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Series GSE17520 Query DataSets for GSE17520
Status Public on Aug 05, 2010
Title M. smegmatis response to energy- and oxygen-limitation in continuous culture
Platform organism Mycolicibacterium smegmatis
Sample organism Mycolicibacterium smegmatis MC2 155
Experiment type Expression profiling by array
Summary Transcriptional profiling of M. smegmatis grown at 69h doubling time compared to 4.6h doubling time both at 50% air saturation. Transcriptional profiling of M. smegmatis grown at 69h doubling time with 50%, 2.5% and 0.6% air saturation.
 
Overall design Two-condition experiment. Biological replicates: 5 independently grown and harvested. One replicate per array.
 
Contributor(s) Berney M, Cook GM
Citation(s) 20062806
Submission date Aug 05, 2009
Last update date Mar 21, 2012
Contact name Michael Berney
Organization name Albert Einstein College of Medicine
Department Department of Microbiology and Immunology
Lab Jacobs lab
Street address 1301 Morris Park Avenue
City Bronx
State/province NY
ZIP/Postal code 10461
Country USA
 
Platforms (1)
GPL5862 JCVI PFGRC Mycobacterium smegmatis 25K v4 array designed primarily based on strain MC2 155
Samples (15)
GSM436644 Slow vs. Fast Replicate 1
GSM436645 Slow vs. Fast Replicate 2
GSM436646 Slow vs. Fast Replicate 3
Relations
BioProject PRJNA118797

Combined means and p-values for biological replicates header descriptions
Locus Locus
GeneN GeneN
GeneS GeneS
mean(slow_50%_vs_fast_50%) Gene mean for slow 50% vs. fast 50%
p-value(slow_50%_vs_fast_50%) Raw p value for slow 50% vs. fast 50%
mean(slow_2.5%_vs_slow 50%) Gene mean for slow 2.5% vs. slow 50%
p-value(slow_2.5%_vs_slow 50%) Raw p value for slow 2.5% vs. slow 50%
mean(slow_0.6%_vs_slow_50%) Gene mean for slow 0.6% vs slow 50%
p-value(slow_0.6%_vs_slow_50%) Raw p value for slow 0.6% vs slow 50%

Data table
Locus GeneN GeneS mean(slow_50%_vs_fast_50%) p-value(slow_50%_vs_fast_50%) mean(slow_2.5%_vs_slow 50%) p-value(slow_2.5%_vs_slow 50%) mean(slow_0.6%_vs_slow_50%) p-value(slow_0.6%_vs_slow_50%)
MSMEG_0001 DNA polymerase III, beta subunit dnaN 0.89412355 0.056874678 0.99200976 0.36326736 1.089381 0.34745502
MSMEG_0002 6-phosphogluconate dehydrogenase, decarboxylating 0.82564706 0.0610316 0.90861624 0.23391482 1.1982563 0.13472235
MSMEG_0003 DNA replication and repair protein RecF 0.86206293 0.021948485 0.91370165 0.25247815 1.7640932 0.10513822
MSMEG_0004 hypothetical protein 0.96577847 0.5010798 0.9455573 0.5631956 1.5897179 0.015242265
MSMEG_0005 DNA gyrase, B subunit gyrB 0.78291667 0.001477015 0.9078165 0.10348561 0.9054095 0.36749762
MSMEG_0006 DNA gyrase, A subunit gyrA 0.45506963 2.13E-05 1.0258269 0.70492387 2.745463 1.15E-04
MSMEG_0007 conserved hypothetical protein 0.67199254 1.17E-04 0.8554634 0.06816649 1.653087 0.094331816
MSMEG_0009 hypothetical protein 1.472009 6.20E-04 0.81853104 0.09648386 1.3081048 0.22786416
MSMEG_0011 FAD-binding 9, siderophore-interacting 0.8389963 0.064668044 1.1592551 0.32114375 1.0821325 0.72825855
MSMEG_0012 ferric enterobactin transport system permease protein FepD 0.53604615 0.030161543 1.7473707 0.29972953 1.7180961 0.14550574
MSMEG_0013 ferric enterobactin transport system permease protein FepG; this gene contains a frame shift which is not the result of sequencing error; identified by match to protein family HMM PF01032 0.6041925 0.005942142 1.2826126 0.14694451 1.4286335 0.1664056
MSMEG_0014 Formyl transferase 1.2881093 0.16461888 0.5960818 0.03950621 0.87796324 0.27502158
MSMEG_0015 ferric enterobactin transport ATP-binding protein FepC 1.4047167 0.18561146 0.6893016 0.011486649 1.1113108 0.5306311
MSMEG_0016 conserved domain protein 0.9001466 0.089516275 0.8271507 0.06382087 0.8873297 0.30701387
MSMEG_0017 ABC transporter, permease/ATP-binding protein 0.75176096 0.088019505 1.3398616 0.08293586 1.1919367 0.43284586
MSMEG_0018 ABC transporter, permease/ATP-binding protein 0.83990014 0.043011498 1.2101566 0.16094781 1.0967762 0.6696072
MSMEG_0019 amino acid adenylation 0.87861407 0.16038224 1.0336895 0.82554907 0.9109067 0.17737311
MSMEG_0020 Periplasmic binding protein 0.6008202 3.51E-04 0.76719 0.007201826 0.11340372 1.11E-06
MSMEG_0021 aspartate 1-decarboxylase panD 0.7655491 0.007296015 1.0015925 0.9866168 0.39127603 0.006853527
MSMEG_0022 L-ornithine 5-monooxygenase 0.5269432 0.002090454 1.0529177 0.6912415 0.3192532 0.002300505

Total number of rows: 6897

Table truncated, full table size 745 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE17520_RAW.tar 17.8 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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