run_metadata: 44522

This data as json

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44522	SRR6261584	SRX3367866	SRS2665508	SRP124289	PRJNA417290	Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints	GSE106474	Transcriptome Analysis	Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5.	parent bioproject:PRJNA417291	pubmed:29700225		WT zebrafish embryo 60% epiboly Rep 1	GSM2838513		tissue:Wild type TLAB Embryo\|developmental stage:60% epiboly\|hpf batch:DS2	WT zebrafish embryo 60% epiboly Rep 1	Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts	Wild type TLAB Embryo		Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction.	Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging.	developmental stage:60% epiboly\|hpf batch:DS2	GSM2838513	GSM2838513: WT zebrafish embryo 60% epiboly Rep 1; Danio rerio; RNA Seq	GSM2838513		1	Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction.	GEO Accession:GSM2838513	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP124289		dangling references:treat as unmapped	ZF60-DS2.bam	bam	9427367847.0	197041685.0	GSM2838513 r1	0:47.84	A:2840380863;C:1954270941;G:2115387210;T:2512438103;N:4890730	47				2840380863	1954270941	2115387210	2512438103	4890730	SRX3367866	SRS2665508	SRA628740	GEO	Schier Lab, Molecular and Cellular Biology, Harvard University	1	0.90013		0.10453		0.84609		0.67284		50		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq		United States	2017-11-02	Gastrula	Embryo	Embryo Imprecise	All anatomical structures