Transposon site hybridization (TraSH) screen in the lungs
Ontology highlight
ABSTRACT:
ORGANISM(S): Francisella tularensis
PROVIDER: GSE22231 | GEO | 2010/06/09
SECONDARY ACCESSION(S): PRJNA128841
REPOSITORIES: GEO
Similar Datasets
Project description:pool 16 and pool 29 arrays represent the Francisella transposon insertion mutants isolated from the spleens of two separate groups of 5 intraperitoneally infected mice. skin arrays represent the Francisella transposon insertion mutants isolated from the skin of 5 individual, subcutaneously infected mice. input arrays represent Francisella transposon insertion mutants surviving after growth in TSB broth. Detailed Materials and Methods from Weiss et al, PNAS, 2007, In vivo negative selection screen identifies genes required for Francisella virulence: Mice and Francisella infections Female C57BL/6 mice (Jackson) between 7 and 10 wk of age were kept under specific pathogen-free conditions in filter-top cages at Stanford University and provided with sterile water and food ad libitum. Experimental studies were in accordance with IACUC Guidelines. Mice were inoculated with 2x105 cfu subcutaneously in 50 ul sterile PBS or intraperitoneally (IP) in 500 ul. Spleens were harvested 2 days post-infection, homogenized, and dilutions were plated on supplemented MH agar plates containing kanamycin (infections with library) or MH plates with and without the appropriate antibiotic (competition experiments). Plates were grown overnight at 37oC, 5% CO2 and colonies were enumerated. After infections with the library, approximately 10^5 cfu were collected in sterile PBS for isolation of DNA. Competitive Index (CI) values were calculated using the formula CI = (mutant cfu in output/wild-type cfu in output)/(mutant cfu in input/wild-type cfu in input). Microarrays Genomic DNA was purified from bacterial pellets by phenol-chloroform extraction. Each DNA sample was divided in two and digested separately with BfaI or RsaI (NEB). The digested DNA was used as the template for in vitro transcription with the AmpliScribe T7-Flash transcription kit (Epicentre) following the manufacturer's protocol, except that 2 ?g of digested DNA was used, and the reaction was allowed to proceed for 12 to 16 h. Purified RNA was used in a RT reaction using Superscript II(?) (Invitrogen) and random hexamers as primers. cDNA was labeled with amino-allyl dUTP using the Klenow (exo-) enzyme. The ssDNA containing amino-allyl dUTP from the mouse output or the library input pools were labeled with Cy3 and Cy5, respectively, prior to hybridization to our Francisella microarray as described previously. Data analysis Normalized data were downloaded from the Stanford Microarray Database according to the median log2 Cy5/Cy3 (logRAT2N). Filters for feature quality, including a Cy3 net median intensity of 150 and regression correlation of >0.6, were applied. To compare data from separate IP infection experiments, each experimental sample was zero-transformed to the input/input control. Features (spots) missing values for 40% of the arrays were removed from the data set. The data sets were analyzed with the SAM program, using the two-class analysis option to identify features that consistently deviated from the input and samples across all of the arrays with a false discovery rate of 1%.
2007-05-02 | E-SMDB-3978 | biostudies-arrayexpress
Project description:The transposon site hybridization (TraSH) technique (Sassetti, CM et al. 2001. PNAS 98:12712-7) was utilized to identify genes important for the survival of Y. pestis within murine macrophages. A transposon library was created with ~31,500 Y. pestis KIM6+ insertion mutants. A portion of the Y. pestis transposon insertion mutant library was used to infect BMMs and the surviving bacteria (output pool) were recovered. TraSH was used to compare the output pool to a portion of the library that was not subjected to selection (input pool) in order to identify Y. pestis genes important for survival in macrophages. Each end of the transposon used for mutagenesis contains an outward-reading T7 RNA polymerase promoter. RNAs transcribed from the T7 promoters are complementary to the chromosomal DNA flanking each transposon in the library, so the RNAs can be used as “targets” to identify the approximate position of each transposon insertion in the mutant pool. Differentially labeled targets generated from the output and input pools are competitively hybridized to the 70-mer oligonucleotide microarrays obtained from Pathogen Functional Genomics Resource Center/J. Craig Venter Institute. Genes important for survival of Y. pestis in macrophages are identified by determining the ratio of the signal intensities for the output and input targets hybridizing to a given probe.
2011-11-30 | GSE33982 | GEO
Project description:We used an inhalation mouse model of infection to query a collection of 2149 mutants in a Francisella tularensis subsp. novicida background for genes required for growth, survival and systemic dissemination. A microarray-based genome-wide negative selection screen (Microarray tracking of transposon mutants = MATT) allowed us to monitor the behavior of transposon insertions in 1371 unique genes. Interestingly most of these genes persisted in lung and colonized liver and spleen. We found 44 (35%) genes negatively selected in lung and 81 (65%) genes negatively selected in liver and/or spleen. If negative selection in lung occurred, the attenuated mutants in general persisted at 24h after infection, disseminated to liver and/or spleen and appeared to be lost in lung after 48 to 72h of infection. These genes with a strong phenotype in lung but also potential for dissemination might be attractive vaccine or drug candidates. Keywords: Genome-Wide Negative Selection Screen 185 arrays, no duplicates/replicates Filtered data (per organ/timepoint) provided as a supplementary file
2008-12-30 | E-GEOD-11297 | biostudies-arrayexpress
Project description:The transposon site hybridization (TraSH) technique (Sassetti, CM et al. 2001. PNAS 98:12712-7) was utilized to identify genes important for the survival of Y. pestis within murine macrophages. A transposon library was created with ~31,500 Y. pestis KIM6+ insertion mutants. A portion of the Y. pestis transposon insertion mutant library was used to infect BMMs and the surviving bacteria (output pool) were recovered. TraSH was used to compare the output pool to a portion of the library that was not subjected to selection (input pool) in order to identify Y. pestis genes important for survival in macrophages. Each end of the transposon used for mutagenesis contains an outward-reading T7 RNA polymerase promoter. RNAs transcribed from the T7 promoters are complementary to the chromosomal DNA flanking each transposon in the library, so the RNAs can be used as “targets” to identify the approximate position of each transposon insertion in the mutant pool. Differentially labeled targets generated from the output and input pools are competitively hybridized to the 70-mer oligonucleotide microarrays obtained from Pathogen Functional Genomics Resource Center/J. Craig Venter Institute. Genes important for survival of Y. pestis in macrophages are identified by determining the ratio of the signal intensities for the output and input targets hybridizing to a given probe. A transposon library was created with ~31,500 Y. pestis KIM6+ insertion mutants. A portion of the Y. pestis transposon insertion mutant library was used to infect BMMs and the surviving bacteria (output pool) were recovered. TraSH was used to compare the output pool to a portion of the library that was not subjected to selection (input pool). Each end of the transposon used for mutagenesis contains an outward-reading T7 RNA polymerase promoter. RNAs transcribed from the T7 promoters are complementary to the chromosomal DNA flanking each transposon in the library, so the RNAs was used as “targets” to identify the approximate position of each transposon insertion in the mutant pool. Differentially labeled targets generated from the output and input pools are competitively hybridized to the 70-mer oligonucleotide microarrays obtained from Pathogen Functional Genomics Resource Center/J. Craig Venter Institute. Genes important for survival of Y. pestis in macrophages are identified by determining the ratio of the signal intensities for the output and input targets hybridizing to a given probe.
2011-11-30 | E-GEOD-33982 | biostudies-arrayexpress
Project description:Francisella tularensis may enter the body thorugh the lungs and cause fatal infection. In this study the inflammatory response to the virulent strain of Francisella (Schu4) was mapped over a 96h time-course using a custom microarray.
2011-03-01 | GSE17248 | GEO
Project description:We used an inhalation mouse model of infection to query a collection of 2149 mutants in a Francisella tularensis subsp. novicida background for genes required for growth, survival and systemic dissemination. A microarray-based genome-wide negative selection screen (Microarray tracking of transposon mutants = MATT) allowed us to monitor the behavior of transposon insertions in 1371 unique genes. Interestingly most of these genes persisted in lung and colonized liver and spleen. We found 44 (35%) genes negatively selected in lung and 81 (65%) genes negatively selected in liver and/or spleen. If negative selection in lung occurred, the attenuated mutants in general persisted at 24h after infection, disseminated to liver and/or spleen and appeared to be lost in lung after 48 to 72h of infection. These genes with a strong phenotype in lung but also potential for dissemination might be attractive vaccine or drug candidates. Keywords: Genome-Wide Negative Selection Screen
2008-12-31 | GSE11297 | GEO
Project description:Salmonella typhimurium 14028s invA::cam Transposon library recovered from spleen 2 days after IP passage of 2.2 x 10^6 through BALB/c mouse, compared to the initial Transposon library grown in LB broth (kanamycin 50ug/ml), O/N at 37°C with aeration Keywords: Transposon tag analysis 6 biological replicates analysed after arbitrarily primed sampling (Klenow, DOPR degenerate primer) + specific PCR amplification (Taq DNA Pol) + T7 in vitro transcription (AmpliScribe T7) + RT labeling (Cy3) + hybridization, compared to identically processed standard library (Cy5)
2008-08-31 | E-GEOD-7059 | biostudies-arrayexpress
Project description:A library of transposon mutants were generated in S.aureus strain SH1000 using a custom Mariner transposon with an outward-facing T7 promoter. Genomic DNA was extracted from the library and digested with an appropriate restriction enzyme (AluI or RsaI). Labelled RNA run-offs were produced from the T7 promoter and hybridised to a tiling microarray to determine the position of the mutant. This was done using a library of a million S. aureus mutants, and genes not disrupted by a transposon were inferred to be essential for replication and growth in vitro.
2009-04-16 | E-MEXP-1588 | biostudies-arrayexpress
Project description:A library of transposon mutants was generated in Salmonella enterica serovar Typhimurium strain SL1344 using custom Tn5 and Mu transposons with outward-facing T7 and SP6 promoters. The library was grown up in vitro, and used as the input pool for mouse infection experiments. An in vivo output pool was obtained from the mouse livers 2 days post-infection.<br><br>Genomic DNA was extracted from the input and output pools and digested with the restriction enzyme RsaI. Cy5-labelled RNA run-offs were produced seperately from the T7 and SP6 promoters and hybridised to a tiling microarray along with the Cy3-labelled in vitro transcription products from an untransposed SL1344 wild type control. Analysis of the microarray data allows the location of the transposon inserts to be determined. Mutants that are present in the input pool but that are absent or less prevalent in the output pools are inferred to be attenuated in vivo.
2009-08-25 | E-MEXP-2076 | biostudies-arrayexpress
Project description:The factors that determine the outcome of clinical tuberculosis lie within both the host and the pathogen, Mycobacterium tuberculosis (Mtb). The advent of recombinant inbred mouse panels and next-generation transposon mutagenesis and sequencing approaches has enabled dissection of the host-pathogen interface for mammalian and pathogen genetic determinants of disease outcome. To identify host and pathogen genetic drivers of Mtb infection, we infected 19 genotypes from the BXD panel, bred from Mtb-resistant C57BL/6J (B6) and Mtb-susceptible DBA/2J (D2), with a comprehensive library of transposon mutants (TnSeq). The survival of each of the ~4000 bacterial mutants within each distinct host was quantified and leveraged as refined “endophenotypes”, directly reporting on the infection microenvironment. We leveraged QTL mapping to associate each varying bacterial fitness endophenotype to the host genome and identified 140 significant host-pathogen quantitative trait loci (hpQTL). This host-pathogen interaction screen reinforces the utility of bacterial mutant libraries as precise reporters of host immunological microenvironment during infection and highlights host gene candidates for further investigation.
2023-06-07 | GSE234093 | GEO