{"database": "metadata", "table": "run_metadata", "rows": [[59237, "SRR12974169", "SRX9426450", "SRS7641321", "SRP261473", "PRJNA632595", "Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways", "GSE150498", "Transcriptome Analysis", "Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish", null, "pubmed:33789339", null, "SNJM06", "GSM4878627", null, "source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS|genotype/variation:wildtype|10x chemistry:V3", "SNJM06", "FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Intestinal dissection", "6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed", "tissue:Intestine|treatment:2X DSS|genotype/variation:wildtype|10x chemistry:V3", "GSM4878627", "GSM4878627: SNJM06; Danio rerio; RNA Seq", "GSM4878627", null, "1", "post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.", "GEO Accession:GSM4878627", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP261473", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM6 0 G S6 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM6 0 G S6 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM6 0 G S6 L002 R2 001.fastq.gz", "JUCH10_SNJM6_0_G_S6_L002_I1_001.fastq.gz JUCH10_SNJM6_0_G_S6_L002_R1_001.fastq.gz JUCH10_SNJM6_0_G_S6_L002_R2_001.fastq.gz", "fastq fastq fastq", 8891805795.0, 95610815.0, "GSM4878627 r2", "0:8 1:29 2:56", "A:2456331697;C:2112784685;G:2006505048;T:2315434557;N:749808", 8, 29, 56, null, 2456331697, 2112784685, 2006505048, 2315434557, 749808, "SRX9426450", "SRS7641321", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96343, null, 0.04559, null, 0.90165, null, 0.84056, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-03", "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": ["59237"], "units": {}, "query_ms": 7.367555997916497}