{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"Oligo-dT\", experiment.library_source = \"TRANSCRIPTOMIC\" and technology = \"10x\"", "rows": [[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", null, "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", null, null, null, null, null, null, null, null, "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", null, "ERP128749", "Illumina NovaSeq 6000 paired end sequencing; 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Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I4-Hiseq_S2_L001_R1_001.fastq.gz S3-I4-Hiseq_S2_L001_R2_001.fastq.gz", "fastq fastq", 3487596300.0, 11625321.0, "S3 I4 Hiseq S2 L001 R1 001.fastq.gz", "0:150 1:150", "A:892777135;C:554604922;G:602698080;T:1437353489;N:162674", 150, 150, null, null, 892777135, 554604922, 602698080, 1437353489, 162674, "SRX6875873", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.20171, 0.89797, 0.05294, 0.15018, 0.98557, 0.78865, 0.5155, 0.57581, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54728, "SRR10150437", "SRX6875872", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of  juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I4S1", "I4S1", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. 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Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I3-Hiseq_S2_L001_R1_001.fastq.gz S3-I3-Hiseq_S2_L001_R2_001.fastq.gz", "fastq fastq", 4273728900.0, 14245763.0, "S3 I3 Hiseq S2 L001 R1 001.fastq.gz", "0:150 1:150", "A:1093044190;C:680068409;G:740119940;T:1760292389;N:203972", 150, 150, null, null, 1093044190, 680068409, 740119940, 1760292389, 203972, "SRX6875871", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.20465, 0.90036, 0.05289, 0.14865, 0.98553, 0.7877, 0.49162, 0.55234, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54730, "SRR10150439", "SRX6875870", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of  juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I3S1", "I3S1", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP222654", null, null, "S3-I3-Hiseq_S1_L001_R1_001.fastq.gz S3-I3-Hiseq_S1_L001_R2_001.fastq.gz", "fastq fastq", 9027772200.0, 30092574.0, "S3 I3 Hiseq S1 L001 R1 001.fastq.gz", "0:150 1:150", "A:2295058606;C:1618993604;G:1725968569;T:3387689160;N:62261", 150, 150, null, null, 2295058606, 1618993604, 1725968569, 3387689160, 62261, "SRX6875870", "SRS5411730", "SRA965192", "Sun Yat- sen University|Life Sicence School", "Sun Yat- sen University", 2, 0.07429, 0.86204, 0.01816, 0.14367, 0.98638, 0.78754, 0.51152, 0.56418, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-09-20", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [54731, "SRR10150440", "SRX6875869", "SRS5411730", "SRP222654", "PRJNA571187", "single cell RNA Seq of juvenile zebrafish", "PRJNA571187", "Other", "single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit", null, null, null, "whole organism single cell RNA seq of  juvenile zebrafish", "SC2S3", null, "strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "single cell RNA Seq of zebrafish: whole organism of juvenile", "I2S2", "I2S2", "A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. 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Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. 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Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA  and transferred into 200 L Dissociation buffer  1  TrypLE Thermo Fisher Scientific in 1  HBSS [Ca+/Mg+ free] GIBCO. Next  the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich  10 mg/mL pronase Sigma Aldrich  10 mg/mL proteinase K Sigma Aldrich were added  and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. 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