run_metadata: 56298

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
56298	SRR10903538	SRX7571707	SRS6007283	SRP242229	PRJNA601746	Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species	GSE143801	Other	Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here we report the development and application of a cross species small molecule screening platform employing zebrafish and mouse which enables rapid direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids lysophosphatidic acid LPA and niflumic acid NFA both linked to activation of intracellular calcium ion flux which showed conserved dose dependent and synergistic effects in promoting muscle engraftment across these vertebrate species. Overall design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.				Zebrafish LPA Rep 2	GSM4274793		tissue:zebrafish myogenic progenitor cells\|cell type:myogenic progenitor cells\|treatment:LPA	Zebrafish LPA Rep 2	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to GRCz11 and GRCm38 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz11 and GRCm38 Supplementary files format and content: FPKM	zebrafish myogenic progenitor cells	Freshly isolated mice muscle stem cells were treated with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at in 78% F10 GIBCO 20% horse serum Atlanta Biologics 1% penicillin streptomycin Invitrogen 1% GlutaMAX Invitrogen and 5 ng/ml bFGF Sigma at 37°C and 5% CO2. Zebrafish myogenic progenitor cells were washed with DPBS and treated in serum and bFGF free growth media with DMSO or 5 uM LPA or 10 uM NFA for 2hrs at 37C and 28C respectively.	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	Freshly isolated mice muscle stem cells were sorted into collagen/laminin coated plate containing treatment media. Zebrafish myogenic progenitor cells were generated in vitro from blastomere cells which were cultured in a zESC medium composed of 70% LDF medium 50% Leibowitz’s L 15 Invitrogen 35% DMEM Invitrogen and 15% Ham’s F 12 Invitrogen with 20% embryo extract and 10% FBS; these were supplemented with 2 ng/ml recombinant human FGF basic protein Sigma Aldrich 15 mM sodium bicarbonate 15 mM HEPES Invitrogen 1% L glutamine Invitrogen 10 nM sodium selenite Sigma Aldrich 1% N2 Invitrogen 2% B27 Invitrogen 0.1 mg/ml Primocin Invivogen and at 28°C without xxx for 48 hours.	cell type:myogenic progenitor cells\|treatment:LPA	GSM4274793	GSM4274793: Zebrafish LPA Rep 2; Danio rerio; RNA Seq	GSM4274793		1	Treated freshly isolated mice muscle stem cells and zebrafish myogenic progenitor cells were washed with DPBS then total RNA was extracted with the micro RNeasy kit QIAGEN. cDNA was prepared using SMART Seq v4 Ultra Low RNA Seq kit Takara and a Nextera kit was used for library construction.	GEO Accession:GSM4274793	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP242229			LPA-Z2_S5_R2_001.fastq.gz LPA-Z2_S5_R1_001.fastq.gz	fastq fastq	3259713731.0	43430992.0	GSM4274793 r1	0:37.53 1:37.53	A:889586274;C:714766857;G:716243885;T:938441843;N:674872	37	37			889586274	714766857	716243885	938441843	674872	SRX7571707	SRS6007283	SRA1027312	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.90057	0.90315	0.2034	0.20364	0.72583	0.72819	0.48128	0.48201	38	38	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	nextera	sc	single_cell_plate	smartseq		United States	2020-01-16	Undetermined	Embryo	Muscle	Muscular System