run_metadata: 63869

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
63869	SRR14144778	SRX10514122	SRS8637874	SRP313536	PRJNA719817	RORa is required for neutrophil migration	GSE171501	Transcriptome Analysis	We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control				RORaDN 3	GSM5226363		tissue:neutrophils\|cell type:neutrophils\|genotype:RORa dominant negative	RORaDN 3	Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 " p Q 10". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis	neutrophils	Transgenic lines expressing RORa dominant negative or mcherry were used.	tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..	zebrafish were grow in circulating system	cell type:neutrophils\|genotype:RORa dominant negative	GSM5226363	GSM5226363: RORaDN 3; Danio rerio; RNA Seq	GSM5226363		1	tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..	GEO Accession:GSM5226363	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP313536		loader:fastq load.py	roraDN-3_S24_R1_001.fastq.gz roraDN-3_S24_R2_001.fastq.gz	fastq fastq	9541970758.0	47237479.0	GSM5226363 r1	0:101 1:101	A:2556115286;C:2215951997;G:2229754627;T:2539986639;N:162209	101	101			2556115286	2215951997	2229754627	2539986639	162209	SRX10514122	SRS8637874	SRA1215296	GEO	Department of Biological Sciences, Purdue University	2	0.94352	0.93947	0.09023	0.08984	0.79224	0.79523	0.45486	0.45588	101	101	B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	trueseq	sc	single_cell_plate	smartseq		United States	2021-04-05	Adult	Adult	Blood	Hematopoietic System