run_metadata: 34507

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
34507	SRR31854002	SRX27213774	SRS23662881	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.				LPS 10hr	GSM8703959		source name:Body\|tissue:Body\|genotype:AB\|age:6 dpf\|treatment:LPS\|geo loc name:missing\|collection date:missing	LPS 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		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.		tissue:Body\|genotype:AB\|age:6 dpf\|treatment:LPS	GSM8703959	GSM8703959: LPS 10hr; Danio rerio; RNA Seq	GSM8703959 r1	GSM8703959	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP554457		loader:fastq load.py	LPS_S11_L004_I1_001.fastq.gz LPS_S11_L004_R1_001.fastq.gz LPS_S11_L004_R2_001.fastq.gz	fastq fastq fastq	27411098848.0	215835424.0	GSM8703959 r4	0:8 1:28 2:91	A:5383218071;C:4459553243;G:5297438054;T:4498601355;N:2212861	8	28	91		5383218071	4459553243	5297438054	4498601355	2212861	SRX27213774	SRS23662881	SRA2042619	Jerison, Physics, University of Chicago	Jerison, Physics, University of Chicago												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2024-12-30	Larval	Larval	Trunk	Surface Structure