run_metadata: 33857

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
33857	SRR30769782	SRX26172015	SRS22716029	SRP534198	PRJNA1164198	Analysis of The Senescence Secretome During Zebrafish Retina Regeneration	GSE277792	Transcriptome Analysis	Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently we discovered that this process is aided by a population of damage induced senescent immune cells. As part of the Senescence Associated Secretory Phenotype SASP senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury including two distinct acute damage regimens as well as a chronic genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3 12 and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.		pubmed:40308558		NMDA Only 12dpi Rep 1	GSM8530618		source name:Retina\|tissue:Retina\|genotype:NMDA Damage\|treatment:Control\|geo loc name:missing\|collection date:missing	NMDA Only 12dpi Rep 1	Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10 a wrapper for CutAdapt v4.8 using the paired and illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters validateMappings and gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode	Retina		RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit		tissue:Retina\|genotype:NMDA Damage\|treatment:Control	GSM8530618	GSM8530618: NMDA Only 12dpi Rep 1; Danio rerio; RNA Seq	GSM8530618 r1	GSM8530618	1	RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus		SRP534198			11384-GK-0007_S1_L005_R1_001.fastq.gz 11384-GK-0007_S1_L005_R2_001.fastq.gz	fastq fastq	14797480862.0	48998281.0	GSM8530618 r1	0:151 1:151	A:3900528784;C:3418459440;G:3652120707;T:3823647040;N:2724891	151	151			3900528784	3418459440	3652120707	3823647040	2724891	SRX26172015	SRS22716029	SRA1977341	Patton Lab, Biological Sciences, Vanderbilt University	Patton Lab, Biological Sciences, Vanderbilt University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		United States	2024-09-23	Undetermined	Undetermined	Eye	Sensory System