{"database": "metadata", "table": "run_metadata", "rows": [[29174, "SRR27237224", "SRX22915658", "SRS19883761", "SRP478464", "PRJNA1053781", "Single cell gene expression profie of developing photoreceptor cells in larval zebrafish", "GSE250379", "Other", "Molecular underpinnings of vertebrate retinal differentiation and maturation are poorly understood  particularly for non mammalian species. We generated single cell transcriptome data from the larval zebrafish retina and characterized gene expression diversity among photoreceptor subtypes and their progenitors. Overall design: GFP positive differentiating photoreceptor cells and bipolar cells were collected from 4 dpf larval transgenic zebrafish  Tgcrx:EGFPstl887  using fluorescence activated cell sorting.", "parent bioproject:PRJNA1050288", "pubmed:39531499", null, "retina  scRNA seq", "GSM7978132", null, "source name:retina|tissue:retina|genotype:Tgcrx:EGFPstl887|developmental stage:4 dpf|geo loc name:missing|collection date:missing", "retina  scRNA seq", "Read alignment and initial quality control were performed using Cell Ranger software version 7.0.0  10X Genomics. Assembly: GRCz11 Supplementary files format and content: Tab separated value file and matrix file", "retina", null, "Fifty heads were dissected from 4 dpf heterozygous Tgcrx:GFPstl887Tg larvae. Following dissection  eyes were stored in ice cold Hanks\u2019 Balanced Salt Solution HBSS until all eyes were harvested. Once the eyes were collected  HBSS was removed and the eyes were incubated in 400 \u00b5l of calcium/magnesium free HBSS containing 0.4 mg papain Worthington Biochem for 15 min at 37\u00b0C. 800 \u00b5l of 10% fetal bovine serum FBS in Dulbecco's Modified Eagle Medium DMEM containing 5mM MgCl2 and 120 units DNaseI Roche were added to the mixture and incubated for 5 min at 37\u00b0C. Cells were then resuspended in 300 \u00b5l of sorting buffer 2.5 mM EDTA  25 mM HEPES  1% bovine serum albumin BSA in calcium/magnesium free HBSS. Cells were sorted on an Aria II FACS machine BD biosciences with gating based on forward scatter  side scatter  and GFP fluorescence and collected in 700 \u03bcl of D PBS without xxx+ and Mg2+  supplemented with 0.4 % BSA D PBS CMF in 1.5 ml microcentrifuge tubes. The collected cells were then centrifuged at 300\u00d7g for 5 min  washed with D PBS CMF  centrifuged  and supernatant reduced to 80 \u00b5l. Cell density was quantified on a hemocytometer  and  5000 cells were used for single cell library preparation. A library for single cell RNA seq was constructed with the Chromium v3  platform  10X  Genomics   Pleasanton   CA according to the manufacturer protocol.", null, "tissue:retina|genotype:Tgcrx:EGFPstl887|developmental stage:4 dpf", "GSM7978132", "GSM7978132: retina  scRNA seq; Danio rerio; RNA Seq", "GSM7978132 r1", "GSM7978132", "1", "Fifty heads were dissected from 4 dpf heterozygous Tgcrx:GFPstl887Tg larvae. Following dissection  eyes were stored in ice cold Hanks' Balanced Salt Solution HBSS until all eyes were harvested. Once the eyes were collected  HBSS was removed and the eyes were incubated in 400 \u00b5l of calcium/magnesium free HBSS containing 0.4 mg papain Worthington Biochem for 15 min at 37\u00b0C. 800 \u00b5l of 10% fetal bovine serum FBS in Dulbecco's Modified Eagle Medium DMEM containing 5mM MgCl2 and 120 units DNaseI Roche were added to the mixture and incubated for 5 min at 37\u00b0C. Cells were then resuspended in 300 \u00b5l of sorting buffer 2.5 mM EDTA  25 mM HEPES  1% bovine serum albumin BSA in calcium/magnesium free HBSS. Cells were sorted on an Aria II FACS machine BD biosciences with gating based on forward scatter  side scatter  and GFP fluorescence and collected in 700 \u03bcl of D PBS without xxx+ and Mg2+  supplemented with 0.4 % BSA D PBS CMF in 1.5 ml microcentrifuge tubes. The collected cells were then centrifuged at 300\u00d7g for 5 min  washed with D PBS CMF  centrifuged  and supernatant reduced to 80 \u00b5l. Cell density was quantified on a hemocytometer  and  5000 cells were used for single cell library preparation. A library for single cell RNA seq was constructed with the Chromium v3  platform  10X  Genomics   Pleasanton   CA according to the manufacturer protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP478464", null, "loader:fastq load.py", "crx.crx_S1_L003_R1_001.fastq.gz crx.crx_S1_L003_R2_001.fastq.gz", "fastq fastq", 45170138494.0, 253764823.0, "GSM7978132 r1", "0:28 1:150", "A:13826023801;C:9023674621;G:9590649474;T:12728940802;N:849796", 28, 150, null, null, 13826023801, 9023674621, 9590649474, 12728940802, 849796, "SRX22915658", "SRS19883761", "SRA1770358", "Pathology and Immunology, Washington University School of Medicine", "Pathology and Immunology, Washington University School of Medicine", 2, 0.0046, 0.87155, 0.00206, 0.2263, 0.99168, 0.77784, 0.30223, 0.50112, 28, 150, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-12-17", "Larval", "Larval", "Eye", "Sensory System"]], "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": ["29174"], "units": {}, "query_ms": 11.212874000193551}