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Sample GSM495676 Query DataSets for GSM495676
Status Public on Jun 13, 2012
Title H37Rv WT + pMVdosR vs dosR KO rep 6
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 WT + pMVdosR
Organism Mycobacterium tuberculosis
Characteristics strain: H37Rv
experiment: WT + 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/2005-10/64954.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
1 390 154 36 35 354 119 398 152 36 36 362 117 0 0 75 34 5 7 100 100 100 100 473 479 2.975 .336 .323 .334 .325 1.381 156 988 .33 .95 140 1900 28010 50 64 39 53 0 372 85 288 .813 368 283 1.23 .782 -.299 -.355
2 142 64 36 35 106 29 144 62 36 36 108 27 0 0 26 16 6 7 100 93 100 81 135 135 3.655 .274 .25 .239 .263 1.816 156 937 .26 .77 140 2130 28010 50 64 62 76 0 155 85 70 .662 150 65 1.511 .605 -.596 -.726
3 290 104 35 35 255 69 296 102 37 36 261 67 0 0 48 26 12 8 100 99 100 99 324 328 3.696 .271 .257 .253 .27 1.523 120 861 .259 .89 130 2370 28000 49 62 86 99 0 252 85 167 .654 247 162 1.528 .621 -.612 -.688
4 113 54 34 35 79 19 116 52 36 36 82 17 0 0 22 12 12 8 98 80 97 50 98 99 4.158 .241 .207 .216 .222 2.209 156 968 .208 .62 140 2620 28010 50 64 111 125 0 131 85 46 .582 126 41 1.719 .501 -.782 -.996
5 603 196 34 35 569 161 604 188 36 36 570 153 0 0 115 56 19 9 100 100 100 100 730 723 3.534 .283 .268 .272 .276 1.285 120 836 .274 .95 130 2850 28000 49 62 134 147 0 474 85 389 .684 455 370 1.461 .649 -.547 -.623
6 261 105 34 35 227 70 262 103 36 36 228 68 0 0 42 23 19 9 100 100 100 99 297 296 3.243 .308 .298 .297 .298 1.397 120 850 .293 .9 130 3090 28000 49 62 158 171 0 254 85 169 .746 249 164 1.341 .721 -.423 -.471
7 120 60 34 36 86 24 122 57 35 36 88 21 0 0 20 15 7 7 100 91 100 75 110 109 3.583 .279 .239 .249 .265 1.838 156 950 .273 .71 140 3340 28010 50 64 183 197 0 145 87 58 .675 138 51 1.482 .577 -.567 -.793
8 169 79 35 35 134 44 172 79 35 36 137 44 0 0 35 19 5 7 100 98 98 96 178 181 3.045 .328 .321 .322 .308 1.746 156 921 .31 .84 140 3580 28010 50 64 207 221 0 191 85 106 .794 191 106 1.259 .777 -.333 -.365
9 125 59 35 35 90 24 124 60 35 36 89 25 0 0 20 12 5 7 100 91 100 76 114 114 3.75 .267 .281 .239 .266 1.988 156 921 .258 .73 140 3820 28010 50 64 231 245 0 143 85 58 .645 145 60 1.551 .679 -.633 -.558
10 88 51 35 35 53 16 87 51 35 36 52 16 0 0 14 11 5 7 100 73 100 54 69 68 3.313 .302 .308 .269 .346 2.363 156 922 .283 .57 140 4060 28010 50 64 255 269 0 123 85 39 .73 123 39 1.37 .744 -.454 -.426
11 118 57 35 36 83 21 121 55 35 36 86 19 0 0 21 12 5 7 99 91 98 67 104 105 3.952 .253 .221 .235 .25 2.136 156 905 .241 .68 140 4290 28010 50 64 278 292 0 138 87 51 .612 133 46 1.634 .534 -.709 -.904
12 107 58 35 36 72 22 108 56 35 36 73 20 0 0 19 14 5 7 99 86 99 67 94 93 3.273 .306 .274 .268 .276 2.195 156 938 .295 .69 140 4530 28000 49 63 302 316 0 140 87 53 .739 135 48 1.353 .663 -.437 -.594
13 175 74 35 36 140 38 182 74 36 36 147 38 0 0 34 15 5 7 100 100 100 96 178 185 3.684 .271 .259 .263 .272 1.686 156 937 .265 .83 140 4770 28010 50 64 326 340 0 179 87 92 .656 179 92 1.523 .625 -.607 -.678
14 102 53 36 36 66 17 104 51 36 37 68 15 0 0 14 16 5 7 100 76 100 51 83 83 3.882 .258 .221 .202 .226 2.182 156 939 .272 .59 140 5020 28000 49 63 351 365 0 128 87 41 .623 123 36 1.605 .533 -.683 -.907
15 211 100 36 37 175 63 207 99 38 38 171 62 0 0 36 24 14 10 100 99 100 97 238 233 2.778 .36 .363 .343 .355 1.502 120 820 .367 .89 130 5240 28000 49 62 373 386 0 242 89 152 .871 239 150 1.149 .877 -.2 -.19
16 345 177 36 37 309 140 337 170 39 38 301 133 0 0 57 40 15 10 100 100 100 100 449 434 2.207 .453 .442 .442 .445 1.271 120 850 .44 .94 130 5480 28000 49 62 397 410 0 428 89 339 1.096 411 322 .913 1.069 .132 .096
17 278 137 36 36 242 101 281 136 38 38 245 100 0 0 37 23 13 9 100 100 100 100 343 345 2.396 .417 .408 .413 .406 1.275 120 876 .413 .94 130 5720 28000 49 62 421 434 0 331 87 244 1.009 329 242 .991 .987 .013 -.019
18 141 64 36 35 105 29 141 63 37 36 105 28 0 0 21 14 6 7 100 94 100 83 134 133 3.621 .276 .267 .245 .27 1.865 156 937 .275 .79 140 1900 28250 74 88 39 53 0 155 85 70 .668 152 68 1.497 .645 -.582 -.633
19 247 98 36 35 211 63 248 99 36 36 212 64 0 0 47 19 5 7 100 100 100 99 274 276 3.349 .299 .302 .297 .309 1.439 156 886 .288 .91 140 2140 28250 74 88 63 77 0 237 85 152 .722 239 155 1.385 .73 -.47 -.454
20 83 45 35 35 48 10 83 44 35 36 48 9 0 0 12 10 6 7 100 56 100 29 58 57 4.8 .208 .188 .196 .219 2.453 120 811 .192 .45 130 2380 28250 74 87 87 100 0 109 85 24 .504 106 22 1.985 .453 -.989 -1.141

Total number of rows: 4608

Table truncated, full table size 929 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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