run_metadata: 40739

This data as json

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40739	SRR3290611	SRX1660377	SRS1360340	SRP072298	PRJNA316318	Analysis of gene expression during the early stages of zebrafish heart valve development	GSE79585	Transcriptome Analysis	We report changes in the levels of gene expression between 48hpf hearts and 56hpf hearts the initial stages of valvulogenesis Overall design: 48hpf and 56hpf hearts were dissected and RNA was extracted. RNA profiles were then generated at each stage using Illumina deep sequencing		pubmed:27221222		56hpf con1 ESD 19 N6	GSM2098627		source name:heart\|line:AB\|tissue:heart\|developmental stage:56hpf	56hpf con1 ESD 19 N6	Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2. Reads were mapped onto the zv9 assembly of Danio rerio genome using Tophat2.0.10 and bowtie 2 2.1.0. Quantification of gene expression has been performed using HTSeq 0.5.4p3. Normalization was performed using DESeq 1.10.1. Genome build: zv9 Supplementary files format and content: tabulated text file containing normalized read counts.	heart		Dissected hearts were lysed and the RNA extracted using a Nucleospin XS kit from Machinery Nagel according to the manufacturers instructions Amplified cDNA was prepared from 5 ng of total RNA using the Ovation RNA seq system V2 NuGEN Technologies Inc. following manufacturer's instructions. Briefly total RNA were reverse transcribed into first strand cDNA using a combination of random and poly T DNA/RNA chimeric SPIA primers. Priming sites created by a heating fragmentation of mRNA within the cDNA/mRNA complex were then used to synthesize the second strand cDNA using a DNA polymerase. The resulting double stranded cDNA with a unique RNA/DNA heteroduplex at one end were purified using Agencourt RNAClean XP beads Beckman Coulter Inc. and used as substrate in the linear amplification process SPIA single primer isothermal amplification. Amplified cDNA was purified using AMPure XP beads Beckman Coulter Inc. and 500 ng was fragmented by sonication using a Covaris E210 instrument with duty cycle: 10X intensity: 5 and cycle/burst: 200 for 180 seconds. The next steps of RNA Seq Library preparation were performed on the Mondrian™ SP Workstation using Ovation® SP Ultralow Library Systems kit NuGEN Technologies Inc. according to manufacturer's instructions. Briefly 100 ng of amplified cDNA were blunted phosphorylated and ligated to indexed adapter dimers. The libraries were then enriched by PCR amplification 2 min at 72 degrees Celsius; [30 sec at 94 degrees Celsius 30 sec at 60 degrees Celsius 1 min at 72 degrees Celsius] x 8 cycles; 5 min at 72 degrees Celsius and surplus PCR primers were removed by purification using AMPure XP beads. DNA libraries were checked for quality using 2100 Bioanalyzer Agilent and quantified using Kapa Sybr Fast Light Cycler 480 qPCR Kit Kapa Biosystems according to manufacturer's recommendations. The libraries were loaded in the flow cell at 7pM concentration and sequenced in the Illumina Hiseq 2500 as single end 50 base reads following Illumina’s instructions.	Embryos were collected staged and grown under standard conditions	line:AB\|tissue:heart\|developmental stage:56hpf	GSM2098627	GSM2098627: 56hpf con1 ESD 19 N6; Danio rerio; RNA Seq	GSM2098627		1	Dissected hearts were lysed and the RNA extracted using a Nucleospin XS kit from Machinery Nagel according to the manufacturers instructions Amplified cDNA was prepared from 5 ng of total RNA using the Ovation RNA seq system V2 NuGEN Technologies Inc. following manufacturer's instructions. Briefly total RNA were reverse transcribed into first strand cDNA using a combination of random and poly T DNA/RNA chimeric SPIA primers. Priming sites created by a heating fragmentation of mRNA within the cDNA/mRNA complex were then used to synthesize the second strand cDNA using a DNA polymerase. The resulting double stranded cDNA with a unique RNA/DNA heteroduplex at one end were purified using Agencourt RNAClean XP beads Beckman Coulter Inc. and used as substrate in the linear amplification process SPIA single primer isothermal amplification. Amplified cDNA was purified using AMPure XP beads Beckman Coulter Inc. and 500 ng was fragmented by sonication using a Covaris E210 instrument with duty cycle: 10X intensity: 5 and cycle/burst: 200 for 180 seconds. The next steps of RNA Seq Library preparation were performed on the Mondrian™ SP Workstation using Ovation® SP Ultralow Library Systems kit NuGEN Technologies Inc. according to manufacturer's instructions. Briefly 100 ng of amplified cDNA were blunted phosphorylated and ligated to indexed adapter dimers. The libraries were then enriched by PCR amplification 2 min at 72 degrees Celsius; [30 sec at 94 degrees Celsius 30 sec at 60 degrees Celsius 1 min at 72 degrees Celsius] x 8 cycles; 5 min at 72 degrees Celsius and surplus PCR primers were removed by purification using AMPure XP beads. DNA libraries were checked for quality using 2100 Bioanalyzer Agilent and quantified using Kapa Sybr Fast Light Cycler 480 qPCR Kit Kapa Biosystems according to manufacturer's recommendations. The libraries were loaded in the flow cell at 7pM concentration and sequenced in the Illumina Hiseq 2500 as single end 50 base reads following Illumina’s instructions.	GEO Accession:GSM2098627	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP072298			ESD-19_N6.fastq.gz	fastq	2100229600.0	42004592.0	GSM2098627 r1	0:50	A:601981170;C:436442080;G:439494399;T:622070663;N:241288	50				601981170	436442080	439494399	622070663	241288	SRX1660377	SRS1360340	SRA395278	GEO	IGBMC	1	0.87598		0.32196		0.74146		0.58008		50		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown		France	2016-03-24	Hatching	Embryo	Heart	Cardiovascular System