rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
44922,SRR6297670,SRX3398649,SRS2692829,SRP125098,PRJNA418729,The CCCH type zinc finger transcription factor Zc3h8 protects hepatocytes from degeneration by repressing the inflammatory response in zebrafish.,GSE106985,Transcriptome Analysis,Transcriptional profile of hepatocytes during the cq5 mutant liver degeneration middle stage 5.5 dpf  and later stage 7.5 dpf. Overall design: Examination of gene expression at two different stages for mutant sample group and wild type control group.,,,,D7.5MUT,GSM2858890,,source name:Hepatocytes|strain:ABGO|tissue:liver|developmental stage:7.5 dpf,D7.5MUT,Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.xls] tab delimited text file includes RPKMs for each Sample.  [Table s1.xls] foldChange between developmental stages in each genotype cells.,Hepatocytes,Choose two different stages 5.5 and 7.5 dpf  of zc3h8 /  mutant and wild type group larves which hepatocytes were markerd by Tglfabp:Dendra2 NTR transgenic line  and the zebrafish livers samples were respectively dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman.,Total RNA was harvested using Trizol reagent. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol.,,strain:ABGO|tissue:liver|developmental stage:7.5 dpf,GSM2858890,GSM2858890: D7.5MUT; Danio rerio; RNA Seq,GSM2858890,,1,Total RNA was harvested using Trizol reagent. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol.,GEO Accession:GSM2858890,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP125098,,,D7_5MUT1_R1.fq.gz D7_5MUT1_R2.fq.gz,fastq fastq,6317511200.0,31587556.0,GSM2858890 r1,0:100 1:100,A:1754225166;C:1427299863;G:1424315769;T:1697747107;N:13923295,100,100,,,1754225166,1427299863,1424315769,1697747107,13923295,SRX3398649,SRS2692829,SRA631311,GEO,Southwest university,2,0.85186,0.83894,0.11172,0.10823,0.82731,0.82852,0.60784,0.60651,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,China,2017-11-16,Larval,Larval,Liver,Liver and Biliary System
44923,SRR6297669,SRX3398648,SRS2692828,SRP125098,PRJNA418729,The CCCH type zinc finger transcription factor Zc3h8 protects hepatocytes from degeneration by repressing the inflammatory response in zebrafish.,GSE106985,Transcriptome Analysis,Transcriptional profile of hepatocytes during the cq5 mutant liver degeneration middle stage 5.5 dpf  and later stage 7.5 dpf. Overall design: Examination of gene expression at two different stages for mutant sample group and wild type control group.,,,,D7.5WT,GSM2858889,,source name:Hepatocytes|strain:ABGO|tissue:liver|developmental stage:7.5 dpf,D7.5WT,Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.xls] tab delimited text file includes RPKMs for each Sample.  [Table s1.xls] foldChange between developmental stages in each genotype cells.,Hepatocytes,Choose two different stages 5.5 and 7.5 dpf  of zc3h8 /  mutant and wild type group larves which hepatocytes were markerd by Tglfabp:Dendra2 NTR transgenic line  and the zebrafish livers samples were respectively dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman.,Total RNA was harvested using Trizol reagent. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol.,,strain:ABGO|tissue:liver|developmental stage:7.5 dpf,GSM2858889,GSM2858889: D7.5WT; Danio rerio; RNA Seq,GSM2858889,,1,Total RNA was harvested using Trizol reagent. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol.,GEO Accession:GSM2858889,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP125098,,,D7_5WT1_R1.fq.gz D7_5WT1_R2.fq.gz,fastq fastq,6300586000.0,31502930.0,GSM2858889 r1,,,,,,,,,,,,SRX3398648,SRS2692828,SRA631311,GEO,Southwest university,2,0.86687,0.85977,0.07521,0.07369,0.85871,0.85888,0.5932,0.59571,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,China,2017-11-16,Larval,Larval,Liver,Liver and Biliary System
44924,SRR6297668,SRX3398647,SRS2692827,SRP125098,PRJNA418729,The CCCH type zinc finger transcription factor Zc3h8 protects hepatocytes from degeneration by repressing the inflammatory response in zebrafish.,GSE106985,Transcriptome Analysis,Transcriptional profile of hepatocytes during the cq5 mutant liver degeneration middle stage 5.5 dpf  and later stage 7.5 dpf. Overall design: Examination of gene expression at two different stages for mutant sample group and wild type control group.,,,,D5.5MUT,GSM2858888,,source name:Hepatocytes|strain:ABGO|tissue:liver|developmental stage:5.5 dpf,D5.5MUT,Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.xls] tab delimited text file includes RPKMs for each Sample.  [Table s1.xls] foldChange between developmental stages in each genotype cells.,Hepatocytes,Choose two different stages 5.5 and 7.5 dpf  of zc3h8 /  mutant and wild type group larves which hepatocytes were markerd by Tglfabp:Dendra2 NTR transgenic line  and the zebrafish livers samples were respectively dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman.,Total RNA was harvested using Trizol reagent. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol.,,strain:ABGO|tissue:liver|developmental stage:5.5 dpf,GSM2858888,GSM2858888: D5.5MUT; Danio rerio; RNA Seq,GSM2858888,,1,Total RNA was harvested using Trizol reagent. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol.,GEO Accession:GSM2858888,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP125098,,,D5_5MUT1_R1.fq.gz D5_5MUT1_R2.fq.gz,fastq fastq,6393315400.0,31966577.0,GSM2858888 r1,0:100 1:100,A:1762470726;C:1454470731;G:1456571327;T:1712530332;N:7272284,100,100,,,1762470726,1454470731,1456571327,1712530332,7272284,SRX3398647,SRS2692827,SRA631311,GEO,Southwest university,2,0.86434,0.86515,0.06559,0.06514,0.84315,0.84275,0.57299,0.44229,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,China,2017-11-16,Larval,Larval,Liver,Liver and Biliary System
44925,SRR6297667,SRX3398646,SRS2692826,SRP125098,PRJNA418729,The CCCH type zinc finger transcription factor Zc3h8 protects hepatocytes from degeneration by repressing the inflammatory response in zebrafish.,GSE106985,Transcriptome Analysis,Transcriptional profile of hepatocytes during the cq5 mutant liver degeneration middle stage 5.5 dpf  and later stage 7.5 dpf. Overall design: Examination of gene expression at two different stages for mutant sample group and wild type control group.,,,,D5.5WT,GSM2858887,,source name:Hepatocytes|strain:ABGO|tissue:liver|developmental stage:5.5 dpf,D5.5WT,Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software  and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and |log2 ratio|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software These data were then subject to GO gene ontology  http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes  http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.xls] tab delimited text file includes RPKMs for each Sample.  [Table s1.xls] foldChange between developmental stages in each genotype cells.,Hepatocytes,Choose two different stages 5.5 and 7.5 dpf  of zc3h8 /  mutant and wild type group larves which hepatocytes were markerd by Tglfabp:Dendra2 NTR transgenic line  and the zebrafish livers samples were respectively dissected  collected  and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then  the supernatant was removed and the cell pellet was resuspended in PBS  followed by cell sorting by flow cytometry Moflo XDP  Beckman.,Total RNA was harvested using Trizol reagent. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol.,,strain:ABGO|tissue:liver|developmental stage:5.5 dpf,GSM2858887,GSM2858887: D5.5WT; Danio rerio; RNA Seq,GSM2858887,,1,Total RNA was harvested using Trizol reagent. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol.,GEO Accession:GSM2858887,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP125098,,,D5_5WT1_R1.fq.gz D5_5WT1_R2.fq.gz,fastq fastq,8603691600.0,43018458.0,GSM2858887 r1,0:100 1:100,A:2356107531;C:1974663463;G:1971836234;T:2292265726;N:8818646,100,100,,,2356107531,1974663463,1971836234,2292265726,8818646,SRX3398646,SRS2692826,SRA631311,GEO,Southwest university,2,0.92814,0.92445,0.06252,0.06384,0.82873,0.82911,0.57879,0.57933,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,China,2017-11-16,Larval,Larval,Liver,Liver and Biliary System
71957,SRR22143711,SRX18123007,SRS15624881,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf cavdra expt2 rep3,GSM6705365,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:ca vdra|time:96 hpf,hepatocytes 96hpf cavdra expt2 rep3,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:fabp10a:ca vdra|time:96 hpf,GSM6705365,GSM6705365: hepatocytes 96hpf cavdra expt2 rep3; Danio rerio; RNA Seq,GSM6705365 r1,GSM6705365,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405931,,,cavdra_expt2_rep3_R1.fastq.gz,fastq,6706002750.0,44706685.0,GSM6705365 r1,0:150 1:0,A:1750156238;C:1597023915;G:1614921548;T:1743765130;N:135919,150,0,,,1750156238,1597023915,1614921548,1743765130,135919,SRX18123007,SRS15624881,,,"Goessling Lab, Brigham and Women's Hospital",1,0.88313,,0.04409,,0.87661,,0.55505,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71958,SRR22143712,SRX18123006,SRS15624880,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf cavdra expt2 rep2,GSM6705364,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:ca vdra|time:96 hpf,hepatocytes 96hpf cavdra expt2 rep2,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:fabp10a:ca vdra|time:96 hpf,GSM6705364,GSM6705364: hepatocytes 96hpf cavdra expt2 rep2; Danio rerio; RNA Seq,GSM6705364 r1,GSM6705364,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405931,,,cavdra_expt2_rep2_R1.fastq.gz,fastq,7680154500.0,51201030.0,GSM6705364 r1,0:150 1:0,A:1982779701;C:1851808902;G:1881749764;T:1963662978;N:153155,150,0,,,1982779701,1851808902,1881749764,1963662978,153155,SRX18123006,SRS15624880,,,"Goessling Lab, Brigham and Women's Hospital",1,0.8513,,0.05087,,0.8756,,0.58342,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71959,SRR22143713,SRX18123005,SRS15624879,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf cavdra expt2 rep1,GSM6705363,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:ca vdra|time:96 hpf,hepatocytes 96hpf cavdra expt2 rep1,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:fabp10a:ca vdra|time:96 hpf,GSM6705363,GSM6705363: hepatocytes 96hpf cavdra expt2 rep1; Danio rerio; RNA Seq,GSM6705363 r1,GSM6705363,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405931,,,cavdra_expt2_rep1_R1.fastq.gz,fastq,8901213300.0,59341422.0,GSM6705363 r1,0:150 1:0,A:2306334188;C:2127419797;G:2168880418;T:2298400416;N:178481,150,0,,,2306334188,2127419797,2168880418,2298400416,178481,SRX18123005,SRS15624879,,,"Goessling Lab, Brigham and Women's Hospital",1,0.90473,,0.05586,,0.88347,,0.56493,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71960,SRR22143714,SRX18123004,SRS15624878,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf wt expt2 rep4,GSM6705362,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf,hepatocytes 96hpf wt expt2 rep4,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:wt|time:96 hpf,GSM6705362,GSM6705362: hepatocytes 96hpf wt expt2 rep4; Danio rerio; RNA Seq,GSM6705362 r1,GSM6705362,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405931,,,wt_expt2_rep4_R1.fastq.gz,fastq,11932077600.0,79547184.0,GSM6705362 r1,0:150 1:0,A:3141493904;C:2835740238;G:2863257406;T:3091339595;N:246457,150,0,,,3141493904,2835740238,2863257406,3091339595,246457,SRX18123004,SRS15624878,,,"Goessling Lab, Brigham and Women's Hospital",1,0.88366,,0.04537,,0.88185,,0.58207,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71961,SRR22143715,SRX18123003,SRS15624877,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf wt expt2 rep3,GSM6705361,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf,hepatocytes 96hpf wt expt2 rep3,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:wt|time:96 hpf,GSM6705361,GSM6705361: hepatocytes 96hpf wt expt2 rep3; Danio rerio; RNA Seq,GSM6705361 r1,GSM6705361,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405931,,,wt_expt2_rep3_R1.fastq.gz,fastq,9232946100.0,61552974.0,GSM6705361 r1,0:150 1:0,A:2407612258;C:2198887087;G:2229947120;T:2396306352;N:193283,150,0,,,2407612258,2198887087,2229947120,2396306352,193283,SRX18123003,SRS15624877,,,"Goessling Lab, Brigham and Women's Hospital",1,0.87181,,0.05876,,0.87864,,0.58855,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71962,SRR22143716,SRX18123002,SRS15624876,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf wt expt2 rep2,GSM6705360,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf,hepatocytes 96hpf wt expt2 rep2,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:wt|time:96 hpf,GSM6705360,GSM6705360: hepatocytes 96hpf wt expt2 rep2; Danio rerio; RNA Seq,GSM6705360 r1,GSM6705360,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405931,,,wt_expt2_rep2_R1.fastq.gz,fastq,6185704050.0,41238027.0,GSM6705360 r1,0:150 1:0,A:1603435702;C:1515988796;G:1488677966;T:1577474793;N:126793,150,0,,,1603435702,1515988796,1488677966,1577474793,126793,SRX18123002,SRS15624876,,,"Goessling Lab, Brigham and Women's Hospital",1,0.78101,,0.04338,,0.88266,,0.5608,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71963,SRR22143717,SRX18123001,SRS15624875,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf wt expt2 rep1,GSM6705359,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf,hepatocytes 96hpf wt expt2 rep1,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:wt|time:96 hpf,GSM6705359,GSM6705359: hepatocytes 96hpf wt expt2 rep1; Danio rerio; RNA Seq,GSM6705359 r1,GSM6705359,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405931,,,wt_expt2_rep1_R1.fastq.gz,fastq,6197680950.0,41317873.0,GSM6705359 r1,0:150 1:0,A:1603637872;C:1495661601;G:1502876654;T:1595377016;N:127807,150,0,,,1603637872,1495661601,1502876654,1595377016,127807,SRX18123001,SRS15624875,,,"Goessling Lab, Brigham and Women's Hospital",1,0.86333,,0.05099,,0.88919,,0.56132,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71964,SRR22143718,SRX18123000,SRS15624874,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf dnvdra expt1 rep4,GSM6705358,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf,hepatocytes 96hpf dnvdra expt1 rep4,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf,GSM6705358,GSM6705358: hepatocytes 96hpf dnvdra expt1 rep4; Danio rerio; RNA Seq,GSM6705358 r1,GSM6705358,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP405931,,loader:fastq load.py,dnvdra_expt1_rep4_R1.fastq.gz dnvdra_expt1_rep4_R2.fastq.gz,fastq fastq,18831415800.0,62771386.0,GSM6705358 r1,0:150 1:150,A:4640361931;C:4661552439;G:4707320281;T:4820985318;N:1195831,150,150,,,4640361931,4661552439,4707320281,4820985318,1195831,SRX18123000,SRS15624874,,,"Goessling Lab, Brigham and Women's Hospital",2,0.94748,0.94729,0.03313,0.03287,0.79719,0.79945,0.47574,0.47792,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71965,SRR22143719,SRX18122999,SRS15624873,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf dnvdra expt1 rep3,GSM6705357,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf,hepatocytes 96hpf dnvdra expt1 rep3,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf,GSM6705357,GSM6705357: hepatocytes 96hpf dnvdra expt1 rep3; Danio rerio; RNA Seq,GSM6705357 r1,GSM6705357,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP405931,,loader:fastq load.py,dnvdra_expt1_rep3_R1.fastq.gz dnvdra_expt1_rep3_R2.fastq.gz,fastq fastq,16955597400.0,56518658.0,GSM6705357 r1,0:150 1:150,A:4191429329;C:4181155612;G:4191314524;T:4390631329;N:1066606,150,150,,,4191429329,4181155612,4191314524,4390631329,1066606,SRX18122999,SRS15624873,,,"Goessling Lab, Brigham and Women's Hospital",2,0.94938,0.94935,0.0338,0.03364,0.79545,0.79695,0.48365,0.48166,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71966,SRR22143720,SRX18122998,SRS15624872,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf dnvdra expt1 rep2,GSM6705356,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf,hepatocytes 96hpf dnvdra expt1 rep2,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf,GSM6705356,GSM6705356: hepatocytes 96hpf dnvdra expt1 rep2; Danio rerio; RNA Seq,GSM6705356 r1,GSM6705356,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP405931,,loader:fastq load.py,dnvdra_expt1_rep2_R1.fastq.gz dnvdra_expt1_rep2_R2.fastq.gz,fastq fastq,17388104700.0,57960349.0,GSM6705356 r1,0:150 1:150,A:4247868125;C:4323132556;G:4325289881;T:4490744969;N:1069169,150,150,,,4247868125,4323132556,4325289881,4490744969,1069169,SRX18122998,SRS15624872,,,"Goessling Lab, Brigham and Women's Hospital",2,0.94837,0.94745,0.03174,0.03157,0.79184,0.79381,0.47513,0.47039,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71967,SRR22143721,SRX18122997,SRS15624871,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf dnvdra expt1 rep1,GSM6705355,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf,hepatocytes 96hpf dnvdra expt1 rep1,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf,GSM6705355,GSM6705355: hepatocytes 96hpf dnvdra expt1 rep1; Danio rerio; RNA Seq,GSM6705355 r1,GSM6705355,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP405931,,loader:fastq load.py,dnvdra_expt1_rep1_R1.fastq.gz dnvdra_expt1_rep1_R2.fastq.gz,fastq fastq,18386589600.0,61288632.0,GSM6705355 r1,0:150 1:150,A:4509534555;C:4473109680;G:4706080457;T:4696713250;N:1151658,150,150,,,4509534555,4473109680,4706080457,4696713250,1151658,SRX18122997,SRS15624871,,,"Goessling Lab, Brigham and Women's Hospital",2,0.94402,0.94369,0.03471,0.03448,0.79478,0.7964,0.43544,0.43575,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71968,SRR22143722,SRX18122996,SRS15624870,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf wt expt1 rep4,GSM6705354,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf,hepatocytes 96hpf wt expt1 rep4,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:wt|time:96 hpf,GSM6705354,GSM6705354: hepatocytes 96hpf wt expt1 rep4; Danio rerio; RNA Seq,GSM6705354 r1,GSM6705354,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP405931,,loader:fastq load.py,wt_expt1_rep4_R1.fastq.gz wt_expt1_rep4_R2.fastq.gz,fastq fastq,14844320700.0,49481069.0,GSM6705354 r1,0:150 1:150,A:3676168506;C:3664928523;G:3671171564;T:3831144092;N:908015,150,150,,,3676168506,3664928523,3671171564,3831144092,908015,SRX18122996,SRS15624870,,,"Goessling Lab, Brigham and Women's Hospital",2,0.94938,0.94888,0.02974,0.02976,0.80444,0.80614,0.47385,0.42037,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71969,SRR22143723,SRX18122995,SRS15624869,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf wt expt1 rep3,GSM6705353,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf,hepatocytes 96hpf wt expt1 rep3,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:wt|time:96 hpf,GSM6705353,GSM6705353: hepatocytes 96hpf wt expt1 rep3; Danio rerio; RNA Seq,GSM6705353 r1,GSM6705353,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP405931,,loader:fastq load.py,wt_expt1_rep3_R1.fastq.gz wt_expt1_rep3_R2.fastq.gz,fastq fastq,16613218800.0,55377396.0,GSM6705353 r1,0:150 1:150,A:4069624360;C:4165320060;G:4040198029;T:4337025346;N:1051005,150,150,,,4069624360,4165320060,4040198029,4337025346,1051005,SRX18122995,SRS15624869,,,"Goessling Lab, Brigham and Women's Hospital",2,0.94839,0.94783,0.03158,0.03154,0.79703,0.79859,0.41789,0.4109,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71970,SRR22143724,SRX18122994,SRS15624868,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf wt expt1 rep2,GSM6705352,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf,hepatocytes 96hpf wt expt1 rep2,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:wt|time:96 hpf,GSM6705352,GSM6705352: hepatocytes 96hpf wt expt1 rep2; Danio rerio; RNA Seq,GSM6705352 r1,GSM6705352,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP405931,,loader:fastq load.py,wt_expt1_rep2_R1.fastq.gz wt_expt1_rep2_R2.fastq.gz,fastq fastq,15406857900.0,51356193.0,GSM6705352 r1,0:150 1:150,A:3790021506;C:3872684076;G:3750856541;T:3992308410;N:987367,150,150,,,3790021506,3872684076,3750856541,3992308410,987367,SRX18122994,SRS15624868,,,"Goessling Lab, Brigham and Women's Hospital",2,0.94749,0.94642,0.02824,0.02814,0.80044,0.80275,0.41703,0.46905,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
71971,SRR22143725,SRX18122993,SRS15624867,SRP405931,PRJNA896973,Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish,GSE217120,Transcriptome Analysis,Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.,,pubmed:38944835,,hepatocytes 96hpf wt expt1 rep1,GSM6705351,,tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf,hepatocytes 96hpf wt expt1 rep1,FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment,hepatocytes sorted,,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.,cell type:hepatocytes sorted|genotype:wt|time:96 hpf,GSM6705351,GSM6705351: hepatocytes 96hpf wt expt1 rep1; Danio rerio; RNA Seq,GSM6705351 r1,GSM6705351,1,Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP405931,,loader:fastq load.py,wt_expt1_rep1_R1.fastq.gz wt_expt1_rep1_R2.fastq.gz,fastq fastq,17241539100.0,57471797.0,GSM6705351 r1,0:150 1:150,A:4266092960;C:4150739925;G:4403086295;T:4420536893;N:1083027,150,150,,,4266092960,4150739925,4403086295,4420536893,1083027,SRX18122993,SRS15624867,,,"Goessling Lab, Brigham and Women's Hospital",2,0.9395,0.93854,0.03615,0.03586,0.79715,0.79906,0.48099,0.46325,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2022-11-02,Multi-stage,Multi-stage,Liver,Liver and Biliary System
76480,SRR24992467,SRX20748471,SRS18037870,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EToH set 1 S14,GSM7505568,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal|geo loc name:missing|collection date:missing,WT EToH set 1 S14,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal,GSM7505568,GSM7505568: WT EToH set 1 S14; Danio rerio; RNA Seq,GSM7505568 r1,GSM7505568,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EToH_set_1_S14_L001_R2_001.fastq.gz WT_EToH_set_1_S14_L001_R1_001.fastq.gz,fastq fastq,4020460944.0,19903272.0,GSM7505568 r1,0:101 1:101,A:1112138605;C:908652797;G:856383523;T:1143254241;N:31778,101,101,,,1112138605,908652797,856383523,1143254241,31778,SRX20748471,SRS18037870,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.91623,0.91517,0.08179,0.08205,0.81866,0.81962,0.65131,0.64895,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76481,SRR24992468,SRX20748471,SRS18037870,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EToH set 1 S14,GSM7505568,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal|geo loc name:missing|collection date:missing,WT EToH set 1 S14,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal,GSM7505568,GSM7505568: WT EToH set 1 S14; Danio rerio; RNA Seq,GSM7505568 r1,GSM7505568,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EToH_set_1_S14_L002_R2_001.fastq.gz WT_EToH_set_1_S14_L002_R1_001.fastq.gz,fastq fastq,3978035894.0,19693247.0,GSM7505568 r2,0:101 1:101,A:1100148408;C:899328962;G:846907469;T:1131626302;N:24753,101,101,,,1100148408,899328962,846907469,1131626302,24753,SRX20748471,SRS18037870,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.91605,0.91389,0.0817,0.08248,0.82067,0.82144,0.64647,0.65761,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76482,SRR24992469,SRX20748470,SRS18037871,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EToH set 4 S17,GSM7505571,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal|geo loc name:missing|collection date:missing,WT EToH set 4 S17,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal,GSM7505571,GSM7505571: WT EToH set 4 S17; Danio rerio; RNA Seq,GSM7505571 r1,GSM7505571,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EToH_set_4_S17_L001_R1_001.fastq.gz WT_EToH_set_4_S17_L001_R2_001.fastq.gz,fastq fastq,3105364180.0,15373090.0,GSM7505571 r1,0:101 1:101,A:856534378;C:703075428;G:661241200;T:884488710;N:24464,101,101,,,856534378,703075428,661241200,884488710,24464,SRX20748470,SRS18037871,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.89958,0.89861,0.09043,0.09111,0.81933,0.82169,0.65043,0.64824,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76483,SRR24992470,SRX20748470,SRS18037871,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EToH set 4 S17,GSM7505571,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal|geo loc name:missing|collection date:missing,WT EToH set 4 S17,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal,GSM7505571,GSM7505571: WT EToH set 4 S17; Danio rerio; RNA Seq,GSM7505571 r1,GSM7505571,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EToH_set_4_S17_L002_R1_001.fastq.gz WT_EToH_set_4_S17_L002_R2_001.fastq.gz,fastq fastq,3081840270.0,15256635.0,GSM7505571 r2,0:101 1:101,A:849789387;C:697928769;G:656330984;T:877771828;N:19302,101,101,,,849789387,697928769,656330984,877771828,19302,SRX20748470,SRS18037871,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.90016,0.8984,0.08969,0.09032,0.82116,0.82359,0.65151,0.63024,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76484,SRR24992471,SRX20748469,SRS18037869,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EToH set 3 S16,GSM7505570,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal|geo loc name:missing|collection date:missing,WT EToH set 3 S16,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal,GSM7505570,GSM7505570: WT EToH set 3 S16; Danio rerio; RNA Seq,GSM7505570 r1,GSM7505570,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EToH_set_3_S16_L001_R1_001.fastq.gz WT_EToH_set_3_S16_L001_R2_001.fastq.gz,fastq fastq,3233955764.0,16009682.0,GSM7505570 r1,0:101 1:101,A:888870359;C:734034367;G:689722656;T:921302895;N:25487,101,101,,,888870359,734034367,689722656,921302895,25487,SRX20748469,SRS18037869,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.91015,0.9079,0.10287,0.10401,0.82298,0.82473,0.66352,0.65432,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76485,SRR24992472,SRX20748469,SRS18037869,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EToH set 3 S16,GSM7505570,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal|geo loc name:missing|collection date:missing,WT EToH set 3 S16,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal,GSM7505570,GSM7505570: WT EToH set 3 S16; Danio rerio; RNA Seq,GSM7505570 r1,GSM7505570,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EToH_set_3_S16_L002_R1_001.fastq.gz WT_EToH_set_3_S16_L002_R2_001.fastq.gz,fastq fastq,3201989466.0,15851433.0,GSM7505570 r2,0:101 1:101,A:880002064;C:726970273;G:682615774;T:912381500;N:19855,101,101,,,880002064,726970273,682615774,912381500,19855,SRX20748469,SRS18037869,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.91072,0.9093,0.10339,0.10403,0.82522,0.82633,0.65967,0.66098,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76486,SRR24992473,SRX20748468,SRS18037868,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EToH set 2 S15,GSM7505569,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal|geo loc name:missing|collection date:missing,WT EToH set 2 S15,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal,GSM7505569,GSM7505569: WT EToH set 2 S15; Danio rerio; RNA Seq,GSM7505569 r1,GSM7505569,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EToH_set_2_S15_L001_R1_001.fastq.gz WT_EToH_set_2_S15_L001_R2_001.fastq.gz,fastq fastq,3082630696.0,15260548.0,GSM7505569 r1,0:101 1:101,A:868065402;C:686482230;G:646173321;T:881885501;N:24242,101,101,,,868065402,686482230,646173321,881885501,24242,SRX20748468,SRS18037868,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.90535,0.90358,0.09667,0.09756,0.82087,0.82306,0.75123,0.75511,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76487,SRR24992474,SRX20748468,SRS18037868,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EToH set 2 S15,GSM7505569,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal|geo loc name:missing|collection date:missing,WT EToH set 2 S15,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:EToH treated animal,GSM7505569,GSM7505569: WT EToH set 2 S15; Danio rerio; RNA Seq,GSM7505569 r1,GSM7505569,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EToH_set_2_S15_L002_R1_001.fastq.gz WT_EToH_set_2_S15_L002_R2_001.fastq.gz,fastq fastq,3061891154.0,15157877.0,GSM7505569 r2,0:101 1:101,A:862151443;C:682033621;G:641773066;T:875913721;N:19303,101,101,,,862151443,682033621,641773066,875913721,19303,SRX20748468,SRS18037868,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.90498,0.90291,0.09556,0.0963,0.82037,0.82442,0.75184,0.75197,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76488,SRR24992475,SRX20748467,SRS18037866,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EF set 4 S8,GSM7505567,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal|geo loc name:missing|collection date:missing,WT EF set 4 S8,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal,GSM7505567,GSM7505567: WT EF set 4 S8; Danio rerio; RNA Seq,GSM7505567 r1,GSM7505567,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EF_set_4_S8_L001_R1_001.fastq.gz WT_EF_set_4_S8_L001_R2_001.fastq.gz,fastq fastq,3057678242.0,15137021.0,GSM7505567 r1,0:101 1:101,A:834997830;C:699939146;G:667516119;T:855201031;N:24116,101,101,,,834997830,699939146,667516119,855201031,24116,SRX20748467,SRS18037866,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.90652,0.90524,0.10378,0.10578,0.82033,0.82126,0.6495,0.64663,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76489,SRR24992476,SRX20748467,SRS18037866,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EF set 4 S8,GSM7505567,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal|geo loc name:missing|collection date:missing,WT EF set 4 S8,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal,GSM7505567,GSM7505567: WT EF set 4 S8; Danio rerio; RNA Seq,GSM7505567 r1,GSM7505567,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EF_set_4_S8_L002_R1_001.fastq.gz WT_EF_set_4_S8_L002_R2_001.fastq.gz,fastq fastq,3054411498.0,15120849.0,GSM7505567 r2,0:101 1:101,A:833807761;C:699489930;G:666989039;T:854105655;N:19113,101,101,,,833807761,699489930,666989039,854105655,19113,SRX20748467,SRS18037866,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.9071,0.90497,0.1051,0.10566,0.82061,0.82209,0.64965,0.65134,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76490,SRR24992477,SRX20748466,SRS18037867,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,MTM1 set 1 S11,GSM7505561,,source name:liver|tissue:liver|genotype:mtm mutant|time:7dpf|geo loc name:missing|collection date:missing,MTM1 set 1 S11,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:mtm mutant|time:7dpf,GSM7505561,GSM7505561: MTM1 set 1 S11; Danio rerio; RNA Seq,GSM7505561 r1,GSM7505561,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,MTM1_set_1_S11_L001_R1_001.fastq.gz MTM1_set_1_S11_L001_R2_001.fastq.gz,fastq fastq,3256411296.0,16120848.0,GSM7505561 r1,0:101 1:101,A:898555395;C:744016486;G:682595206;T:931218480;N:25729,101,101,,,898555395,744016486,682595206,931218480,25729,SRX20748466,SRS18037867,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.90146,0.90035,0.09697,0.0986,0.84786,0.85159,0.74169,0.73867,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76491,SRR24992480,SRX20748466,SRS18037867,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,MTM1 set 1 S11,GSM7505561,,source name:liver|tissue:liver|genotype:mtm mutant|time:7dpf|geo loc name:missing|collection date:missing,MTM1 set 1 S11,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:mtm mutant|time:7dpf,GSM7505561,GSM7505561: MTM1 set 1 S11; Danio rerio; RNA Seq,GSM7505561 r1,GSM7505561,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,MTM1_set_1_S11_L002_R1_001.fastq.gz MTM1_set_1_S11_L002_R2_001.fastq.gz,fastq fastq,3238888402.0,16034101.0,GSM7505561 r2,0:101 1:101,A:893743513;C:739918856;G:678932023;T:926273381;N:20629,101,101,,,893743513,739918856,678932023,926273381,20629,SRX20748466,SRS18037867,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.90035,0.89785,0.09722,0.09743,0.84626,0.84991,0.74299,0.73866,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76492,SRR24992479,SRX20748465,SRS18037864,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,MTM1 set 2 S12,GSM7505562,,source name:liver|tissue:liver|genotype:mtm mutant|time:7dpf|geo loc name:missing|collection date:missing,MTM1 set 2 S12,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:mtm mutant|time:7dpf,GSM7505562,GSM7505562: MTM1 set 2 S12; Danio rerio; RNA Seq,GSM7505562 r1,GSM7505562,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,MTM1_set_2_S12_L001_R1_001.fastq.gz MTM1_set_2_S12_L001_R2_001.fastq.gz,fastq fastq,3916993918.0,19391059.0,GSM7505562 r1,0:101 1:101,A:1093091636;C:883988956;G:806093205;T:1133789115;N:31006,101,101,,,1093091636,883988956,806093205,1133789115,31006,SRX20748465,SRS18037864,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.9103,0.90923,0.12955,0.13114,0.78946,0.79344,0.68013,0.68109,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76493,SRR24992482,SRX20748465,SRS18037864,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,MTM1 set 2 S12,GSM7505562,,source name:liver|tissue:liver|genotype:mtm mutant|time:7dpf|geo loc name:missing|collection date:missing,MTM1 set 2 S12,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:mtm mutant|time:7dpf,GSM7505562,GSM7505562: MTM1 set 2 S12; Danio rerio; RNA Seq,GSM7505562 r1,GSM7505562,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,MTM1_set_2_S12_L002_R1_001.fastq.gz MTM1_set_2_S12_L002_R2_001.fastq.gz,fastq fastq,3885204370.0,19233685.0,GSM7505562 r2,0:101 1:101,A:1084311794;C:876602929;G:799411838;T:1124853442;N:24367,101,101,,,1084311794,876602929,799411838,1124853442,24367,SRX20748465,SRS18037864,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.9112,0.90807,0.12919,0.12955,0.79133,0.79563,0.68103,0.67452,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76494,SRR24992481,SRX20748464,SRS18037865,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,MTM1 set 3 S13,GSM7505563,,source name:liver|tissue:liver|genotype:mtm mutant|time:7dpf|geo loc name:missing|collection date:missing,MTM1 set 3 S13,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:mtm mutant|time:7dpf,GSM7505563,GSM7505563: MTM1 set 3 S13; Danio rerio; RNA Seq,GSM7505563 r1,GSM7505563,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,MTM1_set_3_S13_L001_R2_001.fastq.gz MTM1_set_3_S13_L001_R1_001.fastq.gz,fastq fastq,4684166890.0,23188945.0,GSM7505563 r1,0:101 1:101,A:1305876899;C:1049544010;G:998943186;T:1329768217;N:34578,101,101,,,1305876899,1049544010,998943186,1329768217,34578,SRX20748464,SRS18037865,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.91585,0.91597,0.09626,0.0969,0.81229,0.80994,0.78116,0.77879,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76495,SRR24992484,SRX20748464,SRS18037865,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,MTM1 set 3 S13,GSM7505563,,source name:liver|tissue:liver|genotype:mtm mutant|time:7dpf|geo loc name:missing|collection date:missing,MTM1 set 3 S13,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:mtm mutant|time:7dpf,GSM7505563,GSM7505563: MTM1 set 3 S13; Danio rerio; RNA Seq,GSM7505563 r1,GSM7505563,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,MTM1_set_3_S13_L002_R2_001.fastq.gz MTM1_set_3_S13_L002_R1_001.fastq.gz,fastq fastq,4610801096.0,22825748.0,GSM7505563 r2,0:101 1:101,A:1284936355;C:1033275021;G:983687726;T:1308875175;N:26819,101,101,,,1284936355,1033275021,983687726,1308875175,26819,SRX20748464,SRS18037865,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.91556,0.91484,0.09713,0.09811,0.81359,0.8116,0.77748,0.77589,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76496,SRR24992483,SRX20748463,SRS18037862,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EF set 1 S5,GSM7505564,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal|geo loc name:missing|collection date:missing,WT EF set 1 S5,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal,GSM7505564,GSM7505564: WT EF set 1 S5; Danio rerio; RNA Seq,GSM7505564 r1,GSM7505564,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EF_set_1_S5_L001_R1_001.fastq.gz WT_EF_set_1_S5_L001_R2_001.fastq.gz,fastq fastq,3974246980.0,19674490.0,GSM7505564 r1,0:101 1:101,A:1088210154;C:910534652;G:850534570;T:1124936042;N:31562,101,101,,,1088210154,910534652,850534570,1124936042,31562,SRX20748463,SRS18037862,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.90291,0.9019,0.11545,0.11601,0.80864,0.81067,0.56739,0.55446,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76497,SRR24992486,SRX20748463,SRS18037862,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EF set 1 S5,GSM7505564,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal|geo loc name:missing|collection date:missing,WT EF set 1 S5,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal,GSM7505564,GSM7505564: WT EF set 1 S5; Danio rerio; RNA Seq,GSM7505564 r1,GSM7505564,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EF_set_1_S5_L002_R1_001.fastq.gz WT_EF_set_1_S5_L002_R2_001.fastq.gz,fastq fastq,3984092258.0,19723229.0,GSM7505564 r2,0:101 1:101,A:1090762749;C:913032811;G:852752708;T:1127518743;N:25247,101,101,,,1090762749,913032811,852752708,1127518743,25247,SRX20748463,SRS18037862,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.90323,0.90101,0.11447,0.11601,0.81089,0.81294,0.56627,0.56009,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76498,SRR24992485,SRX20748462,SRS18037860,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EF set 2 S6,GSM7505565,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal|geo loc name:missing|collection date:missing,WT EF set 2 S6,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal,GSM7505565,GSM7505565: WT EF set 2 S6; Danio rerio; RNA Seq,GSM7505565 r1,GSM7505565,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EF_set_2_S6_L001_R1_001.fastq.gz WT_EF_set_2_S6_L001_R2_001.fastq.gz,fastq fastq,3473301322.0,17194561.0,GSM7505565 r1,0:101 1:101,A:961074551;C:779266356;G:749129347;T:983803528;N:27540,101,101,,,961074551,779266356,749129347,983803528,27540,SRX20748462,SRS18037860,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.91581,0.9143,0.09069,0.09084,0.80215,0.80574,0.57298,0.564,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76499,SRR24992488,SRX20748462,SRS18037860,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EF set 2 S6,GSM7505565,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal|geo loc name:missing|collection date:missing,WT EF set 2 S6,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal,GSM7505565,GSM7505565: WT EF set 2 S6; Danio rerio; RNA Seq,GSM7505565 r1,GSM7505565,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EF_set_2_S6_L002_R1_001.fastq.gz WT_EF_set_2_S6_L002_R2_001.fastq.gz,fastq fastq,3478783400.0,17221700.0,GSM7505565 r2,0:101 1:101,A:961974452;C:780943249;G:750816401;T:985027271;N:22027,101,101,,,961974452,780943249,750816401,985027271,22027,SRX20748462,SRS18037860,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.91555,0.91386,0.09051,0.09088,0.80032,0.80507,0.57167,0.5731,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76500,SRR24992487,SRX20748461,SRS18037863,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EF set 3 S7,GSM7505566,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal|geo loc name:missing|collection date:missing,WT EF set 3 S7,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal,GSM7505566,GSM7505566: WT EF set 3 S7; Danio rerio; RNA Seq,GSM7505566 r1,GSM7505566,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EF_set_3_S7_L001_R1_001.fastq.gz WT_EF_set_3_S7_L001_R2_001.fastq.gz,fastq fastq,3404569408.0,16854304.0,GSM7505566 r1,0:101 1:101,A:939122584;C:776537363;G:719167525;T:969714940;N:26996,101,101,,,939122584,776537363,719167525,969714940,26996,SRX20748461,SRS18037863,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.89948,0.89796,0.09392,0.09451,0.81988,0.8224,0.64148,0.63729,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76501,SRR24992491,SRX20748461,SRS18037863,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT EF set 3 S7,GSM7505566,,source name:liver|tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal|geo loc name:missing|collection date:missing,WT EF set 3 S7,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf|treatment:overfed animal,GSM7505566,GSM7505566: WT EF set 3 S7; Danio rerio; RNA Seq,GSM7505566 r1,GSM7505566,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,WT_EF_set_3_S7_L002_R2_001.fastq.gz WT_EF_set_3_S7_L002_R1_001.fastq.gz,fastq fastq,3447871138.0,17068669.0,GSM7505566 r2,0:101 1:101,A:950903607;C:786509232;G:728497589;T:981938662;N:22048,101,101,,,950903607,786509232,728497589,981938662,22048,SRX20748461,SRS18037863,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.90032,0.89782,0.09527,0.09578,0.81964,0.82199,0.64643,0.63964,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76502,SRR24992489,SRX20748460,SRS18037861,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,MTM1 3R resub Jan18 21 S22,GSM7505559,,source name:liver|tissue:liver|genotype:mtm mutant|time:7dpf|geo loc name:missing|collection date:missing,MTM1 3R resub Jan18 21 S22,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:mtm mutant|time:7dpf,GSM7505559,GSM7505559: MTM1 3R resub Jan18 21 S22; Danio rerio; RNA Seq,GSM7505559 r1,GSM7505559,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,MTM1_3R_resub_Jan18_21_S22_L001_R2_001.fastq.gz MTM1_3R_resub_Jan18_21_S22_L001_R1_001.fastq.gz,fastq fastq,3511872414.0,17385507.0,GSM7505559 r1,0:101 1:101,A:971950894;C:784831408;G:734665623;T:1020396717;N:27772,101,101,,,971950894,784831408,734665623,1020396717,27772,SRX20748460,SRS18037861,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.89108,0.88878,0.13494,0.13644,0.79604,0.80042,0.62708,0.6341,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76503,SRR24992493,SRX20748460,SRS18037861,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,MTM1 3R resub Jan18 21 S22,GSM7505559,,source name:liver|tissue:liver|genotype:mtm mutant|time:7dpf|geo loc name:missing|collection date:missing,MTM1 3R resub Jan18 21 S22,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:mtm mutant|time:7dpf,GSM7505559,GSM7505559: MTM1 3R resub Jan18 21 S22; Danio rerio; RNA Seq,GSM7505559 r1,GSM7505559,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,MTM1_3R_resub_Jan18_21_S22_L002_R1_001.fastq.gz MTM1_3R_resub_Jan18_21_S22_L002_R2_001.fastq.gz,fastq fastq,3529431870.0,17472435.0,GSM7505559 r2,0:101 1:101,A:976486882;C:789093326;G:738751664;T:1025077844;N:22154,101,101,,,976486882,789093326,738751664,1025077844,22154,SRX20748460,SRS18037861,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.89182,0.88867,0.13537,0.13611,0.795,0.79892,0.64424,0.64087,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76504,SRR24992478,SRX20748459,SRS18037858,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,MTM1 R1 resub Jan11 21 S20,GSM7505560,,source name:liver|tissue:liver|genotype:mtm mutant|time:7dpf|geo loc name:missing|collection date:missing,MTM1 R1 resub Jan11 21 S20,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:mtm mutant|time:7dpf,GSM7505560,GSM7505560: MTM1 R1 resub Jan11 21 S20; Danio rerio; RNA Seq,GSM7505560 r1,GSM7505560,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,MTM1_R1_resub_Jan11_21_S20_L002_R1_001.fastq.gz MTM1_R1_resub_Jan11_21_S20_L002_R2_001.fastq.gz,fastq fastq,3032700134.0,15013367.0,GSM7505560 r2,0:101 1:101,A:837556405;C:687623964;G:639701989;T:867798693;N:19083,101,101,,,837556405,687623964,639701989,867798693,19083,SRX20748459,SRS18037858,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.85194,0.851,0.1212,0.12225,0.80884,0.81065,0.752,0.75338,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76505,SRR24992492,SRX20748459,SRS18037858,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,MTM1 R1 resub Jan11 21 S20,GSM7505560,,source name:liver|tissue:liver|genotype:mtm mutant|time:7dpf|geo loc name:missing|collection date:missing,MTM1 R1 resub Jan11 21 S20,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:mtm mutant|time:7dpf,GSM7505560,GSM7505560: MTM1 R1 resub Jan11 21 S20; Danio rerio; RNA Seq,GSM7505560 r1,GSM7505560,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,MTM1_R1_resub_Jan11_21_S20_L001_R1_001.fastq.gz MTM1_R1_resub_Jan11_21_S20_L001_R2_001.fastq.gz,fastq fastq,3024768200.0,14974100.0,GSM7505560 r1,0:101 1:101,A:835627991;C:685529458;G:637812333;T:865774549;N:23869,101,101,,,835627991,685529458,637812333,865774549,23869,SRX20748459,SRS18037858,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.8513,0.85179,0.11982,0.12156,0.809,0.81142,0.39928,0.7531,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76506,SRR24992490,SRX20748458,SRS18037859,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,MTM1 2R resub Jan18 21 S21,GSM7505558,,source name:liver|tissue:liver|genotype:mtm mutant|time:7dpf|geo loc name:missing|collection date:missing,MTM1 2R resub Jan18 21 S21,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:mtm mutant|time:7dpf,GSM7505558,GSM7505558: MTM1 2R resub Jan18 21 S21; Danio rerio; RNA Seq,GSM7505558 r1,GSM7505558,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,MTM1_2R_resub_Jan18_21_S21_L002_R1_001.fastq.gz MTM1_2R_resub_Jan18_21_S21_L002_R2_001.fastq.gz,fastq fastq,5959522372.0,29502586.0,GSM7505558 r2,0:101 1:101,A:1672708319;C:1338852492;G:1228646272;T:1719277497;N:37792,101,101,,,1672708319,1338852492,1228646272,1719277497,37792,SRX20748458,SRS18037859,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.87692,0.87501,0.09282,0.09365,0.85705,0.85817,0.84614,0.82992,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76507,SRR24992494,SRX20748458,SRS18037859,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,MTM1 2R resub Jan18 21 S21,GSM7505558,,source name:liver|tissue:liver|genotype:mtm mutant|time:7dpf|geo loc name:missing|collection date:missing,MTM1 2R resub Jan18 21 S21,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:mtm mutant|time:7dpf,GSM7505558,GSM7505558: MTM1 2R resub Jan18 21 S21; Danio rerio; RNA Seq,GSM7505558 r1,GSM7505558,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,MTM1_2R_resub_Jan18_21_S21_L001_R1_001.fastq.gz MTM1_2R_resub_Jan18_21_S21_L001_R2_001.fastq.gz,fastq fastq,5870454310.0,29061655.0,GSM7505558 r1,0:101 1:101,A:1648422142;C:1318380219;G:1209787536;T:1693817921;N:46492,101,101,,,1648422142,1318380219,1209787536,1693817921,46492,SRX20748458,SRS18037859,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.87677,0.87638,0.09298,0.09404,0.85839,0.85987,0.86181,0.8606,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76508,SRR24992495,SRX20748457,SRS18037855,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,AB set 4 S4,GSM7505557,,source name:liver|tissue:liver|genotype:WT|time:7dpf|geo loc name:missing|collection date:missing,AB set 4 S4,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf,GSM7505557,GSM7505557: AB set 4 S4; Danio rerio; RNA Seq,GSM7505557 r1,GSM7505557,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,AB_set_4_S4_L001_R1_001.fastq.gz AB_set_4_S4_L001_R2_001.fastq.gz,fastq fastq,2811984632.0,13920716.0,GSM7505557 r1,0:101 1:101,A:761877078;C:653908398;G:616500536;T:779675779;N:22841,101,101,,,761877078,653908398,616500536,779675779,22841,SRX20748457,SRS18037855,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.93398,0.93163,0.07105,0.0715,0.82081,0.82386,0.66748,0.67357,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76509,SRR24992496,SRX20748457,SRS18037855,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,AB set 4 S4,GSM7505557,,source name:liver|tissue:liver|genotype:WT|time:7dpf|geo loc name:missing|collection date:missing,AB set 4 S4,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf,GSM7505557,GSM7505557: AB set 4 S4; Danio rerio; RNA Seq,GSM7505557 r1,GSM7505557,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,AB_set_4_S4_L002_R1_001.fastq.gz AB_set_4_S4_L002_R2_001.fastq.gz,fastq fastq,2909746572.0,14404686.0,GSM7505557 r2,0:101 1:101,A:787910287;C:676999016;G:638579652;T:806239151;N:18466,101,101,,,787910287,676999016,638579652,806239151,18466,SRX20748457,SRS18037855,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.93335,0.93084,0.07097,0.07169,0.81905,0.82394,0.6707,0.65758,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76510,SRR24992497,SRX20748456,SRS18037857,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,AB set 3 S3,GSM7505556,,source name:liver|tissue:liver|genotype:WT|time:7dpf|geo loc name:missing|collection date:missing,AB set 3 S3,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf,GSM7505556,GSM7505556: AB set 3 S3; Danio rerio; RNA Seq,GSM7505556 r1,GSM7505556,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,AB_set_3_S3_L001_R1_001.fastq.gz AB_set_3_S3_L001_R2_001.fastq.gz,fastq fastq,3191104292.0,15797546.0,GSM7505556 r1,0:101 1:101,A:878666438;C:727494260;G:696078030;T:888839531;N:26033,101,101,,,878666438,727494260,696078030,888839531,26033,SRX20748456,SRS18037857,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.9163,0.91466,0.07603,0.07685,0.82219,0.82694,0.62499,0.63626,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76511,SRR24992498,SRX20748456,SRS18037857,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,AB set 3 S3,GSM7505556,,source name:liver|tissue:liver|genotype:WT|time:7dpf|geo loc name:missing|collection date:missing,AB set 3 S3,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf,GSM7505556,GSM7505556: AB set 3 S3; Danio rerio; RNA Seq,GSM7505556 r1,GSM7505556,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,AB_set_3_S3_L002_R1_001.fastq.gz AB_set_3_S3_L002_R2_001.fastq.gz,fastq fastq,3284554744.0,16260172.0,GSM7505556 r2,0:101 1:101,A:903945352;C:749150399;G:717237639;T:914200124;N:21230,101,101,,,903945352,749150399,717237639,914200124,21230,SRX20748456,SRS18037857,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.91592,0.91314,0.07772,0.07814,0.82457,0.82771,0.63792,0.63988,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76512,SRR24992499,SRX20748455,SRS18037853,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,AB set 2 S2,GSM7505555,,source name:liver|tissue:liver|genotype:WT|time:7dpf|geo loc name:missing|collection date:missing,AB set 2 S2,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf,GSM7505555,GSM7505555: AB set 2 S2; Danio rerio; RNA Seq,GSM7505555 r1,GSM7505555,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,AB_set_2_S2_L001_R2_001.fastq.gz AB_set_2_S2_L001_R1_001.fastq.gz,fastq fastq,3144262512.0,15565656.0,GSM7505555 r1,0:101 1:101,A:866305870;C:716843798;G:670289504;T:890798418;N:24922,101,101,,,866305870,716843798,670289504,890798418,24922,SRX20748455,SRS18037853,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.88837,0.88743,0.13777,0.14005,0.83613,0.83824,0.74582,0.73723,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76513,SRR24992500,SRX20748455,SRS18037853,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,AB set 2 S2,GSM7505555,,source name:liver|tissue:liver|genotype:WT|time:7dpf|geo loc name:missing|collection date:missing,AB set 2 S2,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf,GSM7505555,GSM7505555: AB set 2 S2; Danio rerio; RNA Seq,GSM7505555 r1,GSM7505555,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,AB_set_2_S2_L002_R2_001.fastq.gz AB_set_2_S2_L002_R1_001.fastq.gz,fastq fastq,3187593936.0,15780168.0,GSM7505555 r2,0:101 1:101,A:877656416;C:727387073;G:680065367;T:902464573;N:20507,101,101,,,877656416,727387073,680065367,902464573,20507,SRX20748455,SRS18037853,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.88957,0.88674,0.13729,0.13763,0.83575,0.83851,0.73958,0.74396,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76514,SRR24992501,SRX20748454,SRS18037854,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,AB set 1 S1,GSM7505554,,source name:liver|tissue:liver|genotype:WT|time:7dpf|geo loc name:missing|collection date:missing,AB set 1 S1,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf,GSM7505554,GSM7505554: AB set 1 S1; Danio rerio; RNA Seq,GSM7505554 r1,GSM7505554,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,AB_set_1_S1_L001_R1_001.fastq.gz AB_set_1_S1_L001_R2_001.fastq.gz,fastq fastq,2892403054.0,14318827.0,GSM7505554 r1,0:101 1:101,A:805968111;C:644115844;G:615359313;T:826936198;N:23588,101,101,,,805968111,644115844,615359313,826936198,23588,SRX20748454,SRS18037854,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.89898,0.89842,0.11346,0.11347,0.80316,0.80507,0.4808,0.61543,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76515,SRR24992502,SRX20748454,SRS18037854,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,AB set 1 S1,GSM7505554,,source name:liver|tissue:liver|genotype:WT|time:7dpf|geo loc name:missing|collection date:missing,AB set 1 S1,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:7dpf,GSM7505554,GSM7505554: AB set 1 S1; Danio rerio; RNA Seq,GSM7505554 r1,GSM7505554,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,loader:fastq load.py,AB_set_1_S1_L002_R1_001.fastq.gz AB_set_1_S1_L002_R2_001.fastq.gz,fastq fastq,2999616776.0,14849588.0,GSM7505554 r2,0:101 1:101,A:835321061;C:668401942;G:638882867;T:856991625;N:19281,101,101,,,835321061,668401942,638882867,856991625,19281,SRX20748454,SRS18037854,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.89734,0.89553,0.11371,0.11318,0.80547,0.80829,0.60947,0.61149,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76516,SRR24992503,SRX20748453,SRS18037850,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT rep3,GSM7505553,,source name:liver|tissue:liver|genotype:WT|time:6 dpf|geo loc name:missing|collection date:missing,WT rep3,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:6 dpf,GSM7505553,GSM7505553: WT rep3; Danio rerio; RNA Seq,GSM7505553 r1,GSM7505553,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,,WTDMSO_2.fastq.gz WTDMSO_1.fastq.gz,fastq fastq,7348566900.0,24495223.0,GSM7505553 r1,0:150 1:150,A:1933671632;C:1729219056;G:1758084185;T:1926687659;N:904368,150,150,,,1933671632,1729219056,1758084185,1926687659,904368,SRX20748453,SRS18037850,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.90886,0.9104,0.05758,0.05819,0.78831,0.79334,0.52128,0.5288,150,150,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76517,SRR24992504,SRX20748452,SRS18037852,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT rep2,GSM7505552,,source name:liver|tissue:liver|genotype:WT|time:6 dpf|geo loc name:missing|collection date:missing,WT rep2,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:6 dpf,GSM7505552,GSM7505552: WT rep2; Danio rerio; RNA Seq,GSM7505552 r1,GSM7505552,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,,WTDMSO2_USR17007344L_HM5FMBBXX_L6_1.fastq.gz WTDMSO2_USR17007344L_HM5FMBBXX_L6_2.fastq.gz,fastq fastq,6998850000.0,23329500.0,GSM7505552 r1,0:150 1:150,A:1833003872;C:1659996567;G:1679877031;T:1824516978;N:1455552,150,150,,,1833003872,1659996567,1679877031,1824516978,1455552,SRX20748452,SRS18037852,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.92955,0.91833,0.07335,0.07308,0.79204,0.80066,0.53683,0.53686,150,150,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76518,SRR24992505,SRX20748451,SRS18037856,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,WT rep1,GSM7505551,,source name:liver|tissue:liver|genotype:WT|time:6 dpf|geo loc name:missing|collection date:missing,WT rep1,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:WT|time:6 dpf,GSM7505551,GSM7505551: WT rep1; Danio rerio; RNA Seq,GSM7505551 r1,GSM7505551,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,,WTDMSO1_USR17007340L_HM5FMBBXX_L6_1.fastq.gz WTDMSO1_USR17007340L_HM5FMBBXX_L6_2.fastq.gz,fastq fastq,7335144300.0,24450481.0,GSM7505551 r1,0:150 1:150,A:1885125117;C:1763608026;G:1815699502;T:1869192219;N:1519436,150,150,,,1885125117,1763608026,1815699502,1869192219,1519436,SRX20748451,SRS18037856,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.89385,0.87012,0.0508,0.04949,0.80249,0.81049,0.47256,0.51837,150,150,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76519,SRR24992506,SRX20748450,SRS18037848,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,abcb11b mutants rep3,GSM7505550,,source name:liver|tissue:liver|genotype:abcb11b mutant|time:6 dpf|geo loc name:missing|collection date:missing,abcb11b mutants  rep3,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:abcb11b mutant|time:6 dpf,GSM7505550,GSM7505550: abcb11b mutants  rep3; Danio rerio; RNA Seq,GSM7505550 r1,GSM7505550,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,,MutDMSO_1.fastq.gz MutDMSO_2.fastq.gz,fastq fastq,7998489300.0,26661631.0,GSM7505550 r1,0:150 1:150,A:2115506889;C:1876524446;G:1899591751;T:2105861863;N:1004351,150,150,,,2115506889,1876524446,1899591751,2105861863,1004351,SRX20748450,SRS18037848,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.91068,0.91272,0.05064,0.05123,0.78399,0.79001,0.50799,0.50065,150,150,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76520,SRR24992507,SRX20748449,SRS18037851,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,abcb11b mutants rep2,GSM7505549,,source name:liver|tissue:liver|genotype:abcb11b mutant|time:6 dpf|geo loc name:missing|collection date:missing,abcb11b mutants  rep2,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:abcb11b mutant|time:6 dpf,GSM7505549,GSM7505549: abcb11b mutants  rep2; Danio rerio; RNA Seq,GSM7505549 r1,GSM7505549,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,,MtDMSO2_USR17007346L_HM5FMBBXX_L6_2.fastq.gz MtDMSO2_USR17007346L_HM5FMBBXX_L6_1.fastq.gz,fastq fastq,8170027500.0,27233425.0,GSM7505549 r1,0:150 1:150,A:2108818327;C:1956603673;G:2017777063;T:2085100355;N:1728082,150,150,,,2108818327,1956603673,2017777063,2085100355,1728082,SRX20748449,SRS18037851,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.88905,0.84348,0.06263,0.06034,0.7792,0.79009,0.48047,0.499,150,150,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System
76521,SRR24992508,SRX20748448,SRS18037846,SRP445344,PRJNA986481,Loss of Mtm1 causes cholestatic liver disease in a model of X linked myotubular myopathy,GSE235571,Transcriptome Analysis,X linked myotubular myopathy XLMTM is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently  there are no approved treatments  though AAV8 mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However  four patients with XLMTM treated with gene therapy have died from progressive liver failure  and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology  we have characterized a novel liver phenotype in a zebrafish model of this disease. Specifically  we have found that loss of function mutations in mtm1 lead to severe liver abnormalities including impaired bile flux  structural abnormalities of the bile canaliculus  and improper endosomal mediated trafficking of canalicular transporters. Using a reporter tagged Mtm1 zebrafish line  we have established localization of Mtm1 in the liver in association with Rab11 and canalicular transport proteins  and demonstrated that hepatocyte specific re expression of Mtm1 can rescue the cholestatic phenotype. Lastly  we completed a targeted chemical screen  and found that Dynasore  a dynamin II inhibitor  is able to partially restore bile flow and transporter localization to the canalicular membrane. In summary  we demonstrate for the first time liver abnormalities that are directly caused by MTM1 mutation in a pre clinical model  thus establishing the critical framework for better understanding and comprehensive treatment of the human disease. Overall design: Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. Samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol. Bioinformatic analysis was performed as described above.,,pubmed:37490339,,abcb11b mutants rep1,GSM7505548,,source name:liver|tissue:liver|genotype:abcb11b mutant|time:6 dpf|geo loc name:missing|collection date:missing,abcb11b mutants  rep1,Fastq files from the different runs were merged using “cat”. The merged paired FASTQ files for each sample were run through FastQC version 0.11.09 to obtain general QC metrics. Adapters were trimmed by Trim Galore version 0.6.6. Salmon3 version 1.4.0 was used for our alignment free pipeline. Adapter trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed at least 5 reads in 80% of the samples. We performed differential expression gene testing with DESeq2 v.1.24.0 R package using default settings. Replicate was used as covariates within the DESeq2 model. Statistical significance was set a 5% FDR Benjamini Hochberg. The Bioconductor package fgsea v 1.10.1 R package  was used for gene set enrichment analysis GSEA. Assembly: Danio Rerio reference genome GRCz11 with associated transcript annotations Gencode version GRCz11.103 was used. Supplementary files format and content: Salmon quant files for liver samples from WT and abcb11b mutants Supplementary files format and content: Raw counts for the 40 livers per replicate,liver,,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor’s standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,tissue:liver|genotype:abcb11b mutant|time:6 dpf,GSM7505548,GSM7505548: abcb11b mutants  rep1; Danio rerio; RNA Seq,GSM7505548 r1,GSM7505548,1,Total mRNAs were extracted from pools of dissected livers from 6 dpf abcb11b mutants and WT siblings  20 livers per replicate and 3 replicates per genotype  by using Arcturus PicoPure RNA isolation kit Applied Biosystems  KIT0204. For the 40 livers per replicate 4 5 replicates per group were dissected under a brightfield microscope at 7dpf and then pooled prior to RNA extraction using the Qiagen RNAeasy Micro kit. Animals in the overfed group were provided with six times the normal amount of food at each feeding from day 5 to 7 while EtOH treated animals were exposed to 2% ethanol for 32 hours prior to sample collection. The presence of hepatic steatosis was confirmed in both groups. WT and abcb11b mutants samples were submitted to Novogene Co for library preparation and RNA sequencing using the vendor's standard protocol.  The 40 samples were  submitted to the Centre for Applied Genomics TCAG  Toronto  Canada. SMART Seq v4 Ultra Low Input RNA kit was used for the cDNA conversion. Library preparation followed the protocol of Nextera XT library prep kit. Libraries were quality controlled QCed run on the Bioanalyzer DNA High Sensitivity chip to check for size and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol. All libraries were pooled and sequenced on 2 lanes on the NovaSeq SP flowcell paired end 2x100bp.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP445344,,,MtDMSO1_USR17007342L_HM5FMBBXX_L6_2.fastq.gz MtDMSO1_USR17007342L_HM5FMBBXX_L6_1.fastq.gz,fastq fastq,9216876000.0,30722920.0,GSM7505548 r1,0:150 1:150,A:2347466060;C:2239533032;G:2293384139;T:2334618631;N:1874138,150,150,,,2347466060,2239533032,2293384139,2334618631,1874138,SRX20748448,SRS18037846,SRA1660605,Hospital for Sick Children,GraphiteBio,2,0.89482,0.86759,0.05454,0.0525,0.79468,0.80068,0.4821,0.4935,150,150,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2023-06-22,Larval,Larval,Liver,Liver and Biliary System