", "GSM4289903: head  2d rw440 mut2; Danio rerio; RNA Seq", "GSM4289903", null, "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", null, "SRP246053", null, null, "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, null, null, 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", null, "Japan", "2020-01-30", "Hatching", "Embryo", "Head", "Nervous System"], [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.", null, null, null, "head  2d rw440 mut1", "GSM4289902", null, "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", null, "Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Head|age:2dpf / ", "GSM4289902", "GSM4289902: head  2d rw440 mut1; Danio rerio; RNA Seq", "GSM4289902", null, "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", null, "SRP246053", null, null, "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, null, null, 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", null, "Japan", "2020-01-30", "Hatching", "Embryo", "Head", "Nervous System"], [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.", null, "pubmed:36396940", null, "T1a1b3", "GSM6613557", null, "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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP400712", null, null, "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, null, null, 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", null, "China", "2022-10-02", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:36396940", null, "T1a1b2", "GSM6613556", null, "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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP400712", null, null, "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, null, null, 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", null, "China", "2022-10-02", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:36396940", null, "T1a1b1", "GSM6613555", null, "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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP400712", null, null, "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, null, null, 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", null, "China", "2022-10-02", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:36396940", null, "WT3", "GSM6613554", null, "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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP400712", null, null, "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, null, null, 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", null, "China", "2022-10-02", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:36396940", null, "WT2", "GSM6613553", null, "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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP400712", null, null, "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, null, null, 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", null, "China", "2022-10-02", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:36396940", null, "WT1", "GSM6613552", null, "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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP400712", null, null, "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, null, null, 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", null, "China", "2022-10-02", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:37437574", null, "pooled hm41 mutant heads  5dpf [MUT 71]", "GSM7208219", null, "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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP433739", null, null, "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, null, null, 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", null, "United States", "2023-04-21", "Larval", "Larval", "Head", "Nervous System"], [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.", null, "pubmed:37437574", null, "pooled hm41 mutant heads  5dpf [MUT 70]", "GSM7208218", null, "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", null, "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.", null, "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. 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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.", null, "pubmed:37437574", null, "pooled wild type heads  5dpf [WT 68]", "GSM7208216", null, "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. 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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.", null, "pubmed:37437574", null, "pooled wild type heads  5dpf [WT 67]", "GSM7208215", null, "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. 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