[{"pmid":"16199573","study_institution":"MIT","public_repository":"GEO","exp_description":"We determined the global gene expression profiles of wildtype, dam, dam mutS, and mutS mutant E. coli strains.; Keywords: Basal gene expression comparison","study_pi":"John Essigmann","exp_title":"Basal gene expression in dam, dam mutS, and mutS mutant E. coli strains","biosets":3,"exp_type":"Transcript Quantification","exp_id":"145915","exp_name":"GSE2928","public_identifier":"GSE2928","measurement_technique":"Microarray","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["GM5555","AB1157","GM5556"],"taxon_lineage_ids":["131567","2","1224","1236","91347","543","561","562","83333","511145"],"organism":["Escherichia coli"],"genome_id":["511145.12"],"treatment_name":["mutant vs wild type"],"treatment_type":["mutant vs wild type"],"taxon_id":[511145],"treatment_duration":[""],"_version_":1809284004994613200},{"pmid":"16913923","public_repository":"GEO","exp_description":"E. coli growing in continuous culture under continuous UVA irradiation exhibits growth inhibition with a subsequent adaptation to the stress.  Transcriptome analysis was performed during transient growth inhibition and in the UVA light-adapted growth state.  The results indicate that UVA light induces stringent response and an additional response that includes the upregulation of the synthesis of valine, isoleucine, leucine, phenylalanine, histidine and glutamate.  The induction of several SOS response-genes strongly points to DNA damage as a result of UVA exposure.  The involvement of oxidative stress was observed with the induction of ahpCF.  Taken together it supports the hypothesis of the production of reactive oxygen species by UVA light.  In the UVA-adapted cell population strong repression of the acid tolerance response was found.  We identified the enzyme chorismate mutase as a possible chromophore for UVA light-inactivation and found strong repression of the pyrBI operon and the gene mgtA encoding for an ATP dependent Mg2+ transporter.  Furthermore, our results indicate that the role of RpoS may not be as important in the adaptation of E. coli to UVA light as it was implicated by previous results with starved cells, but that RpoS might be of crucial importance for the resistance under transient light exposure.","study_institution":"Swiss Federal Institute for Aquatic Science and Technology","biosets":3,"study_pi":"Thomas Egli","exp_title":"Gene expression of E. coli in continuous culture during adaptation to artificial sunlight","exp_type":"Transcript Quantification","exp_id":"83613","exp_name":"GSE4569","public_identifier":"GSE4569","measurement_technique":"Microarray","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["MG1655"],"taxon_lineage_ids":["131567","2","1224","1236","91347","543","561","562","83333","511145"],"organism":["Escherichia coli"],"genome_id":["511145.12"],"treatment_name":["UV"],"treatment_type":["UV"],"taxon_id":[511145],"treatment_duration":[""],"_version_":1809284005031313400},{"study_institution":"university of Groningen","public_repository":"GEO","exp_description":"Comparison of Streptococcus pneumoniae D39 ccpA mutant compared to D39 wild type in CDM with glucose as sole carbon source to define the regulon of carbon catabolite control protein CcpA under this condition; Details described in Carvalho SM, Kloosterman TG, Neves AR, Kuipers OP. CcpA Ensures Optimal Metabolic Fitness of Streptococcus pneumoniae. Plos One 2011","pmid":"22039538","exp_title":"ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + Glucose at MID-log growth phase","study_pi":"Ana R Neves","biosets":1,"exp_id":"491657","exp_type":"Transcript Quantification","public_identifier":"GSE31815","measurement_technique":"Microarray","exp_name":"GSE31815","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["D39"],"taxon_lineage_ids":["131567","2","1783272","1239","91061","186826","1300","1301","1313","373153"],"organism":["Streptococcus pneumoniae"],"genome_id":["373153.27"],"treatment_name":["mutant vs wild type"],"treatment_type":["mutant vs wild type"],"taxon_id":[373153],"treatment_duration":[""],"_version_":1809284005034459100},{"public_identifier":"GSE79731","measurement_technique":"Microarray","exp_name":"GSE79731","exp_id":"2000001","exp_type":"Transcript Quantification","biosets":4,"exp_title":"Gene expression data from Mycobacterium tuberculosis-infected bone-marrow derived mouse macrophages [timecourse]","public_repository":"GEO","exp_description":"How the complex interaction between Mycobacterium tuberculosis (Mtb) and the host is regulated during infection is still not well understood. Using a systems biology approach, we demonstrate here that miR-155 is one of several microRNAs that regulate host gene expression over the first 48 hours of Mtb infection in macrophages. miR-155 regulates the cell survival of Mtb-infected macrophages through SHIP1/AKT signaling. Using timecourse gene expression data, we constructed a miRNA regulatory network for the innate immune response to Mtb infection by WT macrophages. The network suggested a role for seven miRNAs in regulating the host response to Mtb, with miR-155 being one of them. We then validated a role for miR-155 by comparing the response between WT and miR-155-/- macrophages.","study_institution":"CIDR","pmid":"27681624","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","taxon_lineage_ids":["131567","2759","33154","33208","6072","33213","33511","7711","89593","7742","7776","117570","117571","8287","1338369","32523","32524","40674","32525","9347","1437010","314146","314147","9989","1963758","337687","10066","39107","10088","862507","10090"],"organism":["Mus musculus"],"genome_id":["10090.24"],"treatment_name":[""],"taxon_id":[10090],"treatment_type":[""],"_version_":1809284005035507700},{"public_repository":"GEO","exp_description":"The unicellular cyanobacterium Synechocystis sp. PCC 6803 is a model system for studying biochemistry, genetics and molecular biology of photobiological processes. Despite its importance in basic and applied research, the genome-wide picture of transcriptional regulation in this bacterium is limited. Characteristic transcriptional responses to changes in the growth environment are expected to provide a scaffold for describing the Synechocystis transcriptional regulatory network as well as efficient means for functional annotation of genes in the genome. We designed, validated and used Synechocystis genome-wide oligonucleotide (70-mer) microarray (representing 96.7% of all chromosomal ORFs) to study transcriptional activity of the cyanobacterial genome in response to S deprivation. The microarray data were verified by quantitative RT-PCR. We made five main observations: 1) Transcriptional changes upon sulfate withdrawal were relatively moderate, but significant and consistent with growth kinetics; 2) S acquisition genes encoding for a high-affinity sulfate transporter were significantly induced, while decreased transcription of genes for phycobilisome, photosystems I and II, cytochrome b6/f, and ATP synthase indicated reduced light-harvesting and photosynthetic activity; 3) S deprivation elicited transcriptional responses associated with general growth arrest and stress; 4) A large number of genes regulated by S availability encode hypothetical proteins or proteins of unknown function; 5) Hydrogenase structural and maturation accessory genes were not identified as differentially expressed, even though increased hydrogen evolution was observed. The expression profiles recorded by using this oligonucleotide-based microarray platform revealed that during transition from the condition of plentiful sulfur to no sulfur, Synechocystis undergoes coordinated transcriptional changes, including genes whose products are involved in sensing nutrient limitations and tuning bacterial metabolism. The transcriptional profile of the nutrient limitation was dominated by decrease in abundances of many transcripts. However, these changes were unlikely due to the across-the-board, non-specific shut down of transcription in a condition of growth arrest. Down-regulation of transcripts encoding proteins whose function depends on a cellular sulfur status indicated that the observed repression has a specific regulatory component. The repression of certain sulfur-related genes was paralleled by activation of genes involved in internal and external S scavenging.; Keywords: stress response, time course","study_institution":"University of Minnesota","pmid":"18644144","biosets":15,"exp_title":"Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803","study_pi":"Arkady Khodursky","exp_id":"851320","exp_type":"Transcript Quantification","public_identifier":"GSE11970","measurement_technique":"Microarray","exp_name":"GSE11970","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["PCC 6803"],"taxon_lineage_ids":["131567","2","1783272","1798711","1117","1890424","1890428","1142","2640012","1148"],"organism":["Synechocystis sp."],"genome_id":["1148.35"],"treatment_name":["growth phase,time point","sulfur starvation,time point"],"treatment_type":["growth phase,time point","sulfur starvation,time point"],"taxon_id":[1148],"treatment_duration":["0 hrs / 11 hrs","12h","1h","72h","0 hrs / 4 hrs","24h","6h","0 hrs / 5 hrs","48h","0 hrs / 1 hrs","0 hrs / 7 hrs","3h"],"_version_":1809284005036556300},{"public_repository":"GEO","exp_description":"Listeria monocytogenes, the etiological agent of listeriosis, is capable of growth and survival at temperatures ranging from 2 to 48oC, reflecting the diverse environments and host species inhabited by this organism. L. monocytogenes expresses up to 29 proteins, termed internalins, whose structure indicates they make good candidates for facilitating bacterial-host cell interactions. Considering the ubiquitous nature of this organism, we speculated that environmental temperature might serve as an important biological signal in controlling their expression. We therefore employed a subgenomic microarray to investigate the expression profiles of 24 members of the internalin gene family identified in L. monocytogenes 10403S. Competitive hybridization was performed between RNA extracted from 10403S grown to early stationary phase at 37oC, and 10403S grown to early stationary phase at 16oC, 30oC and 42oC. The data reveal that internalin genes can be divided into four broad categories such that (i) four internalin genes inlC2, inlD, lmo0331 and lmo0610 show temperature-dependent expression similar to sigB and the ¿B-dependent gene opuCA; (ii) three internalin genes inlA, inlB and inlC show temperature-dependent expression similar to the PrfA-dependent gene plcA; (iii) five internalin-like genes inlG, inlJ, lmo0327, lmo0514 and lmo1290 show unique temperature-dependent expression and (iv) twelve internalin genes show no difference in expression under the conditions investigated in this study. Our data also shows that the expression of many housekeeping genes can vary considerably under different temperatures, and normalization of both microarray and qRT-PCR data using housekeeping genes should be based on comprehensive experimental validation.; Keywords: Listeria monocytogenes, internalins, temperature, sub-genomic microarrays","study_institution":"Cornell University","pmid":"17337561","biosets":3,"exp_title":"\"Temperature-dependent expression of internalin and internalin-like genes  \"","study_pi":"Kathryn J Boor","exp_id":"647235","exp_type":"Transcript Quantification","public_identifier":"GSE6471","measurement_technique":"Microarray","exp_name":"GSE6471","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["10403S"],"taxon_lineage_ids":["131567","2","1783272","1239","91061","1385","186820","1637","1639","169963"],"organism":["Listeria monocytogenes"],"genome_id":["169963.11"],"treatment_name":["temperature"],"treatment_type":["temperature"],"taxon_id":[169963],"treatment_duration":[""],"_version_":1809284005040750600},{"exp_name":"GSE30415","measurement_technique":"Microarray","public_identifier":"GSE30415","exp_type":"Transcript Quantification","exp_id":"490077","study_pi":"Oscar P Kuipers","exp_title":"Transcriptional response of Streptococcus pneumoniae to copper","biosets":1,"pmid":"21736642","study_institution":"GBB","exp_description":"This SuperSeries is composed of the following subset Series:; GSE30413: High low copper; GSE30414: copY Mutant compared to D39 wild-type","public_repository":"GEO","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","taxon_lineage_ids":["131567","2","1783272","1239","91061","186826","1300","1301","1313","373153"],"strain":["D39"],"organism":["Streptococcus pneumoniae"],"genome_id":["373153.27"],"treatment_name":["copper"],"taxon_id":[373153],"treatment_type":["copper"],"treatment_duration":[""],"_version_":1809284005042847700},{"exp_name":"GSE8084","public_identifier":"GSE8084","measurement_technique":"Microarray","exp_type":"Transcript Quantification","exp_id":"762216","biosets":14,"study_pi":"Wei-Shou Hu","exp_title":"S. coelicolor Wild Type Time-course Study in R5- medium (Culture#1)","pmid":"17959654","public_repository":"GEO","exp_description":"Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators.  Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined.  In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) M145 wild type and disruption mutants of regulatory genes (afsS and absA1) known to affect antibiotic biosynthesis.; Keywords: Time course","study_institution":"University of Minnesota","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","taxon_lineage_ids":["131567","2","1783272","201174","1760","85011","2062","1883","1477431","1902","100226"],"strain":["M145"],"organism":["Streptomyces coelicolor"],"genome_id":["100226.15"],"treatment_name":["time point"],"taxon_id":[100226],"treatment_type":["time point"],"treatment_duration":["26 / 43 hrs","15 / 35 hrs","22 / 35 hrs","24 / 26 hrs","26 / 35 hrs","35 / 43 hrs","15 / 22 hrs","15 / 26 hrs","15 / 43 hrs","22 / 26 hrs","22 / 43 hrs","24 / 35 hrs","15 / 24 hrs","22 / 24 hrs"],"_version_":1809284005043896300},{"pmid":"20444105","exp_description":"Enterohemorrhagic E. coli (EHEC) colonizes the large intestine and causes attaching and effacing lesions (AE). Most of the genes involved in the formation of AE lesions are encoded within a chromosomal pathogenicity island termed the Locus of Enterocyte Effacement (LEE). The LysR-like transcriptional factor QseA regulates the LEE by binding directly to the regulatory region of ler. Here, we performed transcriptome analyses comparing WT EHEC and the isogenic qseA mutant in order to elucidate the extent of QseA¿s role in gene regulation in EHEC. The following results compare genes that were up-regulated and down-regulated ! 2-fold in the qseA mutant strain compared to the WT strain. At mid-exponential growth, 222 genes were up-regulated and 1874 were downregulated. At late-exponential growth, a total of 55 genes were up-regulated and 605 genes were down-regulated. During mid-exponential growth, QseA represses its own transcription, whereas during late-logarithmic growth, QseA activates expression of the LEE genes as well as non-LEE encoded effector proteins. During both growth phases, several genes carried in O-islands, were activated by QseA, whereas genes involved in cell metabolism were repressed. We also performed electrophoretic mobility shift assays, competition experiments, and DNAseI footprints, and the results suggested that QseA directly binds both the ler proximal and distal promoters, its own promoter, as well as promoters of genes encoded in EHEC-specific O-islands. Additionally, we mapped the transcriptional start site of qseA, leading to the identification of two promoter sequences. Taken together, these results indicate that QseA acts as a global regulator in EHEC, coordinating expression of virulence genes.","public_repository":"GEO","study_institution":"University of Texas Southwestern Medical Center","biosets":1,"exp_title":"\"QseA regulation of virulence factors in EHEC \"","study_pi":"Vanessa Sperandio","exp_type":"Transcript Quantification","exp_id":"14144","exp_name":"GSE18118","measurement_technique":"Microarray","public_identifier":"GSE18118","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["8624"],"taxon_lineage_ids":["131567","2","1224","1236","91347","543","561","562","83334","155864","386585","83333","511145"],"organism":["Escherichia coli"],"genome_id":["155864.8","199310.4","386585.9","511145.12"],"treatment_name":["mutant"],"treatment_type":["mutant"],"taxon_id":[155864,386585,511145],"treatment_duration":[""],"_version_":1809284005045993500},{"biosets":1,"exp_title":"Microarray analysis for differential gene expression in M1-SDHHbtail","study_pi":"Hong Jin","pmid":"21628503","public_repository":"GEO","exp_description":"A total of 215 gene were found to be differentially expressed; 90 of them were up regulated and 125 genes were down regulated. Most notably the functional categories that were affected include Virulence genes, carbohydrate genes and lipid synthesis genes. Some of the virulence genes were down regulated by more than 16-32 fold. These results indicate that SDH plays an important role in the regulation of virulence.","study_institution":"Ohio State University","exp_name":"GSE15231","public_identifier":"GSE15231","measurement_technique":"Microarray","exp_type":"Transcript Quantification","exp_id":"668309","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","taxon_lineage_ids":["131567","2","1783272","1239","91061","186826","1300","1301","1314","301451","186103"],"strain":["SF370"],"organism":["Streptococcus pyogenes"],"genome_id":["186103.3"],"treatment_name":["mutant vs wild type"],"taxon_id":[186103],"treatment_type":["mutant vs wild type"],"treatment_duration":[""],"_version_":1809284005049139200},{"study_institution":"University of Groningen","public_repository":"GEO","exp_description":"Comparison of the Bacillus cereus with induced ComK1 (pATK31 in sample 1-3) or ComK2 (pATK32 in sample 4-6) proteins vs Bacillus cereus carrying empty plasmid (pLM5 in all samples)","pmid":"21747963","study_pi":"Oscar P Kuipers","exp_title":"Distinct roles of ComK1 and ComK2 in gene regulation in Bacillus cereus (induced ComK1 or ComK2)","biosets":2,"exp_id":"690917","exp_type":"Transcript Quantification","public_identifier":"GSE27264","measurement_technique":"Microarray","exp_name":"GSE27264","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["ATCC 14579"],"taxon_lineage_ids":["131567","2","1783272","1239","91061","1385","186817","1386","86661","1396","226900"],"organism":["Bacillus cereus"],"genome_id":["226900.8"],"treatment_name":["overexpression"],"treatment_type":["overexpression"],"taxon_id":[226900],"treatment_duration":[""],"_version_":1809284005050187800},{"exp_name":"GSE25521","public_identifier":"GSE25521","measurement_technique":"Microarray","exp_type":"Transcript Quantification","exp_id":"479058","biosets":2,"study_pi":"","exp_title":"Effect of sigH in the growth phase transition of Clostridium difficile","pmid":"21572003","public_repository":"GEO","exp_description":"This SuperSeries is composed of the following subset Series:; GSE25474: Comparison of the expression profiles of 630E strain after 4h and 10h of growth; GSE25475: Comparison of the expression profiles of 630E strain and a sigH mutant after 10h of growth; This study is based on two microarray datasets, in one hand a phase transition comparison using the expression profiles of 630E strain after 4h and 10h of growth. In other hand a comparison at 10h of growth between a mutant of the sigH gene and the WT strains. This experimental procedure was designed to investigate the effect of sigH in the growth phase transition of Clostridium difficile.","study_institution":"Institut Pasteur","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","taxon_lineage_ids":["131567","2","1783272","1239","186801","186802","186804","1870884","1496","272563"],"strain":["C630E"],"organism":["Clostridium difficile"],"genome_id":["272563.8"],"treatment_name":["time point","mutant vs wild type"],"taxon_id":[272563],"treatment_type":["time point","mutant vs wild type"],"treatment_duration":[""],"_version_":1809284005052285000},{"exp_name":"GSE6444","public_identifier":"GSE6444","measurement_technique":"Microarray","exp_type":"Transcript Quantification","exp_id":"23995","biosets":6,"study_pi":"Carol Gross","exp_title":"Steady-state analysis of genes regulated by the E. coli RNA chaperone, Hfq","pmid":"17158661","public_repository":"GEO","exp_description":"cDNA microarray analysis to identify genes regulated by the RNA chaperone, Hfq. Four experiments were performed: 1/ Hfq+ vs Hfq- strains. 269 significantly differentially regulated genes were identified by SAM (Statistical Analysis of Microarrays), of which 120 changed more than 1.5 fold (48 increased and 72 decreased in hfq-). Amongst other genes, these experiments identified significant regulation of the sigma E and sigma 32 regulons. However, only genes induced by sigma E were similarly induced in hfq-; 8 operons repressed by sigma E were not repressed in hfq-. 2/ wt vs delta rseA. RseA is the antisigma factor for sigmaE. This comparison results in elevated steady-state levels of sigma E, and confirmed induction and repression of target regulon members. 3/ hfq+ vs hfq+ rpoE overexpression. RpoE encoding sigma E was overexpressed in an hfq+ background, confirming normal regulation of the sigma E regulon. 4/ hfq+ vs hfq- rpoE overexpression. Sigma E was overexpressed in an hfq- background. This demonstrated that 8 operons normally repressed by sigma E require hfq for this repression. The simple conclusion is that sigma E regulates small RNAs that, together with Hfq, bind target mRNAs and results in their rapid degradation. This study is detailed in Guisbert et al 2007 (J Bacteriol, 189:1963-73)","study_institution":"University of California San Francisco","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","taxon_lineage_ids":["131567","2","1224","1236","91347","543","561","562","83333","511145"],"strain":["MG1655"],"organism":["Escherichia coli"],"genome_id":["511145.12"],"treatment_name":["mutant vs wild type","overexpression"],"taxon_id":[511145],"treatment_type":["mutant vs wild type","overexpression"],"treatment_duration":["","20 mins"],"_version_":1809284005053333500},{"exp_type":"Transcript Quantification","exp_id":"739567","exp_name":"GSE18051","measurement_technique":"Microarray","public_identifier":"GSE18051","pmid":"20923418","exp_description":"Proteus mirabilis is a primary cause of complicated urinary tract infections (UTI).  Surprisingly, iron acquisition systems have been poorly characterized in this uropathogen despite the urinary tract being iron-limited.  In this report the transcriptome of strain HI4320, cultured under iron limitation, was examined using microarray analysis.  Of genes upregulated at least 2-fold, 45 were statistically significant and comprise 21 putative iron-regulated systems.  Two of these systems, PMI0229-0239 and PMI2596-2605, are organized in operons and appear to encode siderophore biosynthesis genes.","public_repository":"GEO","study_institution":"University of Michigan","biosets":1,"exp_title":"Functional redundancy of iron acquisition systems is required for Proteus mirabilis pathogenesis during UTI","study_pi":"Harry L Mobley","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["HI4320"],"taxon_lineage_ids":["131567","2","1224","1236","91347","1903414","583","584","529507"],"organism":["Proteus mirabilis"],"genome_id":["529507.6"],"treatment_name":["iron"],"treatment_type":["iron"],"taxon_id":[529507],"treatment_duration":[""],"_version_":1809284005055430700},{"study_institution":"UCLA/VAGLAHS","public_repository":"GEO","exp_description":"Transcriptional profiling of Helicobacter pylori comparing 26695 wild-type strain and a HP0244-deficient mutant 26695/¿HP0244::km treated at three different pH conditions (pH 7.4, pH 4.5 without urea, or pH 2.5 with 30 mM urea) for 30 min to define the HP0244 acid-responsive regulon; Keywords: Genetic modification and stress response","pmid":"18978046","exp_title":"Identification of HP0244 regulon at different pH conditions","study_pi":"George Sachs","biosets":3,"exp_id":"695896","exp_type":"Transcript Quantification","public_identifier":"GSE12900","measurement_technique":"Microarray","exp_name":"GSE12900","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["26695"],"taxon_lineage_ids":["131567","2","1224","68525","29547","213849","72293","209","210","85962"],"organism":["Helicobacter pylori"],"genome_id":["85962.8"],"treatment_name":["mutant vs wild type"],"treatment_type":["mutant vs wild type"],"taxon_id":[85962],"treatment_duration":["30 mins"],"_version_":1809284005057527800},{"biosets":1,"study_pi":"Sarah Harcum","exp_title":"Serine hydroxamate and the transcriptome of high cell density recombinant E. coli MG1655","public_repository":"GEO","exp_description":"For over 30 years, serine hydroxamate has been used to chemically stimulate a stringent response in Escherichia coli and other bacteria. These studies have elucidated numerous characteristics of the classical stringent response beyond the simple cellular response to an amino acid shortage, including phospholipid synthesis and protease up-regulation. In this study, the effects of a serine hydroxamate addition on high cell density recombinant E. coli were examined and compared to the effects of recombinant protein production to determine overlaps, as recombinant protein production stress has often been attributed to amino acid shortages.  Both the transcriptome and growth characteristics were evaluated and compared. The serine hydroxamate addition profoundly decreased the culture growth rate, whereas, recombinant protein production did not.  Conversely, the transcriptome profile of the recombinant E. coli cultures were relatively unaffected by the serine hydroxamate addition, yet recombinant protein production dramatically changed the transcriptome profile.  A subset of the classical stringent response genes were effected by the serine hydroxamate addition, whereas, recombinant protein production regulated numerous classical stringent response genes; however, not all.  The genes that were regulated by the serine hydroxamate addition include numerous fatty acid synthesis genes, in agreement with altered phospholipids synthesis reports. These results indicate that recombinant protein production and the stringent response have many overlapping responses; however, are far from identical.; It was hypothesized that recombinant protein production leads to a stringent response due to the high amino acid synthesis demands related to recombinant protein synthesis.  A comparison of the transcriptomes during recombinant protein production and a chemical imposed stringent response would assist with determining what portion of the ¿metabolic burden¿ associated with recombinant protein production is due to amino acid shortages. In this study, the transcriptome profiles of recombinant E. coli were examined and compared for the three culture conditions: 1) Normal growth, no external stress; 2) L-serine hydroxamate addition (to mediate a stringent response); and 3) IPTG-induction to produce the recombinant protein chloramphenicol acetyltransferase (CAT). The transcriptome profiles from these three conditions were analyzed using Affymetrix Anti-sense E. coli GeneChip® microarrays.","study_institution":"Clemson University","pmid":"18612598","public_identifier":"GSE17506","measurement_technique":"Microarray","exp_name":"GSE17506","exp_id":"94743","exp_type":"Transcript Quantification","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","taxon_lineage_ids":["131567","2","1224","1236","91347","543","561","562","83333","511145"],"strain":["MG1655"],"organism":["Escherichia coli"],"genome_id":["511145.12"],"treatment_name":["serine hydroxamate"],"taxon_id":[511145],"treatment_type":["serine hydroxamate"],"treatment_duration":[""],"_version_":1809284005058576400},{"exp_id":"688340","exp_type":"Transcript Quantification","measurement_technique":"Microarray","public_identifier":"GSE15546","exp_name":"GSE15546","exp_description":"A total of 163 genes were found to be differentially expressed; 38 genes of them were up regulated and 125 genes were down regulated. Most notably the functional categories that were affected include Virulence genes (18 genes  11% of the total significantly differentiated genes), carbohydrate metabolism  and cell envelop realted genes ( 31, 19.1% of the total),  and aminoacid transport genes (21genes, 12.9%).  Among the virulence-related genes, the most notable one were those belong to the production of capsule, the M protein, exotoxin, NAD glycohydrolase and Streptolysin S. Some of the capsule related genes were down regulated by more than 64 fold. These results indicate that CdhA (group A Streptococcal Cell division controlling and Chain-forming cell wall hydrolase) plays an important role in the regulation of virulence.","public_repository":"GEO","study_institution":"Ohio State University","pmid":"20643653","biosets":1,"exp_title":"Microarray analysis for Streptococcus pyogenes M1-CdhA (-) mutant","study_pi":"Hong Jin","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["SF370"],"taxon_lineage_ids":["131567","2","1783272","1239","91061","186826","1300","1301","1314","301451","186103"],"organism":["Streptococcus pyogenes"],"genome_id":["186103.3"],"treatment_name":["mutant vs wild type"],"treatment_type":["mutant vs wild type"],"taxon_id":[186103],"treatment_duration":[""],"_version_":1809284005060673500},{"exp_name":"GSE17788","measurement_technique":"Microarray","public_identifier":"GSE17788","exp_type":"Transcript Quantification","exp_id":"155797","exp_title":"RNA expression for ethanologenic E coli strains LY180 and LY180 del yqhC in the absence and presence of furfural","study_pi":"Lonnie Ingram","biosets":4,"pmid":"20676725","study_institution":"University of Florida","exp_description":"The data explore the transcription of strain LY180 and the yqhC deletion mutant LY180 del yqhC without and with 0.5 g/L furfural.; LY180 and LY180 del yqhC are described in Turner, PC, EN Miller, LR Jarboe, P Pharkya, KT Shanmugam, and LO Ingram. 2009. Escherichia coli YqhC regulates transcription of the adjacent   yqhD and dkgA genes, and mutations in yqhC contribute to furfural resistance in ethanologenic strains (in preparation for submission to Appl Env Microbiol)","public_repository":"GEO","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","taxon_lineage_ids":["131567","2","1224","1236","91347","543","561","562","83333","511145"],"strain":["LY180"],"organism":["Escherichia coli"],"genome_id":["511145.12"],"treatment_name":["furfural","mutant"],"taxon_id":[511145],"treatment_type":["furfural","mutant"],"treatment_duration":[""],"_version_":1809284005062770700},{"public_identifier":"E-GEOD-20302","measurement_technique":"Microarray","exp_name":"E-GEOD-20302","exp_id":"2000006","exp_type":"Transcript Quantification","exp_title":"B bifidum actively changes the gene expression profile induced by L acidophilus in murine dendritic cells","biosets":3,"study_institution":"Technical University of Denmark","public_repository":"GEO","exp_description":"Dendritic cells (DC) play a pivotal regulatory role in activation of the innate as well as the adaptive part of the immune system by responding to environmental microorganisms. We have previously shown that some lactobacilli strains induce a strong production of the pro-inflammatory and Th1 polarizing cytokine IL-12 in DC. Contrary, bifidobacteria do not induce IL-12, but are able to inhibit the IL-12 production induced by lactobacilli. In the present study, genome wide microarrays were used to investigate the maturation and gene expression pattern murine bone marrow derived DC stimulated with Lactobacillus acidophilus NCFM and Bifidobacterium bifidum Z9. L. acidophilus NCFM strongly induced expression of interferon (IFN)-β, multiple virus defence genes, and cytokine and chemokine genes related to both the adaptive and the innate immune response. Contrary, B. bifidum Z9 mostly up-regulated genes encoding cytokines and chemokines related to the innate immune response. Moreover, B. bifidum Z9 inhibited the expression of the genes initiating the adaptive immune response induced by L. acidophilus NCFM and had an additive effect on genes of the innate immune response and some Th2 skewing genes. The gene encoding Jun dimerization protein 2 (JDP2), a key regulator in cell signalling, was one of the few genes only induced by B. bifidum Z9. Blocking of the JNK1/2 pathway completely inhibited the gene expression of Ifn-β. We suggest that B. bifidum Z9 employs an active mechanism to inhibit induction of genes in DC triggering the adaptive immune system and that JPD2 is involved in the regulatory mechanism. In the experiment saline control, Lactobacillus acidophilus NCFM, Bifidobacterium bifidum Z9 or both bacteria were were added to murine dendritic cells and stimulated for 10 hours. Experiments were run in triplicates and analyzed in a Two-way ANOVA design.","pmid":"20548777","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","taxon_lineage_ids":["131567","2759","33154","33208","6072","33213","33511","7711","89593","7742","7776","117570","117571","8287","1338369","32523","32524","40674","32525","9347","1437010","314146","314147","9989","1963758","337687","10066","39107","10088","862507","10090"],"organism":["Mus musculus"],"genome_id":["10090.24"],"treatment_name":[""],"taxon_id":[10090],"treatment_type":[""],"_version_":1809284005064867800},{"exp_name":"GSE15598","measurement_technique":"Microarray","public_identifier":"GSE15598","exp_type":"Transcript Quantification","exp_id":"508066","exp_title":"Microarray analysis of S. pyogenes Type M1-CdhA55(-) mutant","study_pi":"Hong Jin","biosets":1,"pmid":"20643653","study_institution":"Ohio State University","exp_description":"A total of 192 genes were found to be differentially expressed; 38 genes of them were up regulated and 154 genes were down regulated. Most notably the functional categories that were affected include carbohydrate metabolism  and cell envelop realted genes ( 56, 29.1% of the total),Virulence genes (12 genes  6.25% of the total significantly differentiated genes),  and aminoacid transport genes (7 genes, 3.6 %).  Among the virulence-related genes, the most notable ones were those belong to the production of capsule, the M protein, exotoxin, NAD glycohydrolase and Streptolysin S.  Some of the capsule related genes were down regulated by more than 64 fold. Additionally 11 differentially expressed lipid metabolism related genes  and four aminoacid transport and metabolism-related genes were upregulated. These results indicate that the C-terminal CHAP domain of CdhA (group A Streptococcal Cell division controlling and Chain-forming cell wall hydrolase) plays an important role in the regulation of virulence. Since these mutant lack cell wall hydrolase activity but are not defective in cell division or growth, we believe that CdhA isa multifunctional protein with N-terminal region controlling cell division and c-terminal region responsible for regulating bacterial virulence.","public_repository":"GEO","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","taxon_lineage_ids":["131567","2","1783272","1239","91061","186826","1300","1301","1314","301451","186103"],"strain":["SF370"],"organism":["Streptococcus pyogenes"],"genome_id":["186103.3"],"treatment_name":["mutant vs wild type"],"taxon_id":[186103],"treatment_type":["mutant vs wild type"],"treatment_duration":[""],"_version_":1809284005066965000},{"exp_id":"63710","exp_type":"Transcript Quantification","public_identifier":"GSE13698","measurement_technique":"Microarray","exp_name":"GSE13698","study_institution":"Texas A&M University","public_repository":"GEO","exp_description":"Metabolically-engineered Escherichia coli has been used previously to degrade the ubiquitous pollutant cis-1,2-dichloroethylene (cis-DCE), and the impact of the metabolic engineering was assessed by investigating the changes in the proteome.  Here, genome-wide transcriptome analysis was performed to confirm that a strong heat shock and/or oxidative stress occurs during enhanced cis-DCE mineralization. Also, seven new stress proteins (YchH, YdeI, YodD, YodC, YgiW, YhcN, and YjaA) that were previously uncharacterized have been identified.","pmid":"19919618","exp_title":"12 microarrays for cis-DCE mineralization and new stress genes","study_pi":"Tom Wood","biosets":5,"date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["BW25113","TG1"],"taxon_lineage_ids":["131567","2","1224","1236","91347","543","561","562","83334","155864","386585","83333","511145"],"organism":["Escherichia coli"],"genome_id":["155864.8","199310.4","386585.9","511145.12"],"treatment_name":["H2O2","mutant"],"treatment_type":["H2O2","mutant"],"taxon_id":[155864,386585,511145],"treatment_duration":["10 mins / 10 mins",""],"_version_":1809284005069062100},{"biosets":5,"exp_title":"M1T1 Streptococcus pyogenes (isolate 5448) WT and Animal-passaged variant in vitro and in vivo","study_pi":"Malak Kotb","exp_description":"Microarray analysis was performed on in vitro and in vivo-derived RNA from the well characterized S. pyogenes strain 5448 WT and animal-passage variant","public_repository":"GEO","study_institution":"Faculty of Pharmacy, Cairo University","pmid":"20418946","measurement_technique":"Microarray","public_identifier":"GSE19103","exp_name":"GSE19103","exp_id":"692534","exp_type":"Transcript Quantification","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","taxon_lineage_ids":["131567","2","1783272","1239","91061","186826","1300","1301","1314","301451","186103"],"strain":["5448"],"organism":["Streptococcus pyogenes"],"genome_id":["186103.3"],"treatment_name":["animal passage","in vivo"],"taxon_id":[186103],"treatment_type":["animal passage","in vivo"],"treatment_duration":[""],"_version_":1809284005070110700},{"exp_id":"413712","exp_type":"Transcript Quantification","public_identifier":"GSE22958","measurement_technique":"Microarray","exp_name":"GSE22958","study_institution":"Massachussetts General Hospital","public_repository":"GEO","exp_description":"In this work, we applied an RNA analysis method, Selective Capture of Transcribed Sequences (SCOTS), and cDNA hybridization-microarray technology to identify S. Paratyphi A transcripts expressed by bacteria in the blood of three patients in Bangladesh.  In total, we detected 1798 S. Paratyphi A mRNAs expressed in the blood of infected humans (43.9% of the ORFeome).  Of these, we identified 868 in at least two patients, and 315 in all three patients.  S. Paratyphi A transcripts identified in at least two patients encode proteins involved in energy metabolism, nutrient and iron acquisition, vitamin biosynthesis, stress responses, oxidative stress resistance, and pathogenesis.  A number of detected transcripts are expressed from PhoP and SlyA-regulated genes associated with intra-macrophage survival, genes contained within Salmonella Pathogenicity Islands (SPIs) 1-4, 6, 10, 13, and 16, as well as RpoS-regulated genes.  The largest category of identified transcripts are those encoding proteins with unknown function.  When comparing level of bacterial mRNA detection using in vivo samples collected from infected patients to samples from in vitro grown organisms, we found significant differences for 347, 391, and 456 S. Paratyphi A transcripts in each of three individual patients (approximately 9.7% of the ORFeome).  Of these, expression of 194 transcripts (4.7% of ORFs) was concordant in two or more patients, and 41 in all patients.  Genes encoding these transcripts are contained within SPI-1, 3, 6 and 10, are PhoP-regulated genes, are involved in energy metabolism, nutrient acquisition, drug resistance, or are uncharacterized genes.  Using quantitative RT-PCR, we confirmed increased gene expression in vivo for a subset of genes identified in our analyses.","pmid":"20573880","study_pi":"Edward T Ryan","exp_title":"High-throughput gene expression profiling of Salmonella enterica serovar Paratyphi A in the blood of bacteremic patients in Bangladesh","biosets":3,"date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["Paratyphi A"],"taxon_lineage_ids":["131567","2","1224","1236","91347","543","590","28901","59201","90371","99287"],"organism":["Salmonella enterica"],"genome_id":["220341.7","295319.15","99287.12"],"treatment_name":["in vitro"],"treatment_type":["in vitro"],"taxon_id":[99287],"treatment_duration":[""],"_version_":1809284005071159300},{"study_institution":"Harvard University","public_repository":"GEO","exp_description":"The cyanobacterium Synechococcus elongatus PCC 7942 exhibits oscillations in mRNA transcript abundance with 24-hour periodicity under continuous light conditions. The mechanism underlying these oscillations remains elusive ¿ neither cis nor trans-factors controlling circadian gene expression phase have been identified. Here we show that the topological status of the chromosome is highly correlated with circadian gene expression state. We also demonstrate that DNA sequence characteristics of genes that appear monotonically activated and monotonically repressed by chromosomal relaxation during the circadian cycle are similar to those of supercoiling responsive genes in E. coli. Furthermore, perturbation of superhelical status within the physiological range elicits global changes in gene expression similar to those that occur during the normal circadian cycle.","pmid":"20018699","exp_title":"Oscillations in supercoiling drive circadian gene expression in cyanobacteria","study_pi":"Erin K O'Shea","biosets":23,"exp_id":"738549","exp_type":"Transcript Quantification","public_identifier":"GSE18902","measurement_technique":"Microarray","exp_name":"GSE18902","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["PCC 7942"],"taxon_lineage_ids":["131567","2","1783272","1798711","1117","1890424","1890426","1129","32046","1140"],"organism":["Synechococcus elongatus"],"genome_id":["1140.7"],"treatment_name":["light,time point","novobiocin,time point"],"treatment_type":["light,time point","novobiocin,time point"],"taxon_id":[1140],"treatment_duration":["40h","56h","64h","84h","150m","90m","24h","44h","52h","68h","72h","80h","28h","48h","76h","5m","32h","36h","60h","10m","30m"],"_version_":1809284005073256400},{"study_pi":"Ted Hackstadt","exp_title":"Developmental stage specific metabolic and transcriptional activity of chlamydial elementary bodies and reticulate bodies in an axenic medium","biosets":6,"study_institution":"NIH","public_repository":"GEO","exp_description":"Chlamydia trachomatis is a significant human pathogen yet their obligate intracellular nature severe restrictions upon research.  Chlamydiae undergo a complex developmental cycle characterized by an infectious cell type known as the  elementary body (EB) and an intracellular active replicative form called the reticulate body (RB).    EBs have historically been described as metabolically dormant.  A cell-free (axenic) culture system was developed which showed high levels of metabolic and biosynthetic activity from both EBs and RBs.  EBs preferentially utilized glucose-6-phosphate as an energy source whereas RBs required ATP. Both developmental forms showed improved activity when incubated under microaerobic conditions.  Incorporation of isotopically-labeled amino acids into proteins from both developmental forms indicated unique expression profiles which were confirmed by genome-wide transcriptional analysis.  The described axenic culture system will greatly enhance  biochemical and physiological analyses of chlamydiae.","pmid":"23129646","public_identifier":"GSE39530","measurement_technique":"Microarray","exp_name":"GSE39530","exp_id":"1150517","exp_type":"Transcript Quantification","date_inserted":"2021-12-20T21:06:51.864Z","date_modified":"2021-12-20T21:06:51.864Z","strain":["LGV434"],"organism":["Chlamydia trachomatis"],"genome_id":["115711.10","176279.9","176280.10","196620.5","198214.7","227377.7","227941.6","243161.6","272561.5","279808.8"],"treatment_name":["growth media"],"treatment_type":["growth media"],"treatment_duration":[""],"_version_":1809284005075353600}]