{"database": "metadata", "table": "run_metadata", "rows": [[33017, "SRR29633215", "SRX25139204", "SRS21831217", "SRP516661", "PRJNA1129181", "A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing", "GSE271002", "Transcriptome Analysis", "To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish  we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation  and DAPI  live cells were sorted by FACS.", null, "pubmed:40252728", null, "Control  ablation 4dpf", "GSM8366960", null, "source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control|geo loc name:missing|collection date:missing", "Control  ablation 4dpf", "Demultiplexing of raw Illumina sequencing files  barcoding processing  gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files", "Dissected larval intestines", null, "Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28\u00b0C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70\u00b5m membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.", null, "tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control", "GSM8366960", "GSM8366960: Control  ablation 4dpf; Danio rerio; RNA Seq", "GSM8366960 r1", "GSM8366960", "1", "Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28\u00b0C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70\u00b5m membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP516661", null, "loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R1 001.fastq.gz   read2PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R2 001.fastq.gz   read3PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I1 001.fastq.gz   read4PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I2 001.fastq.gz", "Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R1_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I1_001.fastq.gz", "fastq fastq fastq fastq", 115286504000.0, 360270325.0, "GSM8366960 r1", "0:150 1:150 2:10 3:10", "A:32679027944;C:17748865933;G:17885040590;T:39764959491;N:3203542", 150, 150, 10, 10, 32679027944, 17748865933, 17885040590, 39764959491, 3203542, "SRX25139204", "SRS21831217", "SRA1911905", "Karolinska Institutet", "Karolinska Institutet", 2, 0.39015, 0.90036, 0.10989, 0.19421, 0.97845, 0.79401, 0.69547, 0.6103, 150, 150, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Sweden", "2024-06-27", "Larval", "Larval", "Gut", "Digestive 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": ["33017"], "units": {}, "query_ms": 6.697967000945937}