run_metadata: 66011

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
66011	SRR15783457	SRX12076336	SRS10057001	SRP336073	PRJNA761449	Myostatin is a negative regulator of adult neurogenesis in zebrafish	GSE183644	Transcriptome Analysis	Intrinsic and extrinsic inhibition of axonal and neuronal regeneration obstruct spinal cord SC repair in mammals. In contrast adult zebrafish achieve functional recovery post SC damage. While studies of innate SC regeneration have focused on axon regrowth as a primary repair mechanism how local neurogenesis impacts functional recovery is unknown. We uncovered dynamic expression of myostatin b mstnb in a niche of dorsal ependymal progenitors post complete SC transection in zebrafish. Genetic loss of function in mstnb impaired functional recovery although glial and axonal bridging across the lesion were unaffected. Using a series of transgenic reporter lines we quantified the numbers of stem progenitor and neuronal cells in the absence of mstnb. We found neural stem cell proliferation was reduced while newborn neurons were increased in mstnb null tissues suggesting mstnb is a negative regulator of neurogenesis. Molecularly neuron differentiation genes were upregulated while the neural stem cell maintenance gene fgf1b was downregulated in mstnb mutants. Finally we show that human FGF1 treatment rescued neuronal gene expression in mstnb mutants. These studies uncover unanticipated neurogenic functions for mstnb in adult zebrafish and establish the importance of local neurogenesis for functional SC repair. Overall design: Gene expression profiling of mstn mutants and wildtype at control and one xxx post injury.		pubmed:36417881		SC mstnb wildtype Uninjured replicate 1	GSM5566276		source name:Spinal cord\|tissue:Spinal cord\|experiment:Uninjured\|time:Control\|genotype:wildtype	SC mstnb wildtype Uninjured replicate 1	Quality QC and trimming of adapters and short sequences were performed using Fastx. Sequencing reads were mapped to the zebrafish genome Zv11 using Bowtie2 then assembled and quantified using the Cufflinks and Cuffdiff algorithms. Genes with log2fold enrichment between 1 and 1 or adjusted p value ≥ 0.01 were considered insignificant. Genome build: Zv11 Supplementary files format and content: Processed data is store csv format files. All files contain FPKM expression values of all the genes in different replicates and experimental condition. Supplementary files format and content: Additionally log2 Fold change is calculate between conditions as indicated in the file name.	Spinal cord	Zebrafish were anaesthetized using MS 222. Fine scissors were used to make a small incision that transects the SC 4 mm caudal to the brainstem region. Complete transection was visually confirmed at the time of surgery. Injured animals were also assessed at 2 or 3 dpi to confirm loss of swim capacity post surgery. For sham injuries animals were anaesthetized and fine scissors were used to transect skin and muscle tissues without xxx SCI.	Two mm SC sections including the lesion site plus additional rostral and caudal tissue proximal to the lesion were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.	Adult zebrafish were maintained at the Washington University Zebrafish Core Facility. All animal experiments were performed in compliance with institutional animal protocols. Male and female animals between 3 month and 9 month of 2 cm in length were used. Experimental fish and control siblings of similar size and equal sex distribution were used for all experiments. SC transection surgeries and regeneration analyses were performed in a blinded manner and 2 to 4 independent experiments were repeated using different clutches of animals.	tissue:Spinal cord\|experiment:Uninjured\|time:Control\|genotype:wildtype	GSM5566276	GSM5566276: SC mstnb wildtype Uninjured replicate 1; Danio rerio; RNA Seq	GSM5566276		1	Two mm SC sections including the lesion site plus additional rostral and caudal tissue proximal to the lesion were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.	GEO Accession:GSM5566276	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP336073		loader:fastq load.py	b6-mstnb-wt-uninj-1.GTCGGTTCAC-ATCCTCGAGT.GTCGGTTCAC-ATCCTCGAGT_S72_L003_R1_001.fastq.gz b6-mstnb-wt-uninj-1.GTCGGTTCAC-ATCCTCGAGT.GTCGGTTCAC-ATCCTCGAGT_S72_L003_R2_001.fastq.gz	fastq fastq	20288059208.0	67179004.0	GSM5566276 r1	0:151 1:151	A:6194227425;C:3762932453;G:4520501753;T:5810174695;N:222882	151	151			6194227425	3762932453	4520501753	5810174695	222882	SRX12076336	SRS10057001	SRA1289934	GEO	Developmental Biology, Washington University in St. Louis	2	0.85748	0.88273	0.16029	0.16517	0.74862	0.76213	0.53814	0.52267	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		United States	2021-09-07	Adult	Adult	Spinal Cord	Nervous System