run_metadata: 41888

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
41888	SRR5320521	SRX2619926	SRS2029889	SRP101558	PRJNA378498	Functional Analysis of Regional Gene Expression in Zebrafish Craniofacial Development	GSE95812	Transcriptome Analysis	Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite their significance for craniofacial development how genetic programs drive this regionalization remains poorly understood. Here we use combinatorial labeling of zebrafish cranial neural crest derived cells CNCCs to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 Edn1 signaling in the intermediate joint forming region yet a surprisingly minor role in ventral most regions. Analysis of co variance across multiple sequencing experiments further reveals clusters of co regulated genes with in situ hybridization confirming the expression of novel genes with domain specific expression. We then performed mutational analysis of a number of these genes which uncovered antagonistic functions of two Edn1 targets follistatin a fsta and emx2 in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders. Overall design: mRNA profiles of 3 distinct populations of zebrafish pharyngeal arch cells isolated using FACS from 36 hpf wild type WT zebrafish. fli1a:GFP+;sox10:DsRed and fli1a:GFP ;sox10:DsRed+ populations were also isolated at the same time and sequenced as controls 3 replicate each. Additionally there are mRNA profiles of zebrafish pharyngeal arches all domains combined isolated by FACS from 36 hpf zebrafish with the following genotypes: edn1 / 2 replicates jag1b / jag1b+/+ control hsp70I:Gal4; UAS:Edn1 hsp70I:Gal4; UAS:Nicd and hsp70I:Gal4 control.		pubmed:28705894		WT sox10 1	GSM2526400		tissue:Mixed/Ear\|developmental stage:20 hpf\|genotype:WT\|treatment:N1	WT sox10 1	Raw sequencing data in Fastq format was imported into the Partek Flow® interface for alignment and quantification. Pre alignment QC showed that the reads from all samples had generally high quality with the average Phred quality score for each sample being above 30. Reads were then trimmed from both ends based on Phred quality score with a minimum end quality level of 20 and a minimum acceptable read length of 25. The TopHat 2 algorithm was used to align the trimmed reads to the zebrafish GRCz10 genome assembly Ensembl v80. Aligned reads were then quantified using the Partek E/M algorithm with default parameters to yield the TPM values. Genome build: GRCz10 Supplementary files format and content: csv text files include TPM values for each gene in each sample	Mixed/Ear		GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.		developmental stage:20 hpf\|genotype:WT\|treatment:N1	GSM2526400	GSM2526400: WT sox10 1; Danio rerio; RNA Seq	GSM2526400		1	GFP/DsRed double positive double negative and single positive populations were collected directly into RLT lysis buffer Qiagen. Total RNA was immediately extracted using the RNeasy Micro kit Qiagen following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip Agilent Santa Clara CA. cDNA was then made from the extracted RNA using the SMARTer kit Clontech Mountain View CA according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator Covaris Woburn MA according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit Kapa Biosystems Wilmington MA and NextFlex adapters Bioo Scientific Austin TX. Libraries were visualized by Bioanalyzer analysis and quantified by qPCR Kapa library quantification kit. Sequencing was performed on Illumina HiSeq 2000 50 bp paired end reads and NextSeq 500 75 bp paired end reads machines Illumina San Diego CA. DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.	GEO Accession:GSM2526400	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP101558					5233486400.0	52334864.0	GSM2526400 r1	0:50 1:50	A:1446820250;C:1072511594;G:1151585599;T:1561438904;N:1130053	50	50			1446820250	1072511594	1151585599	1561438904	1130053	SRX2619926	SRS2029889	SRA543392	GEO	Crump Lab, Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California	2	0.92493	0.72674	0.15162	0.12408	0.73551	0.76349	0.5106	0.51362	50	50	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown		United States	2017-03-08	Segmentation	Embryo	Undetermined	Embryo Imprecise