{"database": "metadata", "table": "run_metadata", "rows": [[71758, "SRR22013539", "SRX17995701", "SRS15506855", "SRP404046", "PRJNA893216", "Insulin like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth", "GSE216359", "Transcriptome Analysis", "We generate a single cell transcriptome dataset to characterize zebrafish fin regenerative outgrowth and explore coordinated cell behaviors. Overall design: Regenerated fin tissue was collected from 3 and 7 dy post amputation zebrafish caudal fins and analyzed using scRNA seq", null, "pubmed:37290497", null, "3 dpa  scRNA seq", "GSM6670934", null, "source name:Caudal fin|tissue:Caudal fin|time:3 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult|geo loc name:missing|collection date:missing", "3 dpa  scRNA seq", "Pseudoalignment and processing of raw reads was done in Kallisto/Bustools https://github.com/pachterlab/kb python to generate a cell data set for Monocle3 https://cole trapnell lab.github.io/monocle3/ Assembly: GRCz11.99 Supplementary files format and content: rds file of cell data set", "Caudal fin", null, "Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 \u03bcm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics. Briefly  cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up  amplified by PCR  and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "tissue:Caudal fin|time:3 dpa|genotype:Tgsp7:EGFP;Tgtph1b:mCherry|Stage:Adult", "GSM6670934", "GSM6670934: 3 dpa  scRNA seq; Danio rerio; RNA Seq", "GSM6670934 r1", "GSM6670934", "1", "Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice  diced  then washed with L 15 media supplemented with 1X GlutaMax  1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml  Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 \u03bcm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer'", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP404046", null, "loader:fastq load.py", "3669_3dpa_S4_L002_I1_001.fastq.gz 3669_3dpa_S4_L002_R1_001.fastq.gz 3669_3dpa_S4_L002_R2_001.fastq.gz", "fastq fastq fastq", 18947450035.0, 138302555.0, "GSM6670934 r2", "0:8 1:28 2:101", "A:4126083375;C:2867407006;G:2991995583;T:3979778947;N:3293144", 8, 28, 101, null, 4126083375, 2867407006, 2991995583, 3979778947, 3293144, "SRX17995701", "SRS15506855", "SRA1525679", "Stankunas, Institute of Molecular Biology, University of Oregon", "Stankunas, Institute of Molecular Biology, University of Oregon", 1, 0.91921, null, 0.19517, null, 0.78524, null, 0.57129, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-10-22", "Adult", "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": ["71758"], "units": {}, "query_ms": 22.392735998437274}