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Sample GSM495684 Query DataSets for GSM495684
Status Public on Jun 13, 2012
Title H37Rv dosR KO + 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 MRO (dosRKO) + pMVdosR
Organism Mycobacterium tuberculosis
Characteristics strain: H37Rv
experiment: MRO (dosRKO) + 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/2005-10/64912.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
1 141 83 51 42 90 41 143 84 51 43 92 42 0 0 23 20 7 9 100 93 99 85 131 134 2.195 .456 .457 .413 .436 1.749 208 1212 .466 .82 160 2180 28150 14 30 49 65 0 151 76 75 .829 153 76 1.207 .83 -.271 -.268
2 115 59 51 42 64 17 116 59 51 43 65 17 0 0 13 12 7 9 100 71 100 43 81 82 3.765 .266 .262 .236 .271 2.108 208 1146 .253 .55 170 2420 28160 14 31 72 89 0 107 76 31 .483 107 31 2.07 .476 -1.05 -1.072
3 134 98 51 42 83 56 135 99 51 43 84 57 0 0 24 22 7 9 100 96 100 93 139 141 1.482 .675 .679 .644 .689 1.679 208 1152 .688 .86 170 2660 28150 13 30 96 113 0 178 76 102 1.227 180 104 .815 1.234 .295 .304
4 101 58 49 41 52 17 100 55 50 42 51 14 0 0 13 13 7 9 100 66 100 40 69 65 3.059 .327 .275 .28 .32 2.38 208 1109 .338 .55 160 2900 28160 15 31 121 137 0 105 75 31 .595 100 25 1.682 .499 -.75 -1.002
5 170 129 48 40 122 89 169 125 49 41 121 85 0 0 21 26 10 9 100 100 100 100 211 206 1.371 .73 .702 .707 .713 1.333 208 1083 .734 .9 160 3140 28160 15 31 145 161 0 235 73 162 1.327 227 155 .754 1.278 .408 .354
6 145 100 48 40 97 60 143 99 48 41 95 59 0 0 16 20 9 9 100 99 100 99 157 154 1.617 .619 .621 .596 .615 1.452 208 1146 .634 .87 170 3380 28160 14 31 168 185 0 182 73 109 1.125 180 107 .889 1.13 .17 .176
7 110 66 48 41 62 25 110 65 48 42 62 24 0 0 13 13 6 9 100 90 100 66 87 86 2.48 .403 .387 .35 .396 2.011 208 1080 .394 .68 160 3620 28160 15 31 193 209 0 120 75 45 .733 118 44 1.364 .704 -.447 -.506
8 129 79 48 42 81 37 128 78 48 42 80 36 0 0 18 17 6 9 100 96 100 88 118 116 2.189 .457 .45 .428 .481 1.655 208 1069 .473 .8 160 3860 28160 15 31 217 233 0 144 76 67 .831 142 65 1.204 .818 -.267 -.289
9 116 71 49 41 67 30 116 69 49 42 67 28 0 0 13 17 7 9 100 91 100 71 97 95 2.233 .448 .418 .388 .414 1.981 156 958 .437 .7 150 4090 28150 14 29 240 255 0 129 75 55 .814 126 51 1.228 .76 -.296 -.396
10 101 60 48 42 53 18 101 58 49 42 53 16 0 0 12 14 7 9 100 69 100 42 71 69 2.944 .34 .302 .291 .32 2.296 156 1033 .355 .56 150 4330 28150 14 29 264 279 0 109 76 33 .618 105 29 1.619 .549 -.695 -.865
11 111 68 47 41 64 27 113 67 48 42 66 26 0 0 18 15 7 9 99 84 99 71 91 92 2.37 .422 .394 .365 .407 2.069 208 1076 .439 .74 160 4580 28160 15 31 289 305 0 124 75 49 .767 122 47 1.303 .717 -.382 -.481
12 102 64 46 42 56 22 102 63 47 43 56 21 0 0 14 14 7 9 100 84 100 57 78 77 2.545 .393 .375 .359 .385 1.979 156 937 .392 .64 150 4800 28150 14 29 311 326 0 116 76 40 .715 115 38 1.399 .682 -.485 -.552
13 130 94 46 42 84 52 132 93 47 43 86 51 0 0 20 21 14 13 99 97 98 89 136 137 1.615 .619 .593 .583 .622 1.617 208 1089 .66 .86 160 5050 28160 15 31 336 352 0 171 76 95 1.126 169 93 .888 1.079 .171 .109
14 98 67 45 41 53 26 98 65 46 42 53 24 0 0 13 15 6 9 100 89 100 69 79 77 2.038 .491 .453 .431 .457 2.135 156 975 .5 .67 150 5280 28150 14 29 359 374 0 122 75 47 .892 118 44 1.121 .824 -.164 -.28
15 138 111 45 41 93 70 139 111 46 42 94 70 0 0 19 22 6 8 100 100 100 100 163 164 1.329 .753 .745 .736 .75 1.472 208 1100 .778 .89 160 5520 28160 15 31 383 399 0 202 75 127 1.369 202 127 .73 1.354 .453 .438
16 178 169 45 42 133 127 178 169 46 43 133 127 0 0 22 33 6 9 100 100 100 99 260 260 1.047 .955 .955 .931 .968 1.414 208 1071 .995 .94 160 5760 28160 15 31 407 423 0 307 76 231 1.737 307 231 .576 1.737 .796 .796
17 131 107 45 41 86 66 132 108 45 42 87 67 0 0 17 23 6 9 100 98 100 96 152 154 1.303 .767 .77 .72 .751 1.596 208 1217 .802 .89 160 6000 28160 15 31 431 447 0 195 75 120 1.396 196 122 .716 1.401 .481 .486
18 112 64 52 43 60 21 113 63 53 43 61 20 0 0 16 14 8 9 99 78 98 54 81 81 2.857 .35 .328 .326 .347 2.132 208 1073 .359 .58 160 2170 28400 39 55 48 64 0 116 78 38 .637 115 36 1.571 .596 -.652 -.746
19 121 70 53 43 68 27 121 68 53 44 68 25 0 0 13 15 8 9 100 90 100 69 95 93 2.519 .397 .368 .359 .379 1.868 208 945 .41 .7 170 2410 28410 39 56 71 88 0 127 78 49 .722 124 45 1.385 .669 -.47 -.581
20 93 63 52 43 41 20 93 60 53 43 41 17 0 0 19 29 9 9 94 74 86 46 61 58 2.05 .488 .415 .438 .442 2.663 208 1023 .729 .42 160 2650 28410 40 56 96 112 0 115 78 36 .887 109 31 1.127 .754 -.173 -.407

Total number of rows: 4608

Table truncated, full table size 900 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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