run_metadata: 67071

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
67071	SRR17048175	SRX13237915	SRS11162459	SRP348087	PRJNA783915	RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection	GSE189627	Transcriptome Analysis	Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected mutant PBS injected WT M. marinum infected mutant M. marinum infected.		pubmed:39916610		WT Inf 7 [210019 15 WT Inf 31 s15 S225]	GSM5704988		source name:WT Inf kidney\|treatment:M. marinum infection\|genotype:wild type\|disease state:low dose 4 wpi\|tissue:Zebrafish kidney	WT Inf 7 [210019 15 WT Inf 31 s15 S225]	Automatic adapter trimming Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx	WT Inf kidney	9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish treated with identical protocol were used as controls.	Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.	The zebrafish were maintained according to the standard protocols.	treatment:M. marinum infection\|genotype:wild type\|disease state:low dose 4 wpi\|tissue:Zebrafish kidney	GSM5704988	GSM5704988: WT Inf 7 [210019 15 WT Inf 31 s15 S225]; Danio rerio; RNA Seq	GSM5704988		1	Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM5704988	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP348087		loader:fastq load.py	210019_15_WT_Inf_31_s15_S225_L004_R1_001.fastq.gz 210019_15_WT_Inf_31_s15_S225_L004_R2_001.fastq.gz	fastq fastq	7195652752.0	36740405.0	GSM5704988 r1	0:97.89 1:97.97	A:1741246591;C:1859016659;G:1883433506;T:1702485351;N:9470645	97	97			1741246591	1859016659	1883433506	1702485351	9470645	SRX13237915	SRS11162459	SRA1335306	GEO	Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center	2	0.96048	0.96135	0.12193	0.11965	0.80803	0.8088	0.65183	0.66177	100	99	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Finland	2021-11-26	Multi-stage	Multi-stage	Kidney	Renal System