run_metadata: 34949

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
34949	SRR32472669	SRX27786997	SRS24165033	SRP565999	PRJNA1227535	Characterization of a novel zebrafish model of MTMR5 associated Charcot Marie Tooth disease type 4B3	GSE290354	Transcriptome Analysis	Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot Marie Tooth CMT Type 4B3. There is an incomplete understanding of the disease pathomechanisms underlying CMT4B3 and despite its severe clinical presentation currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However starting by 10 dpf mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination changes reminiscent of the nerve pathology in human CMT4B3. Importantly RNA sequencing from brain enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis chromatin remodeling/organization and synaptic membrane homeostasis. Overall our mtmr5 knockout zebrafish mirror genetic clinical and pathologic features of human CMT4B3. As such it represents a first pre clinical model to phenocopy the disease and an ideal tool for future studies on disease pathomechanisms and therapy development. Overall design: Bulk RNA sequencing of 7 dpf mtmr5 knockout and wild type brain enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.		pubmed:40066109		Brain enriched wild type biol rep4	GSM8811133		source name:head\|tissue:head\|genotype:wild type\|geo loc name:missing\|collection date:missing	Brain enriched wild type biol rep4	Adaptors trimmed using Trim Galore! Galaxy Version 0.6.7+galaxy0 Raw trimmed reads aligned to reference genome using RNA STAR Galaxy Version 2.7.11a+galaxy1 Filtered STAR alignments processed to extract raw read counts for genes using htseq count Galaxy Version 2.0.5+galaxy0 mode: intersection nonempty Normalized count matrix was generated using DESeq2 v3.2 in R v4.4.0. Minimum expression cut off: 10 read counts in at least 3 samples. Assembly: GRCz11/Ensembl release 113 primary assembly downloaded on October 21 2024. Supplementary files format and content: raw counts allSamples.csv includes raw counts for every gene for all samples Supplementary files format and content: normalized counts allSamples.csv includes normalized counts for genes above minimum expression cutoff for all samples	head		Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.	Zebrafish AB strain were raised and maintained at 28.5°C at the Zebrafish Facility at the Hospital for Sick Children Toronto ON Canada. Zebrafish embryos were grown in blue water 0.3 g/L Instant Ocean 1 mg/L methylene blue pH 7.0 from the one cell stage up to 7 dpf. All zebrafish procedures were performed in strict accordance with the Animals for Research Act of Ontario and the Guidelines of the Canadian Council on Animal Care.	tissue:head\|genotype:wild type	GSM8811133	GSM8811133: Brain enriched wild type biol rep4; Danio rerio; RNA Seq	GSM8811133 r1	GSM8811133	1	Zebrafish larvae were fin clipped and genotyped at 4 dpf 6 dpf. At 7 dpf n=11 17 zebrafish heads were dissected per genotype and immediately frozen at 80C. RNA extraction was performed for all samples 4x WT and 4x mtmr5 KO using the RNeasy kit Qiagen. Quality control RNA library preparation cDNA synthesis and library validation were performed by The Centre for Applied Genomics—Next Generation Sequencing Facility PGCRL The Hospital for Sick Children Toronto.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP565999			mtmr5_WT_4_S44_L002_R1_001.fastq.gz mtmr5_WT_4_S44_L002_R2_001.fastq.gz	fastq fastq	12990872770.0	43016135.0	GSM8811133 r1	0:151 1:151	A:3923529419;C:2571621367;G:2649969483;T:3845735356;N:17145	151	151			3923529419	2571621367	2649969483	3845735356	17145	SRX27786997	SRS24165033	SRA2083091	Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning	Dowling Lab, Genetics & Genome Biology, Peter Gilgan Centre for Research and Learning	2	0.89808	0.89653	0.27845	0.2761	0.74479	0.74412	0.52081	0.52503	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk		Canada	2025-02-24	Larval	Larval	Head	Nervous System