{"database": "metadata", "table": "run_metadata", "rows": [[64216, "SRR14326883", "SRX10681832", "SRS8775211", "SRP316409", "PRJNA725224", "Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]", "GSE173350", "Transcriptome Analysis", "The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so  we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24  36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.", null, "pubmed:34303700", null, "scRNAseq olig2 eGFP 24hpf [reanalysis]", "GSM5266258", null, "tissue:spinal cord cells|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8", "scRNAseq olig2 eGFP 24hpf [reanalysis]", "Generated cell feature counts for each single cell RNAseq library using cellranger count   transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X  CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData  FindVariableFeaturesselection.method = 'vst'  nfeatures = 2000  ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference'  RunPCAnpcs=100  RunUMAPdims = 1:40  FindNeighborsreduction   'pca'  dims = 1:40  FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf  dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData  FindVariableFeaturesselection.method = 'vst'  nfeatures = 2000  ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference'  RunPCAnpcs=100  RunUMAPdims = 1:40  FindNeighborsreduction = 'pca'  dims = 1:40  FindClustersresolution=  1.2  dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells", "spinal cord cells", "No treatment was applied to the samples.", "24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 \u03bcl of pre chilled Ca free Ringers solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES  pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 \u03bcl of protease solution 10 mg/ml BI protease  125 U/ml DNase  2.5 mM EDTA  1X PBS was added  to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 \u03bcl of STOP solution 30% FBS  0.8 mM CaCl2  1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4\u00b0C and supernatant was removed. On ice  1 ml of chilled suspension media 1% FBS  0.8 mM CaCl2  50 U/ml Penicillin  0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4\u00b0C. Supernatant was removed  and 400 \u03bcl of chilled suspension media was added and solution was filtered through a 35 \u03bcm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 \u03bcl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075.\u00a0 Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.\u00a0", "Embryos were raised at 28.5\u00b0C in E3 media 5 mM NaCl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4 at pH 7.4  with sodium bicarbonate  sorted for good health and staged accordingly to developmental morphological features and hpf", "developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8", "GSM5266258", "GSM5266258: scRNAseq olig2 eGFP 24hpf [reanalysis]; Danio rerio; RNA Seq", "GSM5266258", null, "1", "24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 \u03bcl of pre chilled Ca free Ringers solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES  pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 \u03bcl of protease solution 10 mg/ml BI protease  125 U/ml DNase  2.5 mM EDTA  1X PBS was added  to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 \u03bcl of STOP solution 30% FBS  0.8 mM CaCl2  1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4\u00b0C and supernatant was removed. On ice  1 ml of chilled suspension media 1% FBS  0.8 mM CaCl2  50 U/ml Penicillin  0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4\u00b0C. Supernatant was removed  and 400 \u03bcl of chilled suspension media was added and solution was filtered through a 35 \u03bcm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 \u03bcl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075.  Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.", "GEO Accession:GSM5266258", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP316409", null, null, "Olig2_eGFP_24hfp_4_S40_L001_R1_001.fastq Olig2_eGFP_24hfp_4_S40_L001_R2_001.fastq", "fastq fastq", 17382967792.0, 57559496.0, "GSM5266258 r4", "0:151 1:151", "A:4767137063;C:3044788720;G:4846983492;T:4723757048;N:301469", 151, 151, null, null, 4767137063, 3044788720, 4846983492, 4723757048, 301469, "SRX10681832", "SRS8775211", "SRA1223938", "GEO", "Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus", 2, 0.0, 0.83086, 0.0, 0.0679, 1.0, 0.83944, null, 0.4968, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-04-26", "Pharyngula", "Embryo", "Spinal Cord", "Nervous 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": ["64216"], "units": {}, "query_ms": 7.437908003339544}