run_metadata: 51017

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
51017	SRR8435109	SRX5242689	SRS4245412	SRP178513	PRJNA514721	Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut	GSE124970	Transcriptome Analysis	The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2 and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples with 3 replicates each.		pubmed:31474562		cldn15la GFP+ f Dex+ LREs 3	GSM3560348		tissue:cldn15la GFP+ f Dex+ LREs\|strain:EK\|genotype/variation:wild type\|age:6 dpf type:cldn15la GFP Alexa Fluor 568 double positive lysosome rich enterocytes LREs	cldn15la GFP+ f Dex+ LREs 3	HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.	cldn15la GFP+ f Dex+ LREs	Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.	At 6 dpf 24 hrs post gavage zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.		strain:EK\|genotype/variation:wild type\|age:6 dpf type:cldn15la GFP Alexa Fluor 568 double positive lysosome rich enterocytes LREs	GSM3560348	GSM3560348: cldn15la GFP+ f Dex+ LREs 3; Danio rerio; RNA Seq	GSM3560348		1	At 6 dpf 24 hrs post gavage zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM3560348	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP178513			LRE_3.fastq.gz	fastq	3319359633.0	65085483.0	GSM3560348 r1	0:51 1:0	A:939171958;C:728294535;G:735458210;T:914956028;N:1478902	51	0			939171958	728294535	735458210	914956028	1478902	SRX5242689	SRS4245412	SRA833636	GEO	Duke University	1	0.92838		0.08491		0.73507		0.45124		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		United States	2019-01-11	Larval	Larval	Undetermined	Undetermined