run_metadata: 53600

This data as json

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53600	SRR9961214	SRX6708747	SRS5262462	SRP218232	PRJNA560046	Anterior Posterior gene expression differences in zebrafish Vagus motor neurons	GSE135780	Transcriptome Analysis	We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the anterior or posterior 1/4 of Kaede expressing Vagus motor neurons dissecting the posterior hindbrain dissociating to single cell suspension and manually picking photoconverted cells. We sequenced 3 replicates of 100 cells per population.		pubmed:32302545		PB	GSM4029957		tissue:Posterior Vagus motor neurons\|cell type:Vagus motor neurons\|developmental stage:28 hpf 30 hpf\|genotype:Tgisl1:Kaede	PB	Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0. Counts were generated from Tophat alignments at the gene level employing the "intersection strict" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count.	Posterior Vagus motor neurons		The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.		cell type:Vagus motor neurons\|developmental stage:28 hpf 30 hpf\|genotype:Tgisl1:Kaede	GSM4029957	GSM4029957: PB; Danio rerio; RNA Seq	GSM4029957		1	The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA. The cell suspension was then transferred onto a glass coverslip covered with mineral oil and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.	GEO Accession:GSM4029957	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP218232			PB.R1.fastq.gz PB.R2.fastq.gz	fastq fastq	1947375800.0	19473758.0	GSM4029957 r1	0:50 1:50	A:540064062;C:431763279;G:436932637;T:538589534;N:26288	50	50			540064062	431763279	436932637	538589534	26288	SRX6708747	SRS5262462	SRA938975	GEO	Fred Hutchinson Cancer Research Center	2	0.87385	0.88639	0.10632	0.10717	0.84025	0.84011	0.46398	0.46592	50	50	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq		United States	2019-08-13	Pharyngula	Embryo	Brain	Nervous System