{"database": "metadata", "table": "run_metadata", "rows": [[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.", null, "pubmed:37490339", null, "WT EF set 4 S8", "GSM7505567", null, "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 \u201ccat\u201d. 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", null, "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\u2019s 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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP445344", null, "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, null, null, 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", null, "United States", "2023-06-22", "Larval", "Larval", "Liver", "Liver and Biliary System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["76489"], "units": {}, "query_ms": 7.587660002172925}