{"database": "metadata", "table": "run_metadata", "rows": [[41746, "SRR5125770", "SRX2440172", "SRS1874759", "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.", null, "pubmed:28096348", null, "Prox 4", "GSM2436978", null, "tissue:Proximal region of caudal fin|strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584693", "Prox 4", "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", "Proximal region of caudal fin", null, "Collected fin regions were flash frozen in liquid nitrogen and stored at  80\u02daC. 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.", null, "strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584693", "GSM2436978", "GSM2436978: Prox 4; Danio rerio; RNA Seq", "GSM2436978", null, "1", "Collected fin regions were flash frozen in liquid nitrogen and stored at  80\u02daC. 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:GSM2436978", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP095533", null, null, "AC6VTYANXX_US-1584693_ACAGTG_L007_R2_001.fastq.gz AC6VTYANXX_US-1584693_ACAGTG_L007_R1_001.fastq.gz", "fastq fastq", 1900457880.0, 18631940.0, "GSM2436978 r1", "0:51 1:51", "A:479961702;C:461532736;G:470280019;T:486828615;N:1854808", 51, 51, null, null, 479961702, 461532736, 470280019, 486828615, 1854808, "SRX2440172", "SRS1874759", "SRA507993", "GEO", "University of Washington", 2, 0.8576, 0.86993, 0.2678, 0.27331, 0.74278, 0.74754, 0.57447, 0.57758, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2016-12-22", "Undetermined", "Adult", "Fin", "Surface Structure"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["41746"], "units": {}, "query_ms": 11.87346400001843}