Escherichia coli str. K-12 substr. W3110
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PROVIDER: PRJNA108529 | ENA |
REPOSITORIES: ENA
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Project description:A time series of whole-genome transcription profiling of E. coli K-12 W3110 was performed to study the dynamic physiological response of E. coli K-12 W3110 to limited carbon conditions. cDNA from eight time intervals after glucose limitation, representing different stages of glucose depletion, along with cDNA of an unrestricted growth were hybridized to whole-genome microarrays of E. coli K-12. Glucose concentrations were gradually reduced in a fed-batch cultivation process with constant feeding rate in a bioreactor. Major focus was put on the dynamic changes in the transcription level of genes involved in the central carbon metabolism (glycolysis, pentose phosphate pathway, TCA cycle and glyoxylate shunt), high-affinity glucose transport systems, movement, growth, and stress response. In total, 40 microarrays were hybridized. The data were statistically analysed using the software R (R, 2005) and the Limma package included (Smyth, 2005). The data were normalized â??print-tip-loessâ??. â??Multiple hypothesis testingâ?? correction was performed with the method of Benjamini and Hochberg (Benjamini and Hochberg, 1995), which controls the â??false discovery rateâ?? (fdr). Genes were regarded as differentially expressed when the â??adjusted p valuesâ?? were < 0.05, therefore nominally controlling the expected fdr to less than 0.05. The reproducibility of dye swap experiments as well as biological replicates was estimated by calculating â??Pearsonâ??s correlation coefficientsâ??. A high correlation was observed for the dye swap pairs (with averaged Pearsonâ??s correlation coefficients of 0.89 ± 0.06 for the reference samples and of 0.87 ± 0.08 for the different points of time) as well as for biological replicates (with averaged Pearsonâ??s correlation coefficients of 0.86 ± 0.04 for the red channel (Cy5) and 0.80 ± 0.09 for the green channel (Cy3)). Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B 57, 289-300. Smyth, G.K. (2005). Limma: Linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, Carrey, V., Dudoit, S., Irizzary, I., Huber, W., ed. (New York, Springer), pp. 397-420. R (2005). R: A language and environment for statistical computing. (R Development Core Team). Supplementary files: Data_table_A: TabelleA_Signifikante.txt Description: Data table with coefficients of the linear model for every gene which was differentially expressed for at least one point in time according to the reference sample. The statistical analysis was performed as described in Series section (GSE10307) based on the normalized log2(test/ref) ratios in the Sample records' VALUE columns. Data_table_B1: Tabelle_B1; /E. coli/, unlimited growth via glucose limitation (glucose concentration < 0.05 gL-1) Data_table_B2: Tabelle_B2; /E. coli/, unlimited growth via glucose limitation, acetate concentration = 0.35 gL-1 Data_table_B3: Tabelle_B3; /E. coli/, unlimited growth via glucose limitation, 30 min after depletion of extracellular acetate Data_table_B4: Tabelle_B4; /E. coli/, unlimited growth via glucose limitation, 50 min after depletion of extracellular acetate Data_table_B5: Tabelle_B5; /E. coli/, unlimited growth via glucose limitation, 110 min after depletion of extracellular acetate Data_table_B6: Tabelle_B6; /E. coli/, unlimited growth via glucose limitation, 170 min after depletion of extracellular acetate Data_table_B7: Tabelle_B7; /E. coli/, unlimited growth via glucose limitation, 230 min after depletion of extracellular acetate Data_table_B8: Tabelle_B8; /E. coli/, unlimited growth via glucose limitation, 350 min after depletion of extracellular acetate Description: Data_tables_B1-B8 report statistical values (A: average intensity value (1/2log2(test*ref)); M: average expression value (log2(test/ref)), t and P.value ('adjusted P.value')) for every point in time (studied conditions are described above for the corresponding table). Every differentially expressed gene of the corresponding point in time according to the reference sample is listed. Genes were regarded as differentially expressed when their 'adjusted P.values' were < 0.05, therefore nominally controlling the expected fdr to less than 0.05. The data are based on maximal three biological replicates (three independent fed-batch cultivations). RT-PCR_results_7genes.txt and RT-PCR_protocol.PDF Keywords: Time course, stress response Hybridization involved the hybridization of a common reference (unlimited growth, batch phase) on all arrays together with each sample of interest. This allowed the direct comparison of the transcripts of a time series taken during fed-batch cultivation with the unlimited reference sample. All samples were taken in duplicates and the experiments were performed as dye swap experiments. The first four samples of the time series (T1 - T4) were taken from three individual fed-batch cultivations (three biological replicates), the subsequent four samples (T5 - T8) were taken only from two individual fed-batch cultivations. On each array, the genes were spotted in duplicates. Therefore, twelve replicates (duplicates on dye swaps for three cultivations) were analyzed for T1 â?? T4 and eight replicates (duplicates on dye swaps for two cultivations) were analyzed for T5 â?? T8.
2010-05-19 | E-GEOD-10307 | biostudies-arrayexpress
Project description:Time-course transcriptomic profilling of the oleaginous yeast Yarrowia lipolytica, during a controlled fed-batch. A nitrogen limitation was applied during the course of the fed-batch to initiate de novo biolipid synthesis.
2011-05-15 | GSE29046 | GEO
Project description:Transcriptome responses to nitrogen starvation and oxygen limitation during fed-batch cultivation of Aurantiochytrium sp. T66
| PRJNA554891 | ENA
Project description:A time series of whole-genome transcription profiling of E. coli K-12 W3110 was performed to study the dynamic physiological response of E. coli K-12 W3110 to limited carbon conditions. cDNA from eight time intervals after glucose limitation, representing different stages of glucose depletion, along with cDNA of an unrestricted growth were hybridized to whole-genome microarrays of E. coli K-12. Glucose concentrations were gradually reduced in a fed-batch cultivation process with constant feeding rate in a bioreactor. Major focus was put on the dynamic changes in the transcription level of genes involved in the central carbon metabolism (glycolysis, pentose phosphate pathway, TCA cycle and glyoxylate shunt), high-affinity glucose transport systems, movement, growth, and stress response. In total, 40 microarrays were hybridized. The data were statistically analysed using the software R (R, 2005) and the Limma package included (Smyth, 2005). The data were normalized “print-tip-loess”. “Multiple hypothesis testing” correction was performed with the method of Benjamini and Hochberg (Benjamini and Hochberg, 1995), which controls the “false discovery rate” (fdr). Genes were regarded as differentially expressed when the “adjusted p values” were < 0.05, therefore nominally controlling the expected fdr to less than 0.05. The reproducibility of dye swap experiments as well as biological replicates was estimated by calculating “Pearson’s correlation coefficients”. A high correlation was observed for the dye swap pairs (with averaged Pearson’s correlation coefficients of 0.89 ± 0.06 for the reference samples and of 0.87 ± 0.08 for the different points of time) as well as for biological replicates (with averaged Pearson’s correlation coefficients of 0.86 ± 0.04 for the red channel (Cy5) and 0.80 ± 0.09 for the green channel (Cy3)). Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B 57, 289-300. Smyth, G.K. (2005). Limma: Linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, Carrey, V., Dudoit, S., Irizzary, I., Huber, W., ed. (New York, Springer), pp. 397-420. R (2005). R: A language and environment for statistical computing. (R Development Core Team). Supplementary files: Data_table_A: TabelleA_Signifikante.txt Description: Data table with coefficients of the linear model for every gene which was differentially expressed for at least one point in time according to the reference sample. The statistical analysis was performed as described in Series section (GSE10307) based on the normalized log2(test/ref) ratios in the Sample records' VALUE columns. Data_table_B1: Tabelle_B1; /E. coli/, unlimited growth via glucose limitation (glucose concentration < 0.05 gL-1) Data_table_B2: Tabelle_B2; /E. coli/, unlimited growth via glucose limitation, acetate concentration = 0.35 gL-1 Data_table_B3: Tabelle_B3; /E. coli/, unlimited growth via glucose limitation, 30 min after depletion of extracellular acetate Data_table_B4: Tabelle_B4; /E. coli/, unlimited growth via glucose limitation, 50 min after depletion of extracellular acetate Data_table_B5: Tabelle_B5; /E. coli/, unlimited growth via glucose limitation, 110 min after depletion of extracellular acetate Data_table_B6: Tabelle_B6; /E. coli/, unlimited growth via glucose limitation, 170 min after depletion of extracellular acetate Data_table_B7: Tabelle_B7; /E. coli/, unlimited growth via glucose limitation, 230 min after depletion of extracellular acetate Data_table_B8: Tabelle_B8; /E. coli/, unlimited growth via glucose limitation, 350 min after depletion of extracellular acetate Description: Data_tables_B1-B8 report statistical values (A: average intensity value (1/2log2(test*ref)); M: average expression value (log2(test/ref)), t and P.value ('adjusted P.value')) for every point in time (studied conditions are described above for the corresponding table). Every differentially expressed gene of the corresponding point in time according to the reference sample is listed. Genes were regarded as differentially expressed when their 'adjusted P.values' were < 0.05, therefore nominally controlling the expected fdr to less than 0.05. The data are based on maximal three biological replicates (three independent fed-batch cultivations). RT-PCR_results_7genes.txt and RT-PCR_protocol.PDF Keywords: Time course, stress response
2008-09-23 | GSE10307 | GEO
Project description:This approach aims at searching unidentified regulatory roles of the AreB transcription factor in the overall carbon metabolism of A. niger. A full areB gene deletion mutant was constructed and characterized in A. niger ATCC 1015. Both strains were grown on glucose or glycerol using ammonia as nitrogen source in batch cultivations and the transcriptome was analyzed using three biological replicated transcriptome experiments. Two areB gene deletion replicates, one on glucose and one on glycerol were discarded due to bad quality and therefore not included in the analysis. Samples for RNA extraction were collected and further processed for hybridization in custom designed Affymetrix microarrays containing probes for three Aspergillus species including A. niger. Triplicate batch fermentations with the two Aspergillus niger strains used, the wild type A. niger strain ATCC 1015 and the areB complete gene deletion strain were carried out and transcriptome analysis was performed. Biomass from each batch cultivation was harvested in the exponential phase of growth and further processed for RNA extraction and hybridization on Affymetrix microarrays.
2011-01-31 | E-GEOD-21015 | biostudies-arrayexpress
Project description:Expression data from batch cultivations of Aspergillus niger wild type strain ATCC 1015 and adrA, facB and creA deletion mutants constructed on ATCC 1015 background strain with glucose or glycerol as carbon sources. Genome-wide transcriptome analysis was used to identify genes either affected directly or indirectly by each transcription factor investigated during growth on a repressing or a derepressing carbon source. For this purpose, batch cultivations under well-controlled conditions were performed with Aspergillus niger wild type strain ATCC 1015 and the three deletion mutants of the corresponding transcription factors AdrA, FacB and CreA. Samples for RNA extraction were collected and further processed for hybridization in custom-designed Affymetrix microarrays containing probes for three Aspergillus species, including A. niger. Triplicate batch fermentations of each of the four Aspergillus niger strains used, the wild type A. niger strain ATCC 1015 and three gene deletion mutants, were carried out using glucose or glycerol as carbon source, and transcriptome analysis was performed. Biomass from each batch cultivation was harvested in the exponential phase of growth and further processed for RNA extraction and hybridization on Affymetrix microarrays.
2011-01-31 | E-GEOD-19952 | biostudies-arrayexpress
Project description:Fed-batch cultivation of recombinant Chinese hamster ovary (CHO) cell lines is one of the most widely used production mode for commercial manufacturing of recombinant protein therapeutics. Furthermore, fed-batch cultivations are often conducted as biphasic processes where culture temperature is decreased to maximize volumetric product yields. However, it still remains to be elucidated which intracellular regulatory elements actually control the observed pro-productive phenotypes. Recently, several studies have revealed microRNAs (miRNAs) to be important molecular switches of cell phenotypes since single miRNAs are capable of regulating entire physiological pathways. In this study, we analyzed miRNA profiles of two different recombinant CHO cell lines (high and low producer), and compared them to a non-producing CHO DG44 host cell line during fed-batch cultivation at 37 versus 30 °C culture temperature. Taking advantage of next-generation sequencing combined with cluster, correlation and differential expression analyses, we could identify 89 different miRNAs, which might be interesting for CHO cell engineering. Functional validation experiments using 19 validated target miRNAs confirmed that these miRNAs indeed induced changes in process relevant phenotypes such as recombinant protein production, apoptosis, necrosis and proliferation. Furthermore, computational miRNA target prediction combined with functional clustering identified putative target genes and cellular pathways, which might be regulated by these miRNAs. Taken together, our study systematically identified novel target miRNAs during different phases and conditions of a biphasic fed-batch process and functionally evaluated their potential for host cell engineering.
2016-04-03 | GSE72945 | GEO
Project description:Glucose Glycerol fed-batch fermentation under elevated pCO2
| PRJNA704781 | ENA
Project description:Time-course transcriptomic profilling of the oleaginous yeast Yarrowia lipolytica, during a controlled fed-batch. A nitrogen limitation was applied during the course of the fed-batch to initiate de novo biolipid synthesis. Dual staining, one replicate per slide. On each slide, a time point sample and a reference sample are spotted. Reference samples were obtained by pooling the RNAs from the time-course samples.
2011-05-15 | E-GEOD-29046 | biostudies-arrayexpress
Project description:Transcriptional profiling of A. nidulans comparing the mutant strains ΔgprB and ΔgprD grown on 1% glucose (w/v) in a batch cultivation medium (BCM) at 37°C for 24 and 48h. The main objective was to identifiy genes related to gprB and gprD gene function. The experiment was further validated by real-time PCR and enzymatic assay.
2012-11-28 | GSE42553 | GEO