run_metadata: 60521

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
60521	SRR12340457	SRX8840228	SRS7103462	SRP273985	PRJNA649260	THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE]	GSE155294	Transcriptome Analysis	Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.		pubmed:34006636		Gross A1 3 1 18 S5 R1 001	GSM4698652		tissue:retinal pigment epithelium\|treatment:MTZ \|time point:7dpi\|replicate:3	Gross A1 3 1 18 S5 R1 001	All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint	retinal pigment epithelium	A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium	≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions	Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.	treatment:MTZ \|time point:7dpi\|replicate:3	GSM4698652	GSM4698652: Gross A1 3 1 18 S5 R1 001; Danio rerio; RNA Seq	GSM4698652		1	≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions	GEO Accession:GSM4698652	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP273985			Gross_A1_3_1_18_S5_R1_001.fastq.gz Gross_A1_3_1_18_S5_R2_001.fastq.gz	fastq fastq	8604655350.0	57364369.0	GSM4698652 r1	0:75 1:75	A:2438039854;C:1874282641;G:1790105674;T:2500628946;N:1598235	75	75			2438039854	1874282641	1790105674	2500628946	1598235	SRX8840228	SRS7103462	SRA1104764	GEO	Ophthalmology, University of Pittsburgh School Of Medicine	2	0.88472	0.88444	0.19788	0.19728	0.79044	0.79403	0.56866	0.56514	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq		United States	2020-07-28	Larval	Larval	Eye	Sensory System