run_metadata: 66954

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
66954	SRR16905280	SRX13097723	SRS11034036	SRP345451	PRJNA779419	Transcriptomic profiling of adult zebrafish photoreceptors	GSE188560	Transcriptome Analysis	Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.		pubmed:36745553		UVc1s02	GSM5685584		tissue:Dissociated adult photoreceptors\|transgenic line:Tgopn1sw1:GFP\|cell type:UV c1s\|age:Adult	UVc1s02	Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples	Dissociated adult photoreceptors	post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.	Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.		transgenic line:Tgopn1sw1:GFP\|cell type:UV c1s\|age:Adult	GSM5685584	GSM5685584: UVc1s02; Danio rerio; RNA Seq	GSM5685584 r1	GSM5685584	1	Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP345451			U2_R1.fastq.gz U2_R2.fastq.gz	fastq fastq	3575236392.0	14187446.0	GSM5685584 r1	0:126 1:126	A:975203222;C:812648233;G:846540921;T:940013729;N:830287	126	126			975203222	812648233	846540921	940013729	830287	SRX13097723	SRS11034036	SRA1538252	Wei Li, Unit of Retinal Neurophysiology, National Eye Institute	Wei Li, Unit of Retinal Neurophysiology, National Eye Institute	2	0.79703	0.80022	0.11068	0.1139	0.88101	0.88162	0.43397	0.42506	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq		United States	2021-11-10	Adult	Adult	Eye	Sensory System