{"database": "metadata", "table": "run_metadata", "rows": [[32788, "SRR29441656", "SRX24954077", "SRS21657735", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "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 therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 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. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  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 or PBS immunized group.", null, "pubmed:39759874", null, "Blank sample3", "GSM8334556", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx|geo loc name:missing|collection date:missing", "Blank sample3", "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 raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 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.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 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:Healthy group|treatment:without xxx", "GSM8334556", "GSM8334556: Blank sample3; Danio rerio; RNA Seq", "GSM8334556 r1", "GSM8334556", "1", "post 7 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, "SRP514436", null, null, "Blank3.R2.fq.gz Blank3.R1.fq.gz", "fastq fastq", 6932407082.0, 23420695.0, "GSM8334556 r1", "0:147.99 1:148.00", "A:1790632840;C:1666849105;G:1684978083;T:1789775995;N:171059", 147, 148, null, null, 1790632840, 1666849105, 1684978083, 1789775995, 171059, "SRX24954077", "SRS21657735", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.94957, 0.94988, 0.05378, 0.05336, 0.70715, 0.70705, 0.52195, 0.51293, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "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": ["32788"], "units": {}, "query_ms": 8.737607990042306}