run_metadata: 62017

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
62017	SRR13115071	SRX9557284	SRS7764916	SRP293760	PRJNA680334	Single cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development	GSE162031	Transcriptome Analysis	Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements. Overall design: Single cell RNA sequencing was performed on pronephric cells from 1 2 dpf and 3 dpf zebrafish larvae.		pubmed:33749326		ZNC151116 10	GSM4930043		source name:Pr1phros\|line:Tgwt1b:GFP; Tgcdh17:GFP\|tissue:pr1phros\|age:2 dpf	ZNC151116 10	For image aquisition intensity extraction and basecalling HiSeq Control Software 2.0.2 RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. Zebrafish gene models were based on Ensembl release 74 http://www.ensembl.org were improved for 3’ UTR annotations as described previously Junker JP et al. Genome wide RNA Tomography in the zebrafish embryo. Cell 159: 662 675 2014 The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics the number of observed UMIs was converted into transcript counts Gruen et al. 2014. Genome build: Ensembl release 74 Supplementary files format and content: CSV files columns represent each cell barcode total barcodes used = 192 rows represent the geneid and the values in the file are the quantified number of transcripts.	Pronephros	The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.	Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol	Tgwt1b:GFP; Tgcdh17:GFP transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division Medical Center Freiburg	line:Tgwt1b:GFP; Tgcdh17:GFP\|tissue:pr1phros\|age:2 dpf	GSM4930043	GSM4930043: ZNC151116 10; Danio rerio; RNA Seq	GSM4930043		1	Pronephric cells were isolated as previously described Yakulov TA et al. Nat Commun 9: 3660 2018. As described in mCEL Seq2 protocol Hashimshony et al. 2016 and Herman et al. 2018 Adapted from TruSeq Small RNA Library Preparation Protocol	GEO Accession:GSM4930043	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP293760			ZNC151116_10_R1.fastq.gz ZNC151116_10_R2.fastq.gz	fastq fastq	1177857100.0	11778571.0	GSM4930043 r1	0:30 1:70	A:285930811;C:206559699;G:218627577;T:465859304;N:879709	30	70			285930811	206559699	218627577	465859304	879709	SRX9557284	SRS7764916	SRA1162774	GEO	Renal Division, Department of Medicine, University Freiburg Medical Center	2	0.45186	0.88321	0.43175	0.19229	0.9946	0.83169	0.80603	0.72758	30	70	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	small_rna	trueseq	sc	single_cell_plate	celseq		Germany	2020-11-23	Hatching	Embryo	Embryo Imprecise	All anatomical structures