{"database": "metadata", "table": "run_metadata", "rows": [[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 1\u00b5g 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.", null, "pubmed:39759874", null, "kidneys  L3T immunized sample1", "GSM8321941", null, "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\u2009mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 \u03bcL for intramuscular i.m immunization. 1\u03bcg 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\u2019s 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\u2019s 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 \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP513122", null, null, "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, null, null, 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", null, "China", "2024-06-11", "Multi-stage", "Multi-stage", "Kidney", "Renal System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["32616"], "units": {}, "query_ms": 8.956180012319237}