run_metadata: 34227

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
34227	SRR31604150	SRX26968913	SRS23437611	SRP549343	PRJNA1192682	Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells	PRJNA1192682	Other	The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.					GF mCherry positive		strain:EK\|age:6 dpf\|collection date:2021\|geo loc name:USA: Durham NC\|sex:not applicable\|tissue:Sorted cells\|Condition:Germ free\|Fluorescence:mCherry positive GFP positive\|BioSampleModel:Model organism or animal									scRNA seq of danio rerio: mCherry positive GFP positive sorted cells from GF larvae	7066 P2	7066 P2	TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM Library & Gel Bead Kit v3.1.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP549343			GF_LRE_2_S2_L001_I1_001.fastq.gz GF_LRE_2_S2_L001_R1_001.fastq.gz GF_LRE_2_S2_L001_R2_001.fastq.gz GF_LRE_2_S2_L002_I1_001.fastq.gz GF_LRE_2_S2_L002_R1_001.fastq.gz GF_LRE_2_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq	16477189470.0	130771345.0	GF LRE 2 S2 L001 I1 001.fastq.gz	0:8 1:28 2:90	A:3664699916;C:2552676887;G:2506770636;T:3044709641;N:563970	8	28	90		3664699916	2552676887	2506770636	3044709641	563970	SRX26968913	SRS23437611	SRA2025080	Duke University\|Cell Biology	Duke University												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2024-12-04	Larval	Larval	Undetermined	Undetermined