run_metadata: 59246

This data as json

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
59246	SRR12974158	SRX9426445	SRS7641316	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		pubmed:33789339		SNJM01	GSM4878622		source name:Intestinal dissection\|tissue:Intestine\|treatment:untreated\|genotype/variation:wildtype\|10x chemistry:V3	SNJM01	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 “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” 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:untreated\|genotype/variation:wildtype\|10x chemistry:V3	GSM4878622	GSM4878622: SNJM01; Danio rerio; RNA Seq	GSM4878622		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:GSM4878622	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP261473		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JUCH10 SNJM1 0 G S1 L001 I1 001.fastq.gz read2PairFiles=JUCH10 SNJM1 0 G S1 L001 R1 001.fastq.gz read3PairFiles=JUCH10 SNJM1 0 G S1 L001 R2 001.fastq.gz	JUCH10_SNJM1_0_G_S1_L001_I1_001.fastq.gz JUCH10_SNJM1_0_G_S1_L001_R1_001.fastq.gz JUCH10_SNJM1_0_G_S1_L001_R2_001.fastq.gz	fastq fastq fastq	9359347578.0	100638146.0	GSM4878622 r1	0:8 1:29 2:56	A:2742192040;C:2208968705;G:2007446927;T:2400535057;N:204849	8	29	56		2742192040	2208968705	2007446927	2400535057	204849	SRX9426445	SRS7641316	SRA1075199	GEO	Cho lab, Institute of Personalized medicine, Mount Sinai hospital	1	0.97296		0.04791		0.91259		0.93709		56		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2020-11-03	Larval	Larval	Gut	Digestive System