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Sample GSM944527 Query DataSets for GSM944527
Status Public on Dec 01, 2015
Title delta dapZ with pBAD-ctr (sample 1)
Sample type mixed
 
Channel 1
Source name delta dapZ with pBAD-ctr
Organism Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Characteristics strain background: S.typhimurium SL1344 dapZ deletant
trasnformed with: pBAD-ctr plasmid (negative control)
Extracted molecule total RNA
Extraction protocol Salmonella RNA was isolated using the Promega SV total RNA purification kit
Label Cy3
Label protocol Total RNA was labelled by random priming according to the protocols described at the IFR (Institute of Food Research, Norwich) website (www.ifr.ac.uk/safety/microarrays/protocols.html). Briefly, 10 µg RNA were reverse transcribed and labeled with Cy3-conjugated dCTP (Pharmacia) using 200 units of StrataScript and random octamers (Invitrogen).
 
Channel 2
Source name wild type
Organism Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Characteristics strain background: S.typhimurium SL1344
genotype/variation: Wild type
Extracted molecule genomic DNA
Extraction protocol Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)
Label Cy5
Label protocol Chromosomal DNA (400 ng) was labeled with Cy5-dCTP using the Klenow fragment.
 
 
Hybridization protocol Labeled samples were mixed and hybridized to 8x15K custom-commercial microarrays overnight at 65ºC using 1x Hi hybridization buffer together with blocking buffer according to the supplier`s recommendations (Agilent Technologies). Washing of the hybridized arrays was done with the SSC protocol according supplier`s protocol (Agilent Technologies).
Scan protocol Scanning of microarrays was performed with 5 µm resolution and extended range using a DNA microarray laser scanner (Agilent Technologies).
Data processing Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies). To compensate for unequal dye incorporation, data centering to zero was performed for each individual microarray on the slide separately. Microarray data were analysed using GeneSpring 7.3 (Agilent) and genes were considered to be differentially expressed if they displayed ≥2-fold changes in both replicates and were statistically significantly different (Student's t-test; p<0.05)
 
Submission date Jun 06, 2012
Last update date Dec 01, 2015
Contact name Hans-Joachim Mollenkopf
E-mail(s) [email protected]
Phone +49 30 28460 482
Organization name Max-Planck-Institute for Infection Biology
Lab Microarray/Genomics Core Facility
Street address Charitéplatz 1
City Berlin
ZIP/Postal code 10117
Country Germany
 
Platform ID GPL11416
Series (1)
GSE38523 Targets of the small regulatory RNA DapZ

Data table header descriptions
ID_REF
Row
Col
chr_coord
accessions
SubTypeMask
SubTypeName
Start
Sequence
ProbeUID
ControlType
ProbeName
GeneName
SystematicName
Description
PositionX
PositionY
LogRatio
LogRatioError
PValueLogRatio
gSurrogateUsed
rSurrogateUsed
gIsFound
rIsFound
gProcessedSignal
rProcessedSignal
gProcessedSigError
rProcessedSigError
gNumPixOLHi
rNumPixOLHi
gNumPixOLLo
rNumPixOLLo
gNumPix
rNumPix
gMeanSignal
rMeanSignal
gMedianSignal
rMedianSignal
gPixSDev
rPixSDev
gPixNormIQR
rPixNormIQR
gBGNumPix
rBGNumPix
gBGMeanSignal
rBGMeanSignal
gBGMedianSignal
rBGMedianSignal
gBGPixSDev
rBGPixSDev
gBGPixNormIQR
rBGPixNormIQR
gNumSatPix
rNumSatPix
gIsSaturated
rIsSaturated
gIsLowPMTScaledUp
rIsLowPMTScaledUp
PixCorrelation
BGPixCorrelation
gIsFeatNonUnifOL
rIsFeatNonUnifOL
gIsBGNonUnifOL
rIsBGNonUnifOL
gIsFeatPopnOL
rIsFeatPopnOL
gIsBGPopnOL
rIsBGPopnOL
IsManualFlag
gBGSubSignal
rBGSubSignal
gBGSubSigError
rBGSubSigError
BGSubSigCorrelation
gIsPosAndSignif
rIsPosAndSignif
gPValFeatEqBG
rPValFeatEqBG
gNumBGUsed
rNumBGUsed
gIsWellAboveBG
rIsWellAboveBG
gBGUsed
rBGUsed
gBGSDUsed
rBGSDUsed
IsNormalization
gDyeNormSignal
rDyeNormSignal
gDyeNormError
rDyeNormError
DyeNormCorrelation
ErrorModel
xDev
gSpatialDetrendIsInFilteredSet
rSpatialDetrendIsInFilteredSet
gSpatialDetrendSurfaceValue
rSpatialDetrendSurfaceValue
SpotExtentX
SpotExtentY
gNetSignal
rNetSignal
gMultDetrendSignal
rMultDetrendSignal
gProcessedBackground
rProcessedBackground
gProcessedBkngError
rProcessedBkngError
IsUsedBGAdjust
gInterpolatedNegCtrlSub
rInterpolatedNegCtrlSub
gIsInNegCtrlRange
rIsInNegCtrlRange
gIsUsedInMD
rIsUsedInMD
gNorm
rNorm
log g/r
norm log
VALUE normalized ratio r/g (Cy5/Cy3)
Median block
Median norm

Data table
ID_REF Row Col chr_coord accessions SubTypeMask SubTypeName Start Sequence ProbeUID ControlType ProbeName GeneName SystematicName Description PositionX PositionY LogRatio LogRatioError PValueLogRatio gSurrogateUsed rSurrogateUsed gIsFound rIsFound gProcessedSignal rProcessedSignal gProcessedSigError rProcessedSigError gNumPixOLHi rNumPixOLHi gNumPixOLLo rNumPixOLLo gNumPix rNumPix gMeanSignal rMeanSignal gMedianSignal rMedianSignal gPixSDev rPixSDev gPixNormIQR rPixNormIQR gBGNumPix rBGNumPix gBGMeanSignal rBGMeanSignal gBGMedianSignal rBGMedianSignal gBGPixSDev rBGPixSDev gBGPixNormIQR rBGPixNormIQR gNumSatPix rNumSatPix gIsSaturated rIsSaturated gIsLowPMTScaledUp rIsLowPMTScaledUp PixCorrelation BGPixCorrelation gIsFeatNonUnifOL rIsFeatNonUnifOL gIsBGNonUnifOL rIsBGNonUnifOL gIsFeatPopnOL rIsFeatPopnOL gIsBGPopnOL rIsBGPopnOL IsManualFlag gBGSubSignal rBGSubSignal gBGSubSigError rBGSubSigError BGSubSigCorrelation gIsPosAndSignif rIsPosAndSignif gPValFeatEqBG rPValFeatEqBG gNumBGUsed rNumBGUsed gIsWellAboveBG rIsWellAboveBG gBGUsed rBGUsed gBGSDUsed rBGSDUsed IsNormalization gDyeNormSignal rDyeNormSignal gDyeNormError rDyeNormError DyeNormCorrelation ErrorModel xDev gSpatialDetrendIsInFilteredSet rSpatialDetrendIsInFilteredSet gSpatialDetrendSurfaceValue rSpatialDetrendSurfaceValue SpotExtentX SpotExtentY gNetSignal rNetSignal gMultDetrendSignal rMultDetrendSignal gProcessedBackground rProcessedBackground gProcessedBkngError rProcessedBkngError IsUsedBGAdjust gInterpolatedNegCtrlSub rInterpolatedNegCtrlSub gIsInNegCtrlRange rIsInNegCtrlRange gIsUsedInMD rIsUsedInMD gNorm rNorm log g/r norm log VALUE Median block Median norm
1 1 1 260 BrightCorner 0 0 1 GE_BrightCorner GE_BrightCorner GE_BrightCorner 6728.18 296.592 -1.48E+00 1.53E-01 4.37E-22 0 0 1 1 4.75E+03 1.58E+02 4.75E+02 1.58E+01 3 1 1 0 61 61 5.86E+04 2.63E+04 56604.2 25253.4 9.58E+03 4.22E+03 1.02E+04 4.51E+03 652 652 5.69E+01 1.09E+02 51.5 108.5 3.09E+01 5.95E+01 2.82E+01 6.75E+01 0 0 0 0 1 1 0.724478 0.423528 0 0 0 0 0 0 0 1 0 58156.4 25538.6 5815.87 2558.01 0 1 1 4.86E-173 5.11E-111 1 1 1 1 401.148 742.781 30.865 59.5092 0 4753.69 157.884 475.387 15.8141 0 1 -9.66E+00 0 0 401.148 742.781 55.5662 55.5662 58548.2 26271.8 0.696487 0.729686 56.9233 108.968 30.865 59.5092 0 58192.8 25961.4 0 0 0 0 56552.7 25144.9 0.352003432 1.373869609 23.65209469 -1.021866177 1
2 1 2 66 Structural 0 1 1 DarkCorner DarkCorner DarkCorner 6753.63 296.596 0.00E+00 1.11E+00 1.00E+00 74.0007 201.439 1 1 6.04E-01 6.34E+00 5.92E-01 6.21E+00 4 4 0 0 58 58 3.52E+02 1.40E+02 346 146 6.19E+01 5.13E+01 7.23E+01 5.32E+01 488 488 6.71E+01 1.21E+02 63 117 3.54E+01 6.93E+01 3.63E+01 7.78E+01 0 0 0 0 0 0 0.4244 0.525086 0 0 0 0 0 0 0 1 0 -49.3723 -591.636 51.2638 145.616 0 0 0 0.0147187 1.72E-15 1 1 0 0 401.355 732.085 35.3755 69.3398 0 0.603604 6.34236 0.591944 6.20511 0 1 9.21E-01 0 0 401.355 732.085 57.8122 57.8122 342.611 130.814 0.706393 0.738868 67.0512 121.33 35.3755 69.3398 0 -11.0755 -174.838 0 0 0 0 283 29 0.989388438 2.011254615 102.6253414
3 1 3 66 Structural 0 1 1 DarkCorner DarkCorner DarkCorner 6779.42 296.573 0.00E+00 1.12E+00 1.00E+00 72.9482 198.936 1 1 5.90E-01 6.31E+00 5.79E-01 6.18E+00 2 0 0 0 62 62 3.89E+02 4.88E+02 373 461.5 8.97E+01 2.07E+02 8.52E+01 2.17E+02 491 491 5.88E+01 1.13E+02 56 112 3.09E+01 6.59E+01 2.89E+01 7.38E+01 0 0 0 0 0 0 0.494513 0.45626 0 0 0 0 0 0 0 1 0 -12.9186 -233.475 51.2638 145.616 0 0 0 0.51458 9.67E-05 1 1 0 0 401.515 721.588 30.8604 65.8614 0 0.590472 6.31179 0.579065 6.1752 0 1 9.22E-01 0 0 401.515 721.588 57.5363 57.5363 379.225 478.478 0.716585 0.748165 58.8004 112.591 30.8604 65.8614 0 27.225 177.5 0 0 0 0 317 349.5 -0.042387918 0.97947826 9.538459928
4 1 4 chr1:4196869-4196928 SL1344|SL3922|SL1344|SL3922|LT2|STM3968|14028S|STM14_4774|protein_id|NP_462853.1 0 0 CGTAACCGCCTCTTCCGACACTTTCTATCCGGGTCAGGAACGTTACGACACCTATTCTGG 3 0 "HSL3922STM3968ATC4,1" udp SL3922 uridine phosphorylase 6804.43 296.724 9.41E-02 6.20E-02 1.29E-01 0 0 1 1 1.54E+03 1.92E+03 1.54E+02 1.92E+02 0 0 0 0 67 67 3.31E+04 1.95E+05 32436.6 189127 5.26E+03 3.45E+04 6.05E+03 3.58E+04 480 480 5.11E+01 1.06E+02 51 105 2.61E+01 6.24E+01 2.74E+01 7.21E+01 0 0 0 0 1 1 0.0805945 0.451466 0 0 0 0 0 0 0 1 0 32667.8 193851 3267.18 19385.7 0 1 1 2.94E-156 1.37E-165 1 1 1 1 401.624 711.266 26.1476 62.4071 0 1542.51 1915.81 154.27 191.587 0 1 1.52E+00 0 0 401.624 711.266 48.5334 48.5334 33060 194553 0.726726 0.757288 51.1417 106.033 26.1476 62.4071 0 32709.6 194256 0 0 0 0 32385.6 189022 -0.766160406 0.255705771 1.801796633
5 1 5 chr1:2100505-2100554 SL1344|SL1998|SL1344|SL1998|LT2|STM2022|14028S|STM14_2510|protein_id|NP_460967.1 0 0 GCAGTATAAACCCTGGTTTCAGCCGTTATATGAACCTGCCAGCGGTGAAA 5 0 "HSL1998STM2022ATC2,2" cbiN SL1998 cobalt transport protein CbiN 6829.89 296.693 6.03E-02 6.19E-02 3.30E-01 0 0 1 1 4.83E+02 5.55E+02 4.87E+01 5.55E+01 0 4 0 0 66 60 4.69E+03 1.38E+05 4624 136643 8.57E+02 2.45E+04 8.62E+02 2.30E+04 486 486 4.83E+01 1.05E+02 47 105 2.43E+01 6.00E+01 2.59E+01 6.71E+01 0 0 0 0 0 1 0.174716 0.498731 0 0 0 0 0 0 0 1 0 4286.81 137719 431.735 13772.6 0 1 1 3.48E-97 2.19E-156 1 1 1 1 400.542 699.023 24.3094 59.9752 0 483.315 555.298 48.6758 55.5329 0 1 9.75E-01 0 0 400.542 699.023 47.8731 47.8731 4677.98 138408 0.737058 0.766464 48.3354 105.241 24.3094 59.9752 0 4329.14 138116 0 0 0 0 4577 136538 -1.474672625 -0.452806447 0.352527948
6 1 6 chr3:71370-71429 SL1344|SLP2_0085|SL1344|SLP2_0085 0 0 GATTTTATATGTCCGATGGATCATGGGTTCGAAGTGTAAACAACAAGGGCATCTATACCG 7 0 "x_SLP2_0085,1" SLP2_0085 SLP2_0085 Unknown 6855.2 296.784 2.77E-01 6.65E-02 3.10E-05 0 0 1 1 5.60E+02 1.06E+03 5.62E+01 1.06E+02 0 0 0 0 65 65 7.13E+03 2.00E+05 7091 189148 9.86E+02 3.76E+04 1.07E+03 4.84E+04 486 486 5.67E+01 1.13E+02 53 108 3.21E+01 6.58E+01 2.97E+01 7.26E+01 0 0 0 0 0 1 0.126533 0.465896 0 0 0 0 0 0 0 1 0 6732.51 198990 675.2 19899.5 0 1 1 2.62E-110 2.70E-166 1 1 1 1 398.748 688.151 32.0807 65.7985 0 560.025 1059.62 56.1646 105.965 0 1 4.17E+00 0 0 398.748 688.151 47.8731 47.8731 7121.89 199669 0.747501 0.775641 56.6893 113.183 32.0807 65.7985 0 6774.58 199381 0 0 0 0 7038 189040 -1.429104446 -0.407238269 0.391527013
7 1 7 unmapped 0 0 ATATTTGCGATATCGTGCCAGAGACGCAGCTTCCTGTCAGCGGGGACAATATCCATGATA 9 0 ctrl_SL0764 ctrl_SL0764 ctrl_SL0764 Unknown 6880.93 296.8 -7.41E-01 9.22E-02 9.40E-16 0 0 1 1 9.52E+02 1.73E+02 9.55E+01 1.73E+01 3 0 0 0 63 63 7.85E+03 5.19E+04 7673 50100.9 1.18E+03 9.88E+03 1.13E+03 1.10E+04 498 498 6.32E+01 1.14E+02 57 116 3.57E+01 6.22E+01 3.32E+01 6.58E+01 0 0 0 0 0 1 0.538184 0.393731 0 0 0 0 0 1 0 1 0 7453.22 51189.5 747.083 5121.02 0 1 1 2.89E-113 9.74E-130 1 1 1 1 397.38 677.763 35.725 62.1566 0 952.34 172.895 95.459 17.2965 0 1 -8.03E+00 0 0 397.38 677.763 46.8651 46.8651 7841.23 51857.6 0.75815 0.784906 63.1526 113.906 35.725 62.1566 0 7495.43 51574.3 0 0 1 1 7616 49984.9 -0.817111892 0.204754285 1.602338564
8 1 8 chr1:578749-578808 SL1344|SL0511|SL1344|SL0511|LT2|STM0518|14028S|STM14_0608|protein_id|NP_459513.1 0 0 TGTTACGTTTCTCTGCCAATCTTTCTATGCTGTTTACGGAATATGATTTCCTGGAACGCT 11 0 "HSL0511STM0518ATC0,1" gip SL0511 hydroxypyruvate isomerase 6906.28 296.905 2.58E-01 6.68E-02 1.16E-04 0 0 1 1 2.02E+02 3.66E+02 2.16E+01 3.66E+01 3 0 0 0 63 64 1.77E+03 1.28E+05 1747 120259 2.64E+02 2.64E+04 2.41E+02 2.90E+04 479 479 6.29E+01 1.13E+02 58 117 2.99E+01 6.23E+01 2.82E+01 7.45E+01 0 0 0 0 0 1 0.166698 0.470786 0 0 0 0 0 0 0 1 0 1375.74 127816 146.815 12782.4 0 1 1 2.73E-64 2.24E-154 1 1 1 1 397.7 667.812 29.9136 62.2771 0 202.192 365.889 21.5773 36.5913 0 1 3.85E+00 0 0 397.7 667.812 48.8603 48.8603 1764.07 128474 0.768744 0.794055 62.8706 112.916 29.9136 62.2771 0 1419.71 128195 0 0 0 0 1689 120142 -1.852065208 -0.83019903 0.147843069
9 1 9 chr1:3434753-3434798 SL1344|SL3218|SL1344|SL3218 0 0 TGCTTATCAGGCCGGTGAAGGGTATAGAGGTTGCAGAAGACGCCAG 13 0 "HSL3218,2" SL3218 SL3218 Unknown 6931.72 296.915 -1.13E-01 6.25E-02 7.16E-02 0 0 1 1 5.66E+02 4.36E+02 5.68E+01 4.36E+01 1 1 2 0 63 65 5.55E+03 1.17E+05 5557 115079 6.65E+02 2.39E+04 6.43E+02 2.41E+04 481 481 8.92E+01 1.18E+02 77 118 5.34E+01 6.52E+01 4.74E+01 7.26E+01 0 0 0 0 0 1 0.189379 0.41173 0 0 0 0 0 0 0 1 0 5155.71 116668 518.113 11667.7 0 1 1 1.50E-102 6.42E-152 1 1 1 1 397.13 659.753 53.3988 65.1515 0 565.504 436.422 56.8292 43.6456 0 1 -1.80E+00 0 0 397.13 659.753 49.8279 49.8279 5543.47 117318 0.779346 0.803142 89.2183 117.936 53.3988 65.1515 0 5200.52 117044 0 0 0 0 5480 114961 -1.321769974 -0.299903797 0.501298267
10 1 10 chr1:1644444-1644503 SL1344|SL1528|SL1344|SL1528|LT2|STM1597|14028S|STM14_1934|protein_id|NP_460556.2 0 0 GAGGGCAAACTGTTGGCGATGTATTGACCGGCCATGAAAAAGTACGCATGGTCTCTTTAA 15 0 "HSL1528STM1597ATC1,2" ydcW SL1528 gamma-aminobutyraldehyde dehydrogenase 6957.28 296.905 -2.03E-02 6.16E-02 7.41E-01 0 0 1 1 6.03E+02 5.76E+02 6.05E+01 5.76E+01 0 0 0 0 66 63 6.68E+03 1.39E+05 6724 136981 1.11E+03 2.59E+04 1.13E+03 3.00E+04 475 475 8.61E+01 1.11E+02 77 110 4.58E+01 6.13E+01 4.26E+01 6.71E+01 0 0 0 0 0 1 0.110477 0.353759 0 0 0 0 0 0 0 1 0 6281.27 138051 630.215 13805.9 0 1 1 2.73E-108 1.89E-156 1 1 1 1 397.535 650.602 45.7713 61.3215 1 603.068 575.504 60.5073 57.5536 0 1 -3.30E-01 0 0 397.535 650.602 48.8603 48.8603 6669.43 138692 0.789994 0.812217 86.0947 111.474 45.7713 61.3215 0 6327.85 138421 0 0 0 0 6647 136871 -1.313685762 -0.291819584 0.51071712
11 1 11 chr1:1286447-1286493 SL1344|SL1180|SL1344|SL1180|LT2|STM1241|14028S|STM14_1492|protein_id|NP_460211.1 0 0 TCCTCAATGAACTCACAAAACGCGTACATCAACTTTTTCCCGATGCG 17 0 "x_SL1180STM1241ATC,1" msgA SL1180 macrophage survival protein 6982.07 296.725 5.80E-02 6.16E-02 3.47E-01 0 0 1 1 4.04E+03 4.61E+03 4.04E+02 4.62E+02 0 0 1 0 63 63 1.77E+05 2.70E+05 177952 269978 1.85E+04 4.40E+04 1.93E+04 5.87E+04 474 474 6.97E+01 1.18E+02 63 115 3.45E+01 6.60E+01 3.41E+01 7.25E+01 0 0 0 0 1 1 1 0.432623 0 0 0 0 0 0 0 1 0 176918 269399 17691.8 26940.3 0 1 1 2.06E-205 1.88E-174 1 1 1 1 397.626 640.131 34.5241 65.9951 1 4037.74 4614.96 403.776 461.503 0 1 9.41E-01 0 0 397.626 640.131 46.1809 46.1809 177306 270030 0.800213 0.820878 69.7152 117.857 34.5241 65.9951 0 176966 269763 0 0 0 0 177889 269863 -0.18099425 0.840871927 6.932213458
12 1 12 chr2:34543-34602 LT2|PSLT043|LT2|PSLT043|14028S|STM14_5566|protein_id|NP_490533.1 0 0 GTCCGACGATGGAGGAAATTGGCTATCGTACCGATATTTTTACACTGGACGGGATCACCG 19 0 "x_PSLT043ATC5566,1" PSLT043 PSLT043 type II secretion system protein 7007.72 296.976 1.72E-01 6.34E-02 6.80E-03 0 0 1 1 6.96E+02 1.03E+03 6.97E+01 1.03E+02 0 0 1 0 64 63 1.02E+04 1.94E+05 9692 188321 1.78E+03 3.80E+04 1.94E+03 4.96E+04 473 473 6.39E+01 1.12E+02 61 113 2.94E+01 6.39E+01 2.82E+01 7.04E+01 0 0 0 0 0 1 0.13169 0.389898 0 0 0 0 0 0 0 1 0 9764.18 193218 977.763 19322.3 0 1 1 4.03E-121 1.67E-165 1 1 1 1 396.728 629.414 29.3547 63.8908 0 696.317 1033.81 69.7276 103.384 0 1 2.71E+00 0 0 396.728 629.414 50.4627 50.4627 10151.5 193838 0.810941 0.829987 63.9027 112.321 29.3547 63.8908 0 9812.52 193575 0 0 0 0 9631 188208 -1.290966697 -0.269100519 0.538145212
13 1 13 chr1:466121-466165 SL1344|SL0406|SL1344|SL0406|LT2|STM0411|14028S|STM14_0486|protein_id|NP_459406.1 0 0 GTGTGCGGACGTTGTTCCCGTGAGTTTGTGTATTCAAATCTGCGT 21 0 "HSL0406STM0411ATC0,2" yajD SL0406 hypothetical protein 7032.83 296.677 3.56E-02 6.15E-02 5.63E-01 0 0 1 1 3.22E+03 3.49E+03 3.22E+02 3.49E+02 0 0 1 0 64 64 1.22E+05 2.48E+05 122359 243142 1.70E+04 4.85E+04 1.99E+04 5.87E+04 476 476 6.54E+01 1.12E+02 61 112 3.11E+01 6.20E+01 3.04E+01 6.75E+01 0 0 0 0 1 1 1 0.462586 0 0 0 0 0 0 0 1 0 121713 247622 12171.4 24762.6 0 1 1 1.57E-194 3.50E-172 1 1 1 1 395.297 618.342 31.1054 61.9788 1 3218.2 3492.95 321.822 349.301 0 1 5.78E-01 0 0 395.297 618.342 45.4864 45.4864 122099 248230 0.821121 0.838567 65.416 111.71 31.1054 61.9788 0 121761 247972 0 0 0 0 122298 243030 -0.298240532 0.723625645 5.292070795
14 1 14 chr1:489979-490025 LT2|STM0436A|LT2|STM0436A|14028S|STM14_0516 0 0 GTTCGCTGACAGTCTGGCTTGACGAGTTCTGCTATTGCAACATGGAG 23 0 "HSTM0436AATC0516,1" STM0436A STM0436A Unknown 7058.39 297.052 -7.26E-02 6.19E-02 2.41E-01 0 0 1 1 6.36E+02 5.38E+02 6.37E+01 5.38E+01 0 0 0 0 64 65 7.33E+03 1.36E+05 7197 130888 1.04E+03 2.57E+04 1.15E+03 3.12E+04 466 466 7.14E+01 1.19E+02 65 122 3.37E+01 6.40E+01 3.19E+01 7.38E+01 0 0 0 0 0 1 0.0915299 0.384932 0 0 0 0 0 0 0 1 0 6932.73 135367 695.165 13537.5 0 1 1 3.69E-111 6.38E-156 1 1 1 1 394.57 607.147 33.7084 64.0444 0 635.685 537.888 63.7421 53.7919 0 1 -1.17E+00 0 0 394.57 607.147 49.1849 49.1849 7317.93 135965 0.831671 0.847533 71.427 118.528 33.7084 64.0444 0 6981.33 135710 0 0 0 0 7132 130766 -1.263283505 -0.241417327 0.57356504
15 1 15 chr1:4866248-4866307 SL1344|SL4516|SL1344|SL4516|LT2|STM4589|14028S|STM14_5510|protein_id|NP_463445.1 0 0 CTGGAAGGCAAGAATGAGATTGAGCAGTATGTGTATGCGTTGACTCATGAGCTGAAAAGT 25 0 "HSL4516STM4589ATC5,1" creC SL4516 sensory histidine kinase CreC 7083.96 297.224 -6.99E-02 6.19E-02 2.58E-01 0 0 1 1 6.05E+02 5.15E+02 6.07E+01 5.15E+01 0 0 0 0 66 65 6.86E+03 1.36E+05 6561.5 128513 1.25E+03 3.05E+04 1.26E+03 3.28E+04 476 476 6.62E+01 1.16E+02 62.5 117 3.12E+01 6.53E+01 3.04E+01 6.91E+01 0 0 0 0 0 1 0.106693 0.397627 0 0 0 0 0 0 0 1 0 6460.58 135398 648.089 13540.6 0 1 1 4.15E-109 6.29E-156 1 1 1 1 394.614 595.766 31.2122 65.2865 0 604.996 515.01 60.6898 51.504 0 1 -1.13E+00 0 0 394.614 595.766 49.1849 49.1849 6845.83 135984 0.841998 0.856306 66.187 116.223 31.2122 65.2865 0 6510.38 135733 0 0 0 0 6499 128396 -1.295704957 -0.27383878 0.532305827
16 1 16 chr1:298314-298373 SL1344|SL0253|SL1344|SL0253|LT2|STM0258|14028S|STM14_0303|protein_id|NP_459256.1 0 0 GAACCGCTAAGCAATGAAGAGCGGATCCGTATCCTCGTGTGGAATATATTCAAGCAGCAG 27 0 "HSL0253STM0258ATC0,2" yafD SL0253 hypothetical protein 7109.16 297.234 -4.57E-02 6.16E-02 4.58E-01 0 0 1 1 9.28E+02 8.35E+02 9.28E+01 8.35E+01 0 0 0 0 66 65 1.44E+04 1.59E+05 14268.5 149351 2.34E+03 3.14E+04 2.54E+03 3.57E+04 459 459 6.42E+01 1.15E+02 58 115 3.29E+01 6.67E+01 2.97E+01 7.45E+01 0 0 0 0 0 1 0.0852829 0.417968 0 0 0 0 0 0 0 1 0 14051.3 158178 1406.06 15818.4 0 1 1 1.04E-131 4.09E-160 1 1 1 1 393.091 584.326 32.8608 66.7023 0 927.797 835.057 92.8414 83.5092 0 1 -7.43E-01 0 0 393.091 584.326 49.5074 49.5074 14435 158752 0.851951 0.864771 64.2026 115.412 32.8608 66.7023 0 14100.7 158505 0 0 0 0 14210.5 149236 -1.021264241 0.000601936 1.001386971
17 1 17 chr1:1721598-1721657 SL1344|SL1601|SL1344|SL1601|LT2|STM1671|14028S|STM14_2018|protein_id|NP_460629.1 0 0 CTCCCTACTGGCTTGACTGTGATGAGCATTATCAGTTCGAAATTTGTCAGCTTACGTCAA 29 0 "HSL1601STM1671ATC2,1" SL1601 SL1601 putative regulatory protein 7134.6 297.151 2.18E-01 6.56E-02 8.87E-04 0 0 1 1 1.97E+02 3.25E+02 2.08E+01 3.25E+01 0 0 1 0 64 63 1.88E+03 1.26E+05 1848 121140 2.86E+02 2.67E+04 2.93E+02 2.68E+04 473 473 5.36E+01 1.13E+02 50 114 2.85E+01 6.41E+01 2.67E+01 7.41E+01 0 0 0 0 0 1 0.319933 0.514256 0 0 0 0 0 0 0 1 0 1491.09 125405 157.676 12541.4 0 1 1 1.33E-66 7.29E-154 1 1 1 1 391.937 572.933 28.5165 64.1197 0 196.546 324.702 20.7837 32.4723 0 1 3.32E+00 0 0 391.937 572.933 48.5334 48.5334 1873.66 125969 0.861787 0.873165 53.5772 113.125 28.5165 64.1197 0 1540.38 125725 0 0 0 0 1798 121026 -1.828088992 -0.806222815 0.156234587
18 1 18 chr1:338988-339032 SL1344|isrA|SL1344|isrA|14028S|STM14_0346|SEN|SEN0274 0 0 ATGACCGCCTGTTACTCACAAATCCCCAGCCAGCACCTTAAGGGT 31 0 "HisrAATC0346SEN027,2" isrA isrA Unknown 7159.99 297.173 4.35E-03 6.17E-02 9.44E-01 0 0 1 1 4.08E+02 4.12E+02 4.12E+01 4.12E+01 1 0 0 0 65 64 4.09E+03 1.37E+05 4043 130076 5.36E+02 2.81E+04 5.92E+02 2.94E+04 486 486 6.15E+01 1.14E+02 58 118 2.93E+01 6.15E+01 2.82E+01 6.58E+01 0 0 0 0 0 1 0.140465 0.521599 0 0 0 0 0 0 0 1 0 3696.95 136233 373.233 13624.1 0 1 1 6.95E-93 4.30E-156 1 1 1 1 392.093 561.205 29.2582 61.5056 1 408.304 412.413 41.2211 41.2437 0 1 7.05E-02 0 0 392.093 561.205 50.1463 50.1463 4079.67 136784 0.871428 0.881457 61.5062 114.257 29.2582 61.5056 0 3747.41 136545 0 0 0 0 3985 129958 -1.513374693 -0.491508516 0.322471609
19 1 19 chr1:4545856-4545915 SL1344|SL4220|SL1344|SL4220|LT2|STM4284|14028S|STM14_5153|protein_id|NP_463149.1 0 0 TGGGCGGGAATGATGTTTTTAAACGGTGAACCGGGCTTTATTGAAAAGAATAAGCAGAAG 33 0 "HSL4220STM4284ATC5,2" yjcO SL4220 TPR repeat-containing protein 7185.48 297.352 -2.90E-01 6.69E-02 1.51E-05 0 0 1 1 1.08E+03 5.54E+02 1.08E+02 5.54E+01 0 2 0 0 65 60 1.57E+04 1.20E+05 15159 116642 2.54E+03 2.13E+04 2.64E+03 2.17E+04 477 477 6.04E+01 1.12E+02 56 111 3.19E+01 6.11E+01 3.26E+01 6.82E+01 0 0 0 0 0 1 0.151312 0.561513 0 0 0 0 0 0 0 1 0 15324.2 118998 1533.27 11900.7 0 1 1 3.11E-134 1.88E-152 1 1 1 1 392.232 549.074 31.9105 61.116 0 1078.84 553.858 107.944 55.3899 0 1 -4.33E+00 0 0 392.232 549.074 47.8731 47.8731 15707 119538 0.880921 0.889708 60.4025 111.677 31.9105 61.116 0 15375.7 119301 0 0 0 0 15103 116531 -0.887378251 0.134487926 1.362975115
20 1 20 unmapped 0 0 TGATTCAGCGCTATAAACGTTTTTTAGCCGATGTGATCACCCCTGACGGTACGACGCTTA 35 0 ctrl_SL0188 ctrl_SL0188 ctrl_SL0188 Unknown 7210.86 297.405 -6.33E-01 8.52E-02 1.17E-13 0 0 1 1 5.51E+02 1.28E+02 5.55E+01 1.29E+01 4 0 1 0 59 63 4.73E+03 5.14E+04 4746 50143.9 7.16E+02 1.04E+04 7.08E+02 1.12E+04 467 467 5.61E+01 1.15E+02 51 115 2.98E+01 6.36E+01 2.82E+01 7.12E+01 0 0 0 0 0 1 0.808376 0.504389 0 0 0 0 0 0 0 1 0 4335.48 50817.3 436.568 5083.82 0 1 1 1.64E-97 1.53E-129 1 1 1 1 391.911 538.486 29.8341 63.5821 0 551.193 128.47 55.5033 12.8523 0 1 -7.42E+00 0 0 391.911 538.486 48.5334 48.5334 4718.02 51346.2 0.89007 0.897725 56.1028 114.764 29.8341 63.5821 0 4387.66 51113.4 0 0 1 1 4695 50028.9 -1.027585357 -0.00571918 0.986917432

Total number of rows: 15738

Table truncated, full table size 12801 Kbytes.




Supplementary file Size Download File type/resource
GSM944527_US22502595_252688110001_S01_GE2_105_Jan09_1_3.txt.gz 5.3 Mb (ftp)(http) TXT
Processed data included within Sample table
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