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
10177,ERR5858456,ERX5504345,ERS6343449,ERP128749,PRJEB44676,scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10390,Transcriptome Analysis,To analyse lesion induced gene regulation in progenitor cells at single cell resolution  we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.,Lesi1d,SAMEA8658903,University Of Edinburgh,ENA first public:2021 05 24|ENA last update:2021 05 24|External Id:SAMEA8658903|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 05 24T00:14:32Z|INSDC last update:2021 05 24T00:14:32Z|INSDC status:public|Submitter Id:E MTAB 10390:Lesi1d|age:4|broker name:ArrayExpress|cell type:ependymo radial glial cell|common name:zebrafish|developmental stage:larval day 4|immunophenotype:Her4.3+ positive|injury:spinal injury lesion|organism part:spinal cord|sample name:E MTAB 10390:Lesi1d|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10390:Lesioned p,Lesioned p,scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.,Experimental Factor: injury:spinal injury lesion,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128749,Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24,Lesioned.bam,bam,49902588630.0,554473207.0,E MTAB 10390:Lesioned,0:90,A:14713351178;C:10191139050;G:10897887675;T:14095967201;N:4243526,90,,,,14713351178,10191139050,10897887675,14095967201,4243526,ERX5504345,ERS6343449,ERA4142789,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.91197,,0.29137,,0.7568,,0.56523,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-05-24,Larval,Larval,Spinal Cord,Nervous System
60587,SRR12424278,SRX8920145,SRS7176693,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.,,pubmed:32680935,,scRNAseq olig2 eGFP 48hpf,GSM4718658,,tissue:spinal cord cells|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 48hpf,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:48 hpf ZFIN ID: ZDB ALT 041129 8,GSM4718658,GSM4718658: scRNAseq olig2 eGFP 48hpf; Danio rerio; RNA Seq,GSM4718658,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM4718658,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP276929,,,olig2_egfp_48hpf_1_S41_L001_R1_001.fastq.gz olig2_egfp_48hpf_1_S41_L001_R2_001.fastq.gz,fastq fastq,18778651430.0,62180965.0,GSM4718658 r1,0:151 1:151,A:6542554044;C:3515052559;G:3489753648;T:5231107020;N:184159,151,151,,,6542554044,3515052559,3489753648,5231107020,184159,SRX8920145,SRS7176693,SRA1111061,GEO,University of Colorado School of Medicine,2,0.0,0.90055,0.0,0.21162,1.0,0.77776,,0.53718,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-08-10,Hatching,Embryo,Spinal Cord,Nervous System
60588,SRR12424279,SRX8920145,SRS7176693,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.,,pubmed:32680935,,scRNAseq olig2 eGFP 48hpf,GSM4718658,,tissue:spinal cord cells|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 48hpf,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:48 hpf ZFIN ID: ZDB ALT 041129 8,GSM4718658,GSM4718658: scRNAseq olig2 eGFP 48hpf; Danio rerio; RNA Seq,GSM4718658,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM4718658,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP276929,,,olig2_egfp_48hpf_2_S42_L001_R1_001.fastq.gz olig2_egfp_48hpf_2_S42_L001_R2_001.fastq.gz,fastq fastq,22242782898.0,73651599.0,GSM4718658 r2,0:151 1:151,A:7753674261;C:4160150132;G:4127581173;T:6201157562;N:219770,151,151,,,7753674261,4160150132,4127581173,6201157562,219770,SRX8920145,SRS7176693,SRA1111061,GEO,University of Colorado School of Medicine,2,0.0,0.90097,0.0,0.2127,1.0,0.77966,,0.54192,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-08-10,Hatching,Embryo,Spinal Cord,Nervous System
60589,SRR12424280,SRX8920145,SRS7176693,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.,,pubmed:32680935,,scRNAseq olig2 eGFP 48hpf,GSM4718658,,tissue:spinal cord cells|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 48hpf,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:48 hpf ZFIN ID: ZDB ALT 041129 8,GSM4718658,GSM4718658: scRNAseq olig2 eGFP 48hpf; Danio rerio; RNA Seq,GSM4718658,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM4718658,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP276929,,,olig2_egfp_48hpf_3_S43_L001_R2_001.fastq.gz olig2_egfp_48hpf_3_S43_L001_R1_001.fastq.gz,fastq fastq,25591190986.0,84739043.0,GSM4718658 r3,0:151 1:151,A:8917343424;C:4797392797;G:4757647263;T:7118554564;N:252938,151,151,,,8917343424,4797392797,4757647263,7118554564,252938,SRX8920145,SRS7176693,SRA1111061,GEO,University of Colorado School of Medicine,2,0.0,0.90089,0.0,0.2095,1.0,0.78078,,0.53755,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-08-10,Hatching,Embryo,Spinal Cord,Nervous System
60590,SRR12424281,SRX8920145,SRS7176693,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.,,pubmed:32680935,,scRNAseq olig2 eGFP 48hpf,GSM4718658,,tissue:spinal cord cells|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 48hpf,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:48 hpf ZFIN ID: ZDB ALT 041129 8,GSM4718658,GSM4718658: scRNAseq olig2 eGFP 48hpf; Danio rerio; RNA Seq,GSM4718658,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM4718658,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP276929,,,olig2_egfp_48hpf_4_S44_L001_R1_001.fastq.gz olig2_egfp_48hpf_4_S44_L001_R2_001.fastq.gz,fastq fastq,25546281170.0,84590335.0,GSM4718658 r4,0:151 1:151,A:8905009196;C:4774524700;G:4734395060;T:7132103501;N:248713,151,151,,,8905009196,4774524700,4734395060,7132103501,248713,SRX8920145,SRS7176693,SRA1111061,GEO,University of Colorado School of Medicine,2,0.0,0.90169,0.0,0.21158,1.0,0.77697,,0.54006,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-08-10,Hatching,Embryo,Spinal Cord,Nervous System
60591,SRR12424274,SRX8920144,SRS7176692,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.,,pubmed:32680935,,scRNAseq olig2 eGFP 36hpf,GSM4718657,,tissue:spinal cord cells|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 36hpf,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:36 hpf ZFIN ID: ZDB ALT 041129 8,GSM4718657,GSM4718657: scRNAseq olig2 eGFP 36hpf; Danio rerio; RNA Seq,GSM4718657,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM4718657,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP276929,,,Olig2_eGFP_36hfp_1_S69_L001_R1_001.fastq.gz Olig2_eGFP_36hfp_1_S69_L001_R2_001.fastq.gz,fastq fastq,13366864582.0,44261141.0,GSM4718657 r1,0:151 1:151,A:3721647646;C:2385939960;G:3494552257;T:3764514262;N:210457,151,151,,,3721647646,2385939960,3494552257,3764514262,210457,SRX8920144,SRS7176692,SRA1111061,GEO,University of Colorado School of Medicine,2,0.0,0.85449,0.0,0.08264,1.0,0.84086,,0.50156,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-08-10,Pharyngula,Embryo,Spinal Cord,Nervous System
60592,SRR12424275,SRX8920144,SRS7176692,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.,,pubmed:32680935,,scRNAseq olig2 eGFP 36hpf,GSM4718657,,tissue:spinal cord cells|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 36hpf,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:36 hpf ZFIN ID: ZDB ALT 041129 8,GSM4718657,GSM4718657: scRNAseq olig2 eGFP 36hpf; Danio rerio; RNA Seq,GSM4718657,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM4718657,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP276929,,,Olig2_eGFP_36hfp_2_S70_L001_R1_001.fastq.gz Olig2_eGFP_36hfp_2_S70_L001_R2_001.fastq.gz,fastq fastq,10606211914.0,35119907.0,GSM4718657 r2,0:151 1:151,A:2974656607;C:1869869441;G:2750621038;T:3010898673;N:166155,151,151,,,2974656607,1869869441,2750621038,3010898673,166155,SRX8920144,SRS7176692,SRA1111061,GEO,University of Colorado School of Medicine,2,0.0,0.84822,0.0,0.08456,1.0,0.83719,,0.51503,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-08-10,Pharyngula,Embryo,Spinal Cord,Nervous System
60593,SRR12424276,SRX8920144,SRS7176692,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.,,pubmed:32680935,,scRNAseq olig2 eGFP 36hpf,GSM4718657,,tissue:spinal cord cells|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 36hpf,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:36 hpf ZFIN ID: ZDB ALT 041129 8,GSM4718657,GSM4718657: scRNAseq olig2 eGFP 36hpf; Danio rerio; RNA Seq,GSM4718657,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM4718657,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP276929,,,Olig2_eGFP_36hfp_3_S71_L001_R1_001.fastq.gz Olig2_eGFP_36hfp_3_S71_L001_R2_001.fastq.gz,fastq fastq,15614508642.0,51703671.0,GSM4718657 r3,0:151 1:151,A:4330312984;C:2826855730;G:4093245712;T:4363847925;N:246291,151,151,,,4330312984,2826855730,4093245712,4363847925,246291,SRX8920144,SRS7176692,SRA1111061,GEO,University of Colorado School of Medicine,2,0.0,0.8543,0.0,0.08219,1.0,0.83727,,0.51892,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-08-10,Pharyngula,Embryo,Spinal Cord,Nervous System
60594,SRR12424277,SRX8920144,SRS7176692,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.,,pubmed:32680935,,scRNAseq olig2 eGFP 36hpf,GSM4718657,,tissue:spinal cord cells|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 36hpf,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:36 hpf ZFIN ID: ZDB ALT 041129 8,GSM4718657,GSM4718657: scRNAseq olig2 eGFP 36hpf; Danio rerio; RNA Seq,GSM4718657,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM4718657,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP276929,,,Olig2_eGFP_36hfp_4_S72_L001_R1_001.fastq.gz Olig2_eGFP_36hfp_4_S72_L001_R2_001.fastq.gz,fastq fastq,10707787198.0,35456249.0,GSM4718657 r4,0:151 1:151,A:2981466900;C:1909696186;G:2797297473;T:3019156550;N:170089,151,151,,,2981466900,1909696186,2797297473,3019156550,170089,SRX8920144,SRS7176692,SRA1111061,GEO,University of Colorado School of Medicine,2,0.0,0.85466,0.0,0.08381,1.0,0.83562,,0.51035,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-08-10,Pharyngula,Embryo,Spinal Cord,Nervous System
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.,,pubmed:32680935,,scRNAseq olig2 eGFP 24hpf,GSM4718656,,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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,,SRP276929,,,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,,,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,,0.5078,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-08-10,Pharyngula,Embryo,Spinal Cord,Nervous System
60596,SRR12424271,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.,,pubmed:32680935,,scRNAseq olig2 eGFP 24hpf,GSM4718656,,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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,,SRP276929,,,Olig2_eGFP_24hfp_2_S20_L001_R1_001.fastq.gz Olig2_eGFP_24hfp_2_S20_L001_R2_001.fastq.gz,fastq fastq,22414094210.0,74218855.0,GSM4718656 r2,0:151 1:151,A:6145677154;C:3904876630;G:6254105391;T:6109049174;N:385861,151,151,,,6145677154,3904876630,6254105391,6109049174,385861,SRX8920143,SRS7176691,SRA1111061,GEO,University of Colorado School of Medicine,2,0.0,0.83148,0.0,0.06914,1.0,0.84033,,0.49666,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-08-10,Pharyngula,Embryo,Spinal Cord,Nervous System
60597,SRR12424272,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.,,pubmed:32680935,,scRNAseq olig2 eGFP 24hpf,GSM4718656,,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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,,SRP276929,,,Olig2_eGFP_24hfp_3_S30_L001_R1_001.fastq.gz Olig2_eGFP_24hfp_3_S30_L001_R2_001.fastq.gz,fastq fastq,16406166006.0,54325053.0,GSM4718656 r3,0:151 1:151,A:4513103872;C:2865727260;G:4569430659;T:4457621166;N:283049,151,151,,,4513103872,2865727260,4569430659,4457621166,283049,SRX8920143,SRS7176691,SRA1111061,GEO,University of Colorado School of Medicine,2,0.0,0.82928,0.0,0.06878,1.0,0.83989,,0.4916,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-08-10,Pharyngula,Embryo,Spinal Cord,Nervous System
60598,SRR12424273,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.,,pubmed:32680935,,scRNAseq olig2 eGFP 24hpf,GSM4718656,,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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,,SRP276929,,,Olig2_eGFP_24hfp_4_S40_L001_R1_001.fastq.gz Olig2_eGFP_24hfp_4_S40_L001_R2_001.fastq.gz,fastq fastq,17382967792.0,57559496.0,GSM4718656 r4,0:151 1:151,A:4767137063;C:3044788720;G:4846983492;T:4723757048;N:301469,151,151,,,4767137063,3044788720,4846983492,4723757048,301469,SRX8920143,SRS7176691,SRA1111061,GEO,University of Colorado School of Medicine,2,0.0,0.83084,0.0,0.06779,1.0,0.83948,,0.49689,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-08-10,Pharyngula,Embryo,Spinal Cord,Nervous System
62942,SRR13447021,SRX9860257,SRS8040688,SRP301983,PRJNA692494,Localized EMT reprograms glial progenitors to promote spinal cord repair [single cell RNA seq],GSE164944,Other,Single nuclear RNA sequencing was performed on spinal cord tissues from Tggfap:EGFP zebrafish at 1 xxx post injury using the 10x Genomics platform. Overall design: Single nuclear RNA sequencing of spinal cord tissue.,parent bioproject:PRJNA692492,pubmed:33609461,,single cell injured spinal cord,GSM5023610,,tissue:5 xxx post injury spinal cord nuclear|tissues:spinal cord|rna population:nuclear|time point:5 xxx post injury,single cell injured spinal cord,Aligned reads were analyzed using the Seurat package v3.1.4 within R v3.6.3. Cells that have unique number of genes between 200 to 4000 and a mitochondrial gene percentage less than five were filtered. The “SCTransform” function was used for normalization  scaling and finding variable features. SCTransform returned 3000 highly variable features for downstream analysis. Significant principal components were determined using “ElbowPlot” function. Forty principal components were selected to create a Shared Nearest Neighbour SNN graph using the “FindNeighbours” function. Clustering was performed by the Louvain algorithm using the function “FindClusters” and the resolution parameter was set to one. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 40 principle components and to visualize the data in two dimensional space “RunUMAP” function Differential gene expression for individual cluster was identified using Wilcoxon rank sum tests in the “FindAllMarkers” function. Supplementary files format and content: RDS file,5 xxx post injury spinal cord nuclear,Adult zebrafish were subjected to complete spinal cord transection.,gfap:EGFP transgenic animals were subjected to SCI and 2 mm SC tissue sections spanning the lesion site were collected at 1 wpi. Nuclei were isolated from 45 pooled SC tissues. For single nuclear library preparation on the 10x Genomics platform  the Chromium Single Cell 3′ GEM Library and Gel Bead Kit v3 cat# 1000092 and the Chromium Chip B Single Cell Kit cat# 1000074 were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits V3 User Guide. The resulting cDNA libraries were quantified on an Agilent Tapestation and sequenced on Illumina HiSeq 3000.,,tissues:spinal cord|rna population:nuclear|time point:5 xxx post injury,GSM5023610,GSM5023610: single cell injured spinal cord; Danio rerio; RNA Seq,GSM5023610,,1,gfap:EGFP transgenic animals were subjected to SCI and 2 mm SC tissue sections spanning the lesion site were collected at 1 wpi. Nuclei were isolated from 45 pooled SC tissues. For single nuclear library preparation on the 10x Genomics platform  the Chromium Single Cell 3′ GEM Library and Gel Bead Kit v3 cat# 1000092 and the Chromium Chip B Single Cell Kit cat# 1000074 were used according to the manufacturer's instructions in the Chromium Single Cell 3′ Reagents Kits V3 User Guide. The resulting cDNA libraries were quantified on an Agilent Tapestation and sequenced on Illumina HiSeq 3000.,GEO Accession:GSM5023610,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP301983,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=ZB nuc S1 L007 I1 001.fastq.gz   read2PairFiles=ZB nuc S1 L007 R1 001.fastq.gz   read3PairFiles=ZB nuc S1 L007 R2 001.fastq.gz,ZB_nuc_S1_L007_R2_001.fastq.gz ZB_nuc_S1_L007_R1_001.fastq.gz ZB_nuc_S1_L007_I1_001.fastq.gz,fastq fastq fastq,134333186988.0,436146711.0,GSM5023610 r1,0:8 1:150 2:150,A:34573306207;C:23174725516;G:24790836286;T:51771968988;N:22349991,8,150,150,,34573306207,23174725516,24790836286,51771968988,22349991,SRX9860257,SRS8040688,SRA1184553,GEO,"Developmental Biology, Washington University",1,0.72186,,0.41754,,0.80551,,0.54979,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-01-15,Adult,Adult,Spinal Cord,Nervous System
64205,SRR14326888,SRX10681834,SRS8775213,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.,,pubmed:34303700,,scRNAseq olig2 eGFP 48hpf [reanalysis],GSM5266260,,tissue:spinal cord cells|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 48hpf [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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:48 hpf ZFIN ID: ZDB ALT 041129 8,GSM5266260,GSM5266260: scRNAseq olig2 eGFP 48hpf [reanalysis]; Danio rerio; RNA Seq,GSM5266260,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM5266260,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP316409,,,olig2_egfp_48hpf_1_S41_L001_R1_001.fastq olig2_egfp_48hpf_1_S41_L001_R2_001.fastq,fastq fastq,18778651430.0,62180965.0,GSM5266260 r1,0:151 1:151,A:6542554044;C:3515052559;G:3489753648;T:5231107020;N:184159,151,151,,,6542554044,3515052559,3489753648,5231107020,184159,SRX10681834,SRS8775213,SRA1223938,GEO,"Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus",2,0.0,0.90056,0.0,0.21167,1.0,0.7781,,0.53738,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-26,Hatching,Embryo,Spinal Cord,Nervous System
64206,SRR14326889,SRX10681834,SRS8775213,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.,,pubmed:34303700,,scRNAseq olig2 eGFP 48hpf [reanalysis],GSM5266260,,tissue:spinal cord cells|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 48hpf [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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:48 hpf ZFIN ID: ZDB ALT 041129 8,GSM5266260,GSM5266260: scRNAseq olig2 eGFP 48hpf [reanalysis]; Danio rerio; RNA Seq,GSM5266260,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM5266260,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP316409,,,olig2_egfp_48hpf_2_S42_L001_R1_001.fastq olig2_egfp_48hpf_2_S42_L001_R2_001.fastq,fastq fastq,22242782898.0,73651599.0,GSM5266260 r2,0:151 1:151,A:7753674261;C:4160150132;G:4127581173;T:6201157562;N:219770,151,151,,,7753674261,4160150132,4127581173,6201157562,219770,SRX10681834,SRS8775213,SRA1223938,GEO,"Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus",2,0.0,0.90096,0.0,0.21256,1.0,0.77928,,0.54059,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-26,Hatching,Embryo,Spinal Cord,Nervous System
64207,SRR14326890,SRX10681834,SRS8775213,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.,,pubmed:34303700,,scRNAseq olig2 eGFP 48hpf [reanalysis],GSM5266260,,tissue:spinal cord cells|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 48hpf [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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:48 hpf ZFIN ID: ZDB ALT 041129 8,GSM5266260,GSM5266260: scRNAseq olig2 eGFP 48hpf [reanalysis]; Danio rerio; RNA Seq,GSM5266260,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM5266260,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP316409,,,olig2_egfp_48hpf_3_S43_L001_R2_001.fastq olig2_egfp_48hpf_3_S43_L001_R1_001.fastq,fastq fastq,25591190986.0,84739043.0,GSM5266260 r3,0:151 1:151,A:8917343424;C:4797392797;G:4757647263;T:7118554564;N:252938,151,151,,,8917343424,4797392797,4757647263,7118554564,252938,SRX10681834,SRS8775213,SRA1223938,GEO,"Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus",2,0.0,0.90089,0.0,0.20934,1.0,0.78086,,0.53725,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-26,Hatching,Embryo,Spinal Cord,Nervous System
64208,SRR14326891,SRX10681834,SRS8775213,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.,,pubmed:34303700,,scRNAseq olig2 eGFP 48hpf [reanalysis],GSM5266260,,tissue:spinal cord cells|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 48hpf [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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:48 hpf ZFIN ID: ZDB ALT 041129 8,GSM5266260,GSM5266260: scRNAseq olig2 eGFP 48hpf [reanalysis]; Danio rerio; RNA Seq,GSM5266260,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM5266260,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP316409,,,olig2_egfp_48hpf_4_S44_L001_R1_001.fastq olig2_egfp_48hpf_4_S44_L001_R2_001.fastq,fastq fastq,25546281170.0,84590335.0,GSM5266260 r4,0:151 1:151,A:8905009196;C:4774524700;G:4734395060;T:7132103501;N:248713,151,151,,,8905009196,4774524700,4734395060,7132103501,248713,SRX10681834,SRS8775213,SRA1223938,GEO,"Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus",2,0.0,0.90171,0.0,0.21154,1.0,0.77674,,0.53902,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-26,Hatching,Embryo,Spinal Cord,Nervous System
64209,SRR14326884,SRX10681833,SRS8775212,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.,,pubmed:34303700,,scRNAseq olig2 eGFP 36hpf [reanalysis],GSM5266259,,tissue:spinal cord cells|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 36hpf [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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:36 hpf ZFIN ID: ZDB ALT 041129 8,GSM5266259,GSM5266259: scRNAseq olig2 eGFP 36hpf [reanalysis]; Danio rerio; RNA Seq,GSM5266259,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM5266259,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP316409,,,Olig2_eGFP_36hfp_1_S69_L001_R1_001.fastq Olig2_eGFP_36hfp_1_S69_L001_R2_001.fastq,fastq fastq,13366864582.0,44261141.0,GSM5266259 r1,0:151 1:151,A:3721647646;C:2385939960;G:3494552257;T:3764514262;N:210457,151,151,,,3721647646,2385939960,3494552257,3764514262,210457,SRX10681833,SRS8775212,SRA1223938,GEO,"Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus",2,0.0,0.85451,0.0,0.08269,1.0,0.84094,,0.5016,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-26,Pharyngula,Embryo,Spinal Cord,Nervous System
64210,SRR14326885,SRX10681833,SRS8775212,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.,,pubmed:34303700,,scRNAseq olig2 eGFP 36hpf [reanalysis],GSM5266259,,tissue:spinal cord cells|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 36hpf [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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:36 hpf ZFIN ID: ZDB ALT 041129 8,GSM5266259,GSM5266259: scRNAseq olig2 eGFP 36hpf [reanalysis]; Danio rerio; RNA Seq,GSM5266259,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM5266259,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP316409,,,Olig2_eGFP_36hfp_2_S70_L001_R1_001.fastq Olig2_eGFP_36hfp_2_S70_L001_R2_001.fastq,fastq fastq,10606211914.0,35119907.0,GSM5266259 r2,0:151 1:151,A:2974656607;C:1869869441;G:2750621038;T:3010898673;N:166155,151,151,,,2974656607,1869869441,2750621038,3010898673,166155,SRX10681833,SRS8775212,SRA1223938,GEO,"Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus",2,0.0,0.84821,0.0,0.08459,1.0,0.83731,,0.51513,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-26,Pharyngula,Embryo,Spinal Cord,Nervous System
64211,SRR14326886,SRX10681833,SRS8775212,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.,,pubmed:34303700,,scRNAseq olig2 eGFP 36hpf [reanalysis],GSM5266259,,tissue:spinal cord cells|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 36hpf [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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:36 hpf ZFIN ID: ZDB ALT 041129 8,GSM5266259,GSM5266259: scRNAseq olig2 eGFP 36hpf [reanalysis]; Danio rerio; RNA Seq,GSM5266259,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM5266259,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP316409,,,Olig2_eGFP_36hfp_3_S71_L001_R1_001.fastq Olig2_eGFP_36hfp_3_S71_L001_R2_001.fastq,fastq fastq,15614508642.0,51703671.0,GSM5266259 r3,0:151 1:151,A:4330312984;C:2826855730;G:4093245712;T:4363847925;N:246291,151,151,,,4330312984,2826855730,4093245712,4363847925,246291,SRX10681833,SRS8775212,SRA1223938,GEO,"Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus",2,0.0,0.85427,0.0,0.08218,1.0,0.83713,,0.51889,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-26,Pharyngula,Embryo,Spinal Cord,Nervous System
64212,SRR14326887,SRX10681833,SRS8775212,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.,,pubmed:34303700,,scRNAseq olig2 eGFP 36hpf [reanalysis],GSM5266259,,tissue:spinal cord cells|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8,scRNAseq olig2 eGFP 36hpf [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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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:36 hpf ZFIN ID: ZDB ALT 041129 8,GSM5266259,GSM5266259: scRNAseq olig2 eGFP 36hpf [reanalysis]; Danio rerio; RNA Seq,GSM5266259,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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:GSM5266259,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP316409,,,Olig2_eGFP_36hfp_4_S72_L001_R1_001.fastq Olig2_eGFP_36hfp_4_S72_L001_R2_001.fastq,fastq fastq,10707787198.0,35456249.0,GSM5266259 r4,0:151 1:151,A:2981466900;C:1909696186;G:2797297473;T:3019156550;N:170089,151,151,,,2981466900,1909696186,2797297473,3019156550,170089,SRX10681833,SRS8775212,SRA1223938,GEO,"Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus",2,0.0,0.85465,0.0,0.08381,1.0,0.8355,,0.51049,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-26,Pharyngula,Embryo,Spinal Cord,Nervous System
64213,SRR14326880,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.,,pubmed:34303700,,scRNAseq olig2 eGFP 24hpf [reanalysis],GSM5266258,,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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,,SRP316409,,,Olig2_eGFP_24hfp_1_S10_L001_R1_001.fastq Olig2_eGFP_24hfp_1_S10_L001_R2_001.fastq,fastq fastq,21279021170.0,70460335.0,GSM5266258 r1,0:151 1:151,A:5842145219;C:3712477572;G:5933108587;T:5790922441;N:367351,151,151,,,5842145219,3712477572,5933108587,5790922441,367351,SRX10681832,SRS8775211,SRA1223938,GEO,"Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus",2,0.0,0.83071,0.0,0.06834,1.0,0.8407,,0.50743,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-26,Pharyngula,Embryo,Spinal Cord,Nervous System
64214,SRR14326881,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.,,pubmed:34303700,,scRNAseq olig2 eGFP 24hpf [reanalysis],GSM5266258,,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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,,SRP316409,,,Olig2_eGFP_24hfp_2_S20_L001_R1_001.fastq Olig2_eGFP_24hfp_2_S20_L001_R2_001.fastq,fastq fastq,22414094210.0,74218855.0,GSM5266258 r2,0:151 1:151,A:6145677154;C:3904876630;G:6254105391;T:6109049174;N:385861,151,151,,,6145677154,3904876630,6254105391,6109049174,385861,SRX10681832,SRS8775211,SRA1223938,GEO,"Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus",2,0.0,0.83142,0.0,0.06899,1.0,0.84029,,0.49666,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-26,Pharyngula,Embryo,Spinal Cord,Nervous System
64215,SRR14326882,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.,,pubmed:34303700,,scRNAseq olig2 eGFP 24hpf [reanalysis],GSM5266258,,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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,,SRP316409,,,Olig2_eGFP_24hfp_3_S30_L001_R1_001.fastq Olig2_eGFP_24hfp_3_S30_L001_R2_001.fastq,fastq fastq,16406166006.0,54325053.0,GSM5266258 r3,0:151 1:151,A:4513103872;C:2865727260;G:4569430659;T:4457621166;N:283049,151,151,,,4513103872,2865727260,4569430659,4457621166,283049,SRX10681832,SRS8775211,SRA1223938,GEO,"Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus",2,0.0,0.8293,0.0,0.06878,1.0,0.84017,,0.49152,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-26,Pharyngula,Embryo,Spinal Cord,Nervous System
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.,,pubmed:34303700,,scRNAseq olig2 eGFP 24hpf [reanalysis],GSM5266258,,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 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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. ,Embryos were raised at 28.5°C 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,,1,24  36  and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl 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 μl 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 μl 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°C 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°C. Supernatant was removed  and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm 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 μl 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,,SRP316409,,,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,,,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,,0.4968,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-04-26,Pharyngula,Embryo,Spinal Cord,Nervous System