run_metadata: 70893
This data as json
| 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 |
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| 70893 | SRR20869075 | SRX16888177 | SRS14475661 | SRP390172 | PRJNA866536 | X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition | GSE210642 | Other | X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present there are no directed therapies for XLMTM and incomplete understanding of disease pathomechanisms. To address these knowledge gaps we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits including valproic acid which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO sodium valproate VPA or trichostatin A. For tissue collection the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction. Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice either treated with PBS or valproic acid VPA starting at 21 days. | pubmed:35844027 | Mtm1 KO DMSO treatment zebrafish rep2 | GSM6434011 | source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment | Mtm1 KO DMSO treatment zebrafish rep2 | Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples. | posterior half of larvae | Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit. | tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment | GSM6434011 | GSM6434011: Mtm1 KO DMSO treatment zebrafish rep2; Danio rerio; RNA Seq | GSM6434011 r1 | GSM6434011 | 1 | Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP390172 | WL1502_KY23_168_33_R1.fastq.gz | fastq | 956592516.0 | 14067537.0 | GSM6434011 r1 | 0:68 1:0 | A:313998032;C:166431578;G:204849712;T:271283994;N:29200 | 68 | 0 | 313998032 | 166431578 | 204849712 | 271283994 | 29200 | SRX16888177 | SRS14475661 | SRA1470408 | Hospital for Sick Children | Hospital for Sick Children | 1 | 0.76427 | 0.08867 | 0.8216 | 0.47678 | 68 | B | usable mapping rate | illumina | hiseq_era | 3prime | cdna_unspecified | lexogen | bulk | bulk | bulk | Canada | 2022-08-05 | Larval | Larval | Trunk | Surface Structure |