run_metadata: 33323

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
33323	SRR29927557	SRX25421493	SRS22081649	SRP521592	PRJNA1139127	Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration	PRJNA1139127	Other	Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.				ONL Control rep1	MCWR 2019 000140		strain:wild type\|dev stage:adult\|collection date:2019 10 18\|geo loc name:USA: Wisconsin Milwaukee\|sex:male\|tissue:retina\|treatment:ONL Control rep1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: naive outer nuclear layer	ONL Control rep1	ONL Control rep1	SMART Seqv4			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP521592			MCWR_2019_000140_S11_L001_R1_001.fastq.gz MCWR_2019_000140_S11_L001_R2_001.fastq.gz MCWR_2019_000140_S11_L002_R1_001.fastq.gz MCWR_2019_000140_S11_L002_R2_001.fastq.gz	fastq fastq fastq fastq	12797441059.0	42498374.0	MCWR 2019 000140 S11 L001 R1 001.fastq.gz	0:150.56 1:150.56	A:3214435348;C:3160301138;G:3218337754;T:3204200743;N:166076	150	150			3214435348	3160301138	3218337754	3204200743	166076	SRX25421493	SRS22081649	SRA1930690	Medical College of Wisconsin\|Cell Biology, Neurobiology, and Anatomy	Medical College of Wisconsin	2	0.95836	0.95804	0.0672	0.06787	0.79255	0.7933	0.37626	0.37493	149	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	smartseq		United States	2024-07-23	Adult	Adult	Eye	Sensory System