run_metadata: 51184

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
51184	SRR8559983	SRX5361482	SRS4352012	SRP185597	PRJNA521808	Effect of PTBA on acute kidney injury during AKI	GSE126418	Transcriptome Analysis	PTBA has been published to increase renal tubular cell proliferation increased survival and increased renal functional recovery in fish and various models of murine models of acute kidney injury. Immunohistological analyses suggested increased cell proliferation is accompanied by increased epithelial to mesenchymal transition in the RTECs. In order to elucidate pathways responsible for the increased repair response post compound treatment larval zebrafish were given AKI and treated with PTBA analogue UPHD25 or DMSO. Results suggests that epithelial related genes were downregulated while mesenchymal related genes were upregulated with injury and compound treatment. Results further validate our immunohistological finding that our compound increase post AKI repair by increasing EMT in renal tubular cells. Overall design: At 3dpf larval zebrafish are given acute kidney injury with gentamicin microinjection. 2 xxx post injury larvae with AKI are selected and treated with 1uM of PTBA analogue UPHD25 or vehicle control 1% DMSO. The fish were treated with UPHD25 or DMSO for 24 hours. Then pronephric kidneys were collected using DDT collagenase I and manual collection. Total 100 larvae were collected per sample per replicate. Each treatment group was repeated with 3 biological replicates. RNA was collected and sequenced.		pubmed:30890583		AKI UPHD25 Rep1	GSM3598108		source name:zebrafish pr1phros\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1uM UPHD25	AKI UPHD25 Rep1	Reads were aligned using Hisat2 v2.1.0 with the UCSC zebrafish genome version danRer11. Reads for multiple lanes of the same sample were pooled together. Gene level counts were calculated using featureCounts in the R package Rsubread v1.24.2 with the Ensembl GTF file. Genome build: danRer11 Supplementary files format and content: Tab delimited text file with gene level counts for all samples.	zebrafish pronephros	At 2dpi 5dpf injured larvae were incubated with 1uM UPHD25 1%DMSO or control 1% DMSO for 24 hours at 28C	100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 rounds of PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample.	Larvae were incubated in E3 medium until treatment at 3dpf.	genotype transgenic line:TgPT:egfp\|tissue:pr1phros\|microinjection:gentamicin\|treatment:1uM UPHD25	GSM3598108	GSM3598108: AKI UPHD25 Rep1; Danio rerio; RNA Seq	GSM3598108		1	70 100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit QIAGEN TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay Qubit and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing approximately 30 40 million reads per sample. Four samples of the first biological replicates were pooled and sequenced on a single flow cell. Second and third replicates were pooled and ran on 2 flow cells.	GEO Accession:GSM3598108	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP185597			1_AKI_UPHD25_R1_001.fastq.gz 1_AKI_UPHD25_R2_001.fastq.gz	fastq fastq	6059912984.0	40145674.0	GSM3598108 r1	0:75.50 1:75.45	A:1580876814;C:1444343868;G:1437343041;T:1596089533;N:1259728	75	75			1580876814	1444343868	1437343041	1596089533	1259728	SRX5361482	SRS4352012	SRA848340	GEO	Hukriede, Developmental Biology, University of Pittsburgh	2	0.95682	0.9573	0.09115	0.08901	0.69643	0.70242	0.49657	0.48863	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown		United States	2019-02-11	Larval	Larval	Kidney	Renal System