run_metadata: 42957

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
42957	SRR5855384	SRX3024623	SRS2373888	SRP113259	PRJNA395253	Nr2f transcription factors promote the identity of the vertebrate upper jaw	GSE101719	Transcriptome Analysis	The jaws are complementary in form and function but develop asymmetrically as the lower but not upper jaw bone forms around a prominent cartilage template. How such differences in skeletal composition are patterned is unclear. Here we identify four Nuclear receptor 2f genes nr2f1a nr2f1b nr2f2 and nr2f5 as enriched in zebrafish upper jaw precursors. Whereas loss of Nr2f genes results in expansion of upper jaw cartilage to resemble that of the lower jaw Nr2f5 misexpression inhibits lower jaw cartilage formation. Genome wide analyses show that Nr2f genes prevent expansion of lower jaw associated gene expression into the upper jaw territory. Further restriction of Nr2f expression by Endothelin1 signaling is critical for lower jaw development as reducing Nr2f dosage fully restores lower jaw development in edn1 mutants. We propose that Nr2f genes drive jaw asymmetry by limiting early cartilage differentiation in the upper jaw to preserve more precursors for later osteogenesis. Overall design: Zebrafish pharyngeal arch cells expressing both fli1a:GFP and sox10:DsRed were isolated by FACS from 36 hpf nr2f2; nr2f5 double mutant embryos 2 replicates: n = 37 & 84; 18 858 & 30 655 cells sox10:Gal4+ embryos n = 69; 86 517 cells sox10:Gal4; UAS:Nr2f5 embryos n = 84; 56 866 cells.		pubmed:29358039		nr2f2; nr2f5 mutant 1 fli1a:GFP+ sox10:DsRed+	GSM2713938		tissue:pharyngeal arch cells\|Stage:36 hpf\|genotype/variation:nr2f2; nr2f5 mutant\|identification:ocular coloboma	nr2f2; nr2f5 mutant 1 fli1a:GFP+ sox10:DsRed+	Raw sequencing data in Fastq format were imported into Partek Flow® for alignment and quantification. In pre alignment QC the reads from all samples were generally of high quality with the average quality score for each sample exceeding 33. The reads were then trimmed at both ends based on the Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. Trimmed reads were aligned to the Danio rerio GRCz10 genome assembly Emsembl v80 using the TopHat 2 algorithm. Aligned reads were quantified with the Partek E/M algorithm using default parameters to generate TPM values. Genome build: GRCz10 Supplementary files format and content: The csv text files have the TPM values for each gene in each sample.	pharyngeal arch cells		GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	Embryos were maintained at 28.5 degrees C until 27 hpf and then transferred to 22 degrees C to slow their development. Embryos were dissociated and sorted once they achieved morphological criteria corresponding to the standard 36 hpf stage	Stage:36 hpf\|genotype/variation:nr2f2; nr2f5 mutant\|identification:ocular coloboma	GSM2713938	GSM2713938: nr2f2; nr2f5 mutant 1 fli1a:GFP+ sox10:DsRed+; Danio rerio; RNA Seq	GSM2713938		1	GFP/DsRed double positive cells populations were collected into RLT lysis buffer Qiagen and total RNA was immediately extracted using the RNeasy Micro kit Qiagen according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip Agilent Santa Clara CA and then reverse transcribed into cDNA using the SMARTer kit Clontech Mountain View CA. cDNA amplification was adjusted based on the RNA input quantity and the size and amount of generated cDNA was measured by BioAnalyzer. The samples were sonicated on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA with NextFlex adapters Bioo Scientific Austin TX. Libraries were assessed by Bioanalyzer and quantified using qPCR Kapa Library Quantification kit. Sequencing was performed on a NextSeq 500 75 bp paired end reads Illumina San Diego CA. Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.	GEO Accession:GSM2713938	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP113259			nr2f25mut1_GC101_S2_R1_001.fastq.gz nr2f25mut1_GC101_S2_R2_001.fastq.gz	fastq fastq	4981028448.0	32769924.0	GSM2713938 r1	0:76 1:76	A:840950063;C:1614355757;G:1644774381;T:880078202;N:870045	76	76			840950063	1614355757	1644774381	880078202	870045	SRX3024623	SRS2373888	SRA589735	GEO	Crump Lab, Stem Cell Biology and Regenerative Medicine, University of Southern California	2	0.92321	0.92152	0.11945	0.11592	0.82627	0.83368	0.7663	0.79383	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	unknown	unknown		United States	2017-07-20	Pharyngula	Embryo	Pharyngeal Arch	Multi-system