run_metadata: 68253

This data as json

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68253	SRR17691955	SRX13855134	SRS11731659	SRP356155	PRJNA799333	RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf	GSE194158	Transcriptome Analysis	This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.				Photoreceptors rep1	GSM5829828		tissue:Retina\|age:42 hpf\|expression of reporter genes:ath5+ crx+ ptf1a	Photoreceptors rep1	Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina Read counting performed using featureCounts version 1.6.3 featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample	Retina	MS 222 0.01% prior to dissection of the retinas.	Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.	Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf.	age:42 hpf\|expression of reporter genes:ath5+ crx+ ptf1a	GSM5829828	GSM5829828: Photoreceptors rep1; Danio rerio; RNA Seq	GSM5829828 r1	GSM5829828	1	Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP356155		loader:fastq load.py	L39833_Track-77360_R1.fastq.gz	fastq	1992015632.0	26210732.0	GSM5829828 r1	0:76	A:567270537;C:418033884;G:425507861;T:580998753;N:204597	76				567270537	418033884	425507861	580998753	204597	SRX13855134	SRS11731659	SRA1360146	Max Planck Institute of Molecular Cell Biology and Genetics	Max Planck Institute of Molecular Cell Biology and Genetics	1	0.88374		0.06752		0.82731		0.54807		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Germany	2022-01-21	Pharyngula	Embryo	Eye	Sensory System