NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM495686 Query DataSets for GSM495686
Status Public on Jun 13, 2012
Title H37Rv WT + 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 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/2005-10/64956.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
1 837 402 39 38 798 364 859 411 39 39 820 373 0 0 159 80 6 8 100 100 100 100 1162 1193 2.192 .456 .455 .456 .451 1.293 156 1005 .449 .97 140 1730 27890 38 52 22 36 0 827 78 749 .939 846 767 1.066 .936 -.092 -.096
2 268 125 39 39 229 86 276 128 40 40 237 89 0 0 47 26 6 8 100 100 100 99 315 326 2.663 .376 .376 .362 .381 1.358 156 921 .365 .93 140 1970 27890 38 52 46 60 0 257 80 177 .773 263 183 1.294 .773 -.372 -.372
3 606 238 39 38 567 200 633 246 39 39 594 208 0 0 134 60 6 8 100 100 100 100 767 802 2.835 .353 .35 .339 .351 1.367 156 968 .351 .96 140 2210 27890 38 52 70 84 0 490 78 412 .726 506 428 1.378 .72 -.462 -.473
4 194 98 39 37 155 61 196 97 39 38 157 60 0 0 32 24 8 8 100 99 100 99 216 217 2.541 .394 .382 .37 .39 1.508 156 953 .387 .89 140 2460 27890 38 52 95 109 0 202 76 126 .81 200 123 1.235 .786 -.304 -.347
5 1104 525 40 38 1064 487 1121 529 40 39 1081 491 0 0 200 104 7 8 100 100 100 100 1551 1572 2.185 .458 .454 .456 .458 1.174 156 921 .455 .97 140 2700 27890 38 52 119 133 0 1080 78 1002 .942 1088 1010 1.062 .935 -.087 -.098
6 462 227 40 38 422 189 469 225 41 39 429 187 0 0 79 41 7 8 100 100 100 100 611 616 2.233 .448 .436 .444 .448 1.294 156 905 .438 .96 140 2930 27890 38 52 142 156 0 467 78 389 .921 463 385 1.085 .897 -.118 -.157
7 176 92 40 37 136 55 178 92 41 39 138 55 0 0 27 19 6 8 100 100 100 100 191 193 2.473 .404 .399 .394 .39 1.496 156 937 .389 .87 140 3170 27890 38 52 166 180 0 189 76 113 .832 189 113 1.202 .82 -.265 -.286
8 258 142 40 37 218 105 262 144 41 38 222 107 0 0 43 33 9 8 100 100 100 100 323 329 2.076 .482 .482 .463 .478 1.41 156 952 .483 .93 140 3420 27890 38 52 191 205 0 292 76 216 .991 296 220 1.009 .992 -.013 -.012
9 144 76 39 38 105 38 142 76 40 38 103 38 0 0 23 19 7 8 100 94 99 89 143 141 2.763 .362 .369 .331 .343 1.854 156 921 .381 .8 140 3660 27890 38 52 215 229 0 156 78 78 .745 156 78 1.343 .759 -.425 -.398
10 122 75 38 37 84 38 121 74 38 38 83 37 0 0 19 17 6 8 100 98 100 89 122 120 2.211 .452 .446 .404 .432 1.804 156 916 .44 .78 140 3900 27890 38 52 239 253 0 154 76 78 .931 152 76 1.074 .917 -.103 -.125
11 156 86 38 37 118 49 156 84 38 38 118 47 0 0 24 19 5 8 100 98 100 96 167 165 2.408 .415 .398 .39 .418 1.608 156 939 .399 .85 140 4140 27890 38 52 263 277 0 177 76 101 .854 173 97 1.17 .82 -.227 -.287
12 127 72 38 38 89 34 125 71 38 38 87 33 0 0 19 17 7 8 100 93 100 83 123 120 2.618 .382 .379 .335 .388 1.865 120 824 .381 .78 130 4370 27880 37 50 286 299 0 148 78 70 .786 146 68 1.272 .78 -.347 -.358
13 211 119 38 38 173 81 218 117 38 39 180 79 0 0 44 27 6 8 100 100 100 100 254 259 2.136 .468 .439 .46 .445 1.495 156 968 .458 .91 140 4610 27890 38 52 310 324 0 245 78 167 .963 241 163 1.038 .903 -.054 -.147
14 109 67 39 38 70 29 109 67 39 39 70 29 0 0 18 14 6 8 99 94 98 81 99 99 2.414 .414 .414 .384 .406 1.793 156 953 .388 .75 140 4860 27890 38 52 335 349 0 138 78 60 .852 138 60 1.173 .852 -.23 -.23
15 223 129 39 38 184 91 226 128 39 39 187 90 0 0 37 26 6 8 100 100 100 100 275 277 2.022 .495 .481 .487 .486 1.42 156 1005 .482 .91 150 5100 27890 37 52 358 373 0 265 78 187 1.018 263 185 .983 .99 .025 -.014
16 535 221 39 39 496 182 308 174 39 40 269 135 0 0 1448 306 6 8 100 100 100 100 678 404 2.725 .367 .502 .481 .503 1.59 156 921 .196 .84 140 5330 27890 38 52 382 396 0 455 80 374 .755 358 278 1.325 1.033 -.405 .046
17 312 158 39 39 273 119 321 158 40 39 282 119 0 0 71 36 8 8 100 99 100 99 392 401 2.294 .436 .422 .431 .435 1.481 156 988 .425 .94 140 5570 27890 38 52 406 420 0 325 80 245 .897 325 245 1.115 .868 -.157 -.204
18 245 125 37 38 208 87 247 125 38 38 210 87 0 0 40 25 6 8 100 100 100 100 295 297 2.391 .418 .414 .406 .417 1.37 156 922 .406 .92 140 1740 28130 62 76 23 37 0 257 78 179 .861 257 179 1.162 .852 -.217 -.23
19 507 218 38 38 469 180 519 226 39 39 481 188 0 0 103 52 6 8 100 99 100 99 649 669 2.606 .384 .391 .372 .384 1.46 156 870 .379 .95 140 1980 28120 61 75 47 61 0 449 78 370 .79 465 387 1.266 .804 -.341 -.314
20 113 60 38 37 75 23 114 58 39 38 76 21 0 0 16 14 6 8 100 84 100 62 98 97 3.261 .307 .276 .26 .274 1.984 120 760 .304 .67 130 2220 28130 62 75 71 84 0 123 76 47 .631 119 43 1.585 .569 -.664 -.815

Total number of rows: 4608

Table truncated, full table size 936 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap