{"database": "metadata", "table": "run_metadata", "rows": [[72138, "SRR22266709", "SRX18243018", "SRS15738743", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver  on both uninjured animals  and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0  1  2  3  and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "3 dpa  replicate 3  scRNAseq", "GSM6727463", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2  Tg 3.5ubb:LOXP EGFP LOXP mCherry  Tgfabp10a:CFP NTR|treatment:3 dpa", "3 dpa  replicate 3  scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools  mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live  nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit  with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp  Read 2: 50 bp  Read 1 Index: 8 bp  Custom Read 1 primer  GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2  Tg 3.5ubb:LOXP EGFP LOXP mCherry  Tgfabp10a:CFP NTR|treatment:3 dpa", "GSM6727463", "GSM6727463: 3 dpa  replicate 3  scRNAseq; Danio rerio; RNA Seq", "GSM6727463 r1", "GSM6727463", "1", "Adult zebrafish livers were enyzmatically dissociated and live  nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit  with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp  Read 2: 50 bp  Read 1 Index: 8 bp  Custom Read 1 primer  GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11Q_IO7720_S5_R1_001.fastq.gz 20200107_LIB11Q_IO7720_S5_R2_001.fastq.gz", "fastq fastq", 4327529324.0, 58480126.0, "GSM6727463 r1", "0:25 1:49", "A:1223359778;C:914892543;G:970000561;T:1218683252;N:593190", 25, 49, null, null, 1223359778, 914892543, 970000561, 1218683252, 593190, "SRX18243018", "SRS15738743", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00899, 0.83745, 0.00188, 0.04633, 0.99431, 0.84492, 0.84148, 0.68261, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["72138"], "units": {}, "query_ms": 15.415143992868252}