run_metadata: 41742

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
41742	SRR5125774	SRX2440174	SRS1874761	SRP095533	PRJNA358533	Transcriptomic Proteomic and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish	GSE92760	Transcriptome Analysis	Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules few of which have been identified. Here we quantified the global abundance of transcripts proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover 32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus the identification of proximodistal differences in levels of RNAs proteins and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.		pubmed:28096348		Mid 1	GSM2436980		tissue:Middle region of caudal fin\|strain:AB WT\|position:middle\|barcode sample name for sequencing:US 1584725	Mid 1	FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample	Middle region of caudal fin		Collected fin regions were flash frozen in liquid nitrogen and stored at 80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina San Diego CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina San Diego CA with 20 30 million 50 base pair paired end sequences per sample. RNA extraction rRNA depletion library construction and sequencing were done by Covance Genomics Laboratory Seattle WA.		strain:AB WT\|position:middle\|barcode sample name for sequencing:US 1584725	GSM2436980	GSM2436980: Mid 1; Danio rerio; RNA Seq	GSM2436980		1	Collected fin regions were flash frozen in liquid nitrogen and stored at 80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina San Diego CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina San Diego CA with 20 30 million 50 base pair paired end sequences per sample. RNA extraction rRNA depletion library construction and sequencing were done by Covance Genomics Laboratory Seattle WA.	GEO Accession:GSM2436980	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP095533			AC6VTYANXX_US-1584725_TAGCTT_L007_R1_001.fastq.gz AC6VTYANXX_US-1584725_TAGCTT_L007_R2_001.fastq.gz	fastq fastq	1913312634.0	18757967.0	GSM2436980 r1	0:51 1:51	A:492780448;C:454166657;G:462802006;T:501720327;N:1843196	51	51			492780448	454166657	462802006	501720327	1843196	SRX2440174	SRS1874761	SRA507993	GEO	University of Washington	2	0.86908	0.87713	0.26839	0.26807	0.73685	0.7433	0.46738	0.45371	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown		United States	2016-12-22	Undetermined	Adult	Fin	Surface Structure