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Sample GSM495672 Query DataSets for GSM495672
Status Public on Jun 13, 2012
Title H37Rv dosR KO + pMVdosR vs dosR KO rep 7
Sample type RNA
 
Channel 1
Source name H37Rv MRO dosR KO
Organism Mycobacterium tuberculosis
Characteristics strain: H37Rv
genotype: MRO dosR KO
Extracted molecule total RNA
Extraction protocol TB-Synthesis and Labeling of cDNA SKlab 01; 1. Bring 0.5-5 ?g RNA (Typically 3 ?g) to 11 ?l and add 2 ?l (~2 mg/ml) random hexamers. 2. Heat 10 min at 65C (or 2 min at 98C), snap cool on ice. 10 rxns 20 rxns 3. Add 11?l 5.0 ?l 5X First-Strand buffer (51) (102) 2.5 ?l 100 mM DTT (25.5) (51) 2.0 ?l dNTP (5 mM A,G,C and 0.2 mM T) (20.5) (41) 1.5 ?l Cy3 or Cy5 (Typically use Cy5 for sample that should change) (15.3) (30.6) Then add 1.2-1.8 ?l Stratascript or 0.8-1.2 ?l Superscript II RTase. 4. Incubate 10m at 25C followed by 90m at 42C in PCR machine. Can freeze or leave at 4C o/n.; Protocol Type = Labeling; Performer: Mario Alberto,,Flores-Valdez
Label Cy3
Label protocol not provided
 
Channel 2
Source name H37Rv MRO (dosRKO) + pMVdosR
Organism Mycobacterium tuberculosis
Characteristics strain: H37Rv
experiment: MRO dosR KO + pMVdosR
Growth protocol Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter OD at Harvest = 0.2; Parameter Growth Temperature = 37oC; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC); Performer: Mario Alberto,,Flores-Valdez
Extracted molecule total RNA
Extraction protocol TB-RNA Isolation and Purification SKlab 01; 1. Centrifuge 20-30 ml of early- to mid-log culture (O.D. 0.1-0.2) 4 min at 3700 rpm, at RT-37C. Pipette off supernatant and immediately freeze on dry ice and store at ?80C. 2. Add 1 ml Trizol (Gibco-BRL) to each of 4-8 pellets, suspend first pellet by vortexing,while other pellets are still frozen. Add suspension to 0.4 ml glass beads in a 2 ml screw cap tube. 3. Shake 30s at maximum speed in bead beater. Suspend next pellet and add to glass beads. Apply next sample to bead beater. Repeat bead beating two more times with each sample.Continue to periodically invert samples for at least 5 min in Trizol. 4. Centrifuge samples 45s at max speed, remove Trizol solution to a 2 ml screw cap tube containing half of the Heavy Phase Lock Gel I, supplied by 5 Prime 3 Prime, Inc. in 1.5 ml tubes and transferred with sterile stick to 2 ml tubes, and 300 ?l Chloroform:isoamyl alcohol (24:1). Invert rapidly for 15s, and continue inverting periodically for 2 min.a 5. Centrifuge 5-10m, remove aqueous layer (540 ?l) and add to a 1.5 ml tube containing 270 ?l isopropanol then add 270 ?l high salt solution (0.8M Na Citrate, 1.2M NaCl). Invert several times and spray with Staphene and remove from the P3. Typically ppted at 4C O/N. 6. Centrifuge 10m at 4C and remove isopropanol. Add 1 ml 75% EtOHb, invert several times and centrifuge 5m. 7. Remove EtOH by aspiration. Then, dry under vacuum for 2 min [Do not over dry]. 8. Suspend RNA in 90 ml RNase free water (don?t suspend in DNaseI buffer), may need to heat 10m at 55-60C to dissolve RNA. (Optional: obtain RNA concentration) 9. Add 10 ?l 10X DNaseI buffer to RNA (use no more than 80 ?g RNA) and add 4 ?l DNaseI (Ambion). Incubate 30m at 37C. Qiagen RNeasy purification. 1. Add 350 ?l RLT buffer (add 10 ?l BME to 1 ml RLT before using) and vortex. Add 260 ?l 95% EtOH (or 250 ?l 100% EtOH) to each sample and vortex. 2. Add to RNeasy spin column, centrifuge 15s, transfer column to a new 2 ml collection tube. Add 500 ?l RPE, centrifuge 15s, discard flow-through, add 500 ?l additional RPE and centrifuge 2m. If column still wet on sides, remove wash solution from tube and spin 1m to dry. 3. Transfer to a 1.5 ml collection tube, elute with 40 ?l RNase free water, centrifuge 1m. 4. Determine RNA concentration with A260/A280 readings. Dilute 1 ?l in 199 ?l TE. [200(dilution factor)x 40 ?g/A260x A260 = ?g/ml]. 5. Run 1 ?l RNA on 2% Agarose TAE gel. Run gel 45m at 100 volts. aIf Phase Lock Gel is not used, decrease Chloroform:isoamyl alcohol to 200?l. The yield will be less. Be careful not to remove any of the interface layer. bUsing 100% EtOH should be avoided in all steps of preparation of RNA intended for array analysis. Instead use 95% EtOH in preparation of solutions. Benzene contamination may fluoresce. cInstead of using the RNeasy purification, the DNaseI can be inactivated at 65-70C for 15m and then EtOH precipitated. The RNeasy purification may not be necessary in all applications. We find the purification gives more consistent results and is less time consuming, compared to precipitation. In addition, other purifications can be used. Note: The RNeasy column will remove much of the small tRNA and degraded RNA.; Protocol Type = Extract preparation; Performer: Mario Alberto,,Flores-Valdez
Label Cy5
Label protocol Amount of extract labeled = 2-3 ug of total RNA
 
 
Hybridization protocol not provided
Scan protocol GenePix
Description Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64957.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 11, 2010
Last update date Jun 13, 2012
Contact name Mario A Flores Valdez
E-mail(s) floresvz@yahoo.com
Organization name Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco, A.C.
Department Col. Colinas de la Normal
Street address Av. Normalistas No. 800
City Guadalajara
State/province Jalisco
ZIP/Postal code CP44270
Country Mexico
 
Platform ID GPL9901
Series (1)
GSE19838 Gene expression profiles of M. tuberculosis constitutively expressing the transcriptional regulator DosR (Rv3133c).

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 331 233 40 38 291 195 331 240 41 40 291 202 0 0 81 61 9 10 100 100 100 99 486 493 1.492 .67 .694 .657 .681 1.383 156 1022 .671 .97 140 1420 27760 32 46 27 41 0 478 78 400 1.375 493 415 .727 1.425 .46 .51
2 131 81 40 38 91 43 131 80 41 39 91 42 0 0 23 22 9 10 100 94 99 88 134 133 2.116 .473 .462 .42 .464 1.921 156 937 .487 .81 140 1670 27760 32 46 52 66 0 166 78 88 .97 164 86 1.031 .947 -.044 -.078
3 258 151 42 38 216 113 267 156 44 40 225 118 0 0 55 36 11 11 100 99 100 99 329 343 1.912 .523 .524 .509 .537 1.458 156 952 .524 .94 140 1910 27760 32 46 76 90 0 310 78 232 1.074 320 242 .931 1.076 .102 .106
4 134 74 42 37 92 37 133 74 43 39 91 37 0 0 21 15 8 10 100 96 100 85 129 128 2.486 .402 .407 .384 .4 1.694 156 938 .395 .81 140 2150 27760 32 46 100 114 0 152 76 76 .825 152 76 1.212 .834 -.277 -.261
5 446 303 39 36 407 267 450 297 40 37 411 261 0 0 114 76 7 9 100 100 100 100 674 672 1.524 .656 .635 .66 .68 1.334 156 954 .642 .96 140 2390 27760 32 46 124 138 0 622 74 548 1.346 609 536 .743 1.303 .429 .382
6 216 126 39 36 177 90 218 126 40 36 179 90 0 0 37 33 6 8 100 98 100 96 267 269 1.967 .508 .503 .473 .511 1.552 156 953 .522 .91 140 2640 27750 31 45 149 163 0 259 74 185 1.043 259 185 .958 1.032 .061 .045
7 105 60 38 36 67 24 106 58 39 36 68 22 0 0 16 14 6 7 100 92 100 76 91 90 2.792 .358 .324 .323 .333 1.908 156 938 .367 .71 140 2880 27760 32 46 173 187 0 123 74 49 .735 119 45 1.36 .664 -.444 -.591
8 152 87 37 36 115 51 153 84 37 37 116 48 0 0 21 21 6 7 100 99 100 96 166 164 2.255 .443 .414 .402 .416 1.761 120 838 .438 .85 130 3120 27750 31 44 197 210 0 179 74 105 .91 172 99 1.099 .849 -.136 -.236
9 105 58 39 38 66 20 106 57 40 40 67 19 0 0 14 12 8 10 100 78 100 42 86 86 3.3 .303 .284 .267 .288 2.102 120 850 .319 .65 130 3360 27750 31 44 221 234 0 119 78 41 .622 117 39 1.608 .582 -.685 -.781
10 92 61 40 38 52 23 93 61 41 40 53 23 0 0 12 13 8 10 100 78 100 53 75 76 2.261 .442 .434 .37 .42 2.179 156 985 .465 .61 140 3610 27750 31 45 246 260 0 125 78 47 .908 125 47 1.102 .891 -.14 -.167
11 114 61 38 37 76 24 115 59 38 37 77 22 0 0 15 13 6 7 100 96 100 71 100 99 3.167 .316 .286 .289 .299 1.729 120 812 .32 .71 130 3840 27750 31 44 269 282 0 125 76 49 .648 121 45 1.543 .586 -.626 -.77
12 100 56 37 37 63 19 102 54 38 37 65 17 0 0 15 13 9 7 100 84 99 57 82 82 3.316 .302 .262 .285 .3 1.973 156 952 .314 .66 140 4080 27750 31 45 293 307 0 115 76 39 .619 111 35 1.616 .537 -.692 -.898
13 133 79 38 36 95 43 138 79 47 37 100 43 0 0 26 18 259 8 0 97 0 94 138 143 2.209 .453 .43 .423 .448 1.662 156 953 -1 -1 140 4330 27750 31 45 318 332 0 162 74 88 .929 162 88 1.077 .882 -.106 -.18
14 91 51 37 36 54 15 91 50 47 37 54 14 0 0 12 10 279 8 0 75 0 42 69 68 3.6 .278 .259 .24 .3 2.344 120 826 .263 .55 130 4570 27750 31 44 342 355 0 105 74 31 .57 103 29 1.754 .532 -.811 -.91
15 149 100 36 36 113 64 147 101 37 37 111 65 0 0 22 18 5 8 100 100 100 100 177 176 1.766 .566 .586 .551 .565 1.372 120 826 .567 .89 130 4800 27750 31 44 365 378 0 205 74 131 1.162 207 133 .86 1.202 .217 .265
16 211 140 36 36 175 104 210 140 37 37 174 104 0 0 43 32 6 8 100 100 100 100 279 278 1.683 .594 .598 .582 .579 1.509 156 956 .59 .91 140 5040 27750 31 45 389 403 0 287 74 213 1.22 287 213 .82 1.227 .286 .295
17 208 135 36 36 172 99 212 135 37 36 176 99 0 0 28 27 7 7 100 100 100 100 271 275 1.737 .576 .563 .56 .561 1.361 120 862 .573 .92 130 5270 27740 30 43 412 425 0 277 74 203 1.181 277 203 .847 1.154 .24 .207
18 136 79 42 39 94 40 137 77 43 41 95 38 0 0 20 17 11 11 100 97 100 87 134 133 2.35 .426 .4 .393 .403 1.659 120 824 .416 .78 130 1430 27990 55 68 28 41 0 162 80 82 .873 158 78 1.145 .821 -.196 -.285
19 224 128 41 37 183 91 226 127 42 39 185 90 0 0 43 31 10 10 100 97 100 95 274 275 2.011 .497 .486 .465 .502 1.578 156 899 .495 .92 140 1680 27990 55 69 53 67 0 263 76 187 1.02 261 185 .98 .998 .029 -.002
20 97 54 41 37 56 17 96 52 42 38 55 15 0 0 17 15 10 9 100 63 100 37 73 70 3.294 .304 .273 .266 .327 2.317 120 786 .351 .59 130 1920 28000 56 69 77 90 0 111 76 35 .623 107 31 1.605 .56 -.683 -.837

Total number of rows: 4608

Table truncated, full table size 908 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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