{"database": "metadata", "table": "run_metadata", "rows": [[34503, "SRR31853998", "SRX27213775", "SRS23662882", "SRP554457", "PRJNA1204318", "Spatially structured inflammatory response in the presence of a uniform stimulus: RNAseq screen", "GSE285534", "Transcriptome Analysis", "Inflammatory responses occur within the complex spatial context of tissues and organs  and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here  we used single cell RNA sequencing to screen for genes differentially expressed under LPS lipopolysaccharide and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis. Overall design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS P. Aeuruginosa  Sigma  or E3 alone vehicle control  for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification.", null, null, null, "Control 10hr", "GSM8703960", null, "source name:Body|tissue:Body|genotype:AB|age:6 dpf|treatment:control|geo loc name:missing|collection date:missing", "Control 10hr", "Sequencing data was aligned to the zebrafish reference genome GRCz11 using 10X Genomics Cellranger software 6.1.2. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Body", null, "Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.", null, "tissue:Body|genotype:AB|age:6 dpf|treatment:control", "GSM8703960", "GSM8703960: Control 10hr; Danio rerio; RNA Seq", "GSM8703960 r1", "GSM8703960", "1", "Collected tissue was transferred to 300 uL of digestion buffer Final concentration .12 mg/mL Liberase TL Millipore Sigma  5401020001 and 22.5 U/mL DNAse I Worthington  LS006331 in .25\\% Trypsin/EDTA Gibco  25200 056 in an eppendorf tube. The tube was placed on a heat block at 30 C for 6 minutes  and a P1000 pipette was used to triturate. The samples were centrifuged at 400 g for 5 minutes and the digestion buffer was removed. Cells were resuspended in 1 mL wash buffer .1\\% BSA in PBS per tube; filtered through a 40 um cell strainer; centrifuged for 5 minutes at 400 g; and resuspended in 30 50 ul wash buffer. Cell density was estimated by counting on a hemocytometer prior to loading into a 10X Genomics lane. The 10X Genomics Chromium three prime platform and reagents v3.1 kit was used for cell encapsulation  reverse transcription  and library preparation  according to manufacturer instructions manual revision D  with 12 cycles of preamplification. For cell encapsulation  one lane of the 10X chip was used for each treatment group LPS and control  at a target of 16 000 cells/lane.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP554457", null, "loader:fastq load.py", "Control_S12_L004_I1_001.fastq.gz Control_S12_L004_R1_001.fastq.gz Control_S12_L004_R2_001.fastq.gz", "fastq fastq fastq", 55438180589.0, 436521107.0, "GSM8703960 r4", "0:8 1:28 2:91", "A:11203472019;C:8826429348;G:9895249162;T:9793520783;N:4749425", 8, 28, 91, null, 11203472019, 8826429348, 9895249162, 9793520783, 4749425, "SRX27213775", "SRS23662882", "SRA2042619", "Jerison, Physics, University of Chicago", "Jerison, Physics, University of Chicago", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-30", "Larval", "Larval", "Trunk", "Surface Structure"]], "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": ["34503"], "units": {}, "query_ms": 10.90248700347729}