{"database": "metadata", "table": "run_metadata", "rows": [[60595, "SRR12424270", "SRX8920143", "SRS7176691", "SRP276929", "PRJNA656271", "Single cell RNA seq analysis of pMN neural progenitors from zebrafish", "GSE155988", "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:32680935", null, "scRNAseq olig2 eGFP 24hpf", "GSM4718656", null, "tissue:spinal cord cells|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8", "scRNAseq olig2 eGFP 24hpf", "Raw sequencing reads were demultiplexed  mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes  more than 5% of UMIs derived from mitochondrial genes  or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation  chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples 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", "GSM4718656", "GSM4718656: scRNAseq olig2 eGFP 24hpf; Danio rerio; RNA Seq", "GSM4718656", 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:GSM4718656", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP276929", null, null, "Olig2_eGFP_24hfp_1_S10_L001_R1_001.fastq.gz Olig2_eGFP_24hfp_1_S10_L001_R2_001.fastq.gz", "fastq fastq", 21279021170.0, 70460335.0, "GSM4718656 r1", "0:151 1:151", "A:5842145219;C:3712477572;G:5933108587;T:5790922441;N:367351", 151, 151, null, null, 5842145219, 3712477572, 5933108587, 5790922441, 367351, "SRX8920143", "SRS7176691", "SRA1111061", "GEO", "University of Colorado School of Medicine", 2, 0.0, 0.83071, 0.0, 0.06828, 1.0, 0.8406, null, 0.5078, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-08-10", "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": ["60595"], "units": {}, "query_ms": 9.573076997185126}