run_metadata: 32616

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
32616	SRR29356865	SRX24871759	SRS21581231	SRP513122	PRJNA1122499	An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy	GSE269547	Transcriptome Analysis	Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control. For mRNA vaccination mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL negative control zebrafish were immunized with LPP GFP mRNA immunized twice with two week intervals week 0 and 2.post 12 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.		pubmed:39759874		kidneys L3T immunized sample1	GSM8321941		source name:kidneys\|tissue:kidneys\|cell type:whole cell immune cell\|group:L3T immunized group\|treatment:2 dose of L3T mRNA immunized\|geo loc name:missing\|collection date:missing	kidneys L3T immunized sample1	The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample	kidneys	For determination of the host immune response induced by mRNA vaccine immunization adult zebrafish AB strain 3 to 4 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL. post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.	post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions.	The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS.	tissue:kidneys\|cell type:whole cell immune cell\|group:L3T immunized group\|treatment:2 dose of L3T mRNA immunized	GSM8321941	GSM8321941: kidneys L3T immunized sample1; Danio rerio; RNA Seq	GSM8321941 r1	GSM8321941	1	post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP513122			L3T1.R1.fq.gz L3T1.R2.fq.gz	fastq fastq	6941829152.0	24117590.0	GSM8321941 r1	0:143.92 1:143.91	A:1756734172;C:1708781793;G:1718505186;T:1757800293;N:7708	143	143			1756734172	1708781793	1718505186	1757800293	7708	SRX24871759	SRS21581231	SRA1896369	Zhang Lab, Department of Microbiology, Fudan University	Zhang Lab, Department of Microbiology, Fudan University	2	0.95019	0.95324	0.05797	0.05755	0.70013	0.69934	0.5137	0.5148	147	147	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		China	2024-06-11	Multi-stage	Multi-stage	Kidney	Renal System