|
Status |
Public on Sep 13, 2007 |
Title |
RDE2_X3339_FlightvsGround_F25_LB_7DS518_2 |
Sample type |
mixed |
|
|
Channel 1 |
Source Name |
Salmonella enterica subsp. enterica serovar Typhimurium X3339 total RNA after flight F25
|
Organism(s) |
Salmonella enterica |
Characteristics |
Salmonella typhimurium X3339 total RNA harvested after exposure to conditions
|
Extracted molecule |
total RNA |
Extraction protocol |
total RNA preparation
|
Label |
Cy3
|
Label protocol |
incorporation of Cy3-dCTP with Reverse Transcriptase
|
|
|
Channel 2 |
Source Name |
Salmonella enterica subsp. enterica serovar Typhimurium X3339 gDNA from overnight cultures in LB
|
Organism(s) |
Salmonella enterica |
Characteristics |
Salmonella typhimurium X3339 grown O/N in LB at 37C with aeration
|
Extracted molecule |
genomic DNA |
Extraction protocol |
total gDNA preparation
|
Label |
Cy5
|
Label protocol |
incorporation of Cy5-dCTP with Klenow enzyme
|
|
|
|
Hybridization protocol |
overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA
|
Scan protocol |
Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv7S_01_051201
|
Description |
biological replicate, Date of Scan Wed Dec 13 09:12:30 2006
|
Data processing |
normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.
|
|
|
Submission date |
Jul 24, 2007 |
Contact name |
Michael McClelland |
E-mail(s) |
mcclelland.michael@gmail.com
|
Phone |
858-450-5990
|
Fax |
858-550-3998
|
Organization name |
Sidney Kimmel Cancer Center
|
Department |
|
Street address |
10835 Road to the Cure
|
City |
San Diego |
State/province |
CA |
ZIP/Postal code |
92121 |
Country |
USA |
|
|
Platform ID |
GPL4805 |
Series (1) |
GSE8573 |
Salmonella Typhimurium transcription profiles in space flight |
|
Data table header descriptions |
ID_REF |
Number |
X_LOCATION |
X-coordinate of spot |
Y_LOCATION |
Y-coordinate of spot |
CH1_MEAN |
Channel 1 mean |
CH1_BKD_MEAN |
Channel 1 mean background |
CH1_SD |
Channel 1 standard deviation |
CH1_BKD_SD |
Channel 1 background standard deviation |
CH1_DIAMETER |
Channel 1 diameter |
CH1_AREA |
Channel 1 area |
CH1_FOOTPRINT |
Channel 1 footprint |
CH1_CIRCULARITY |
Channel 1 circularity |
CH1_SPOT_UNIFORMITY |
Channel 1 spot uniformity |
CH1_BKD_UNIFORMITY |
Channel 1 background uniformity |
CH1_SIGNAL_NOISE_RATIO |
Channel 1 signal to noise ratio |
CH1_CONFIDENCE |
Channel 1 confidence |
CH2_MEAN |
Channel 2 mean |
CH2_BKD_MEAN |
Channel 2 mean background |
CH2_SD |
Channel 2 standard deviation |
CH2_BKD_SD |
Channel 2 background standard deviation |
CH2_DIAMETER |
Channel 2 diameter |
CH2_AREA |
Channel 2 area |
CH2_FOOTPRINT |
Channel 2 footprint |
CH2_CIRCULARITY |
Channel 2 circularity |
CH2_SPOT_UNIFORMITY |
Channel 2 spot uniformity |
CH2_BKD_UNIFORMITY |
Channel 2 background uniformity |
CH2_SIGNAL_NOISE_RATIO |
Channel 2 signal to noise ratio |
CH2_CONFIDENCE |
Channel 2 confidence |
CH1_DIAMETER_FILTER |
Channel 1 diameter filter |
CH1_AREA_FILTER |
Channel 1 area filter |
CH1_CIRCULARITY_FILTER |
Channel 1 circularity filter |
CH1_SPOT_UNIFORMITY_FILTER |
Channel 1 spot uniformity filter |
CH1_BKD_UNIFORMITY_FILTER |
Channel 1 background uniformity filter |
CH1_SIGNAL_NOISE_RATIO_FILTER |
Channel 1 signal to noise ratio filter |
CH2_DIAMETER_FILTER |
Channel 2 diameter filter |
CH2_AREA_FILTER |
Channel 2 area filter |
CH2_CIRCULARITY_FILTER |
Channel 2 circularity filter |
CH2_SPOT_UNIFORMITY_FILTER |
Channel 2 spot uniformity filter |
CH2_BKD_UNIFORMITY_FILTER |
Channel 2 background uniformity filter |
CH2_SIGNAL_NOISE_RATIO_FILTER |
Channel 2 signal to noise ratio filter |
IGNORE_FILTER |
Ignore filter |
CH1_BKD_CORR |
Channel 1 background correlation |
CH2_BKD_CORR |
Channel 2 background correlation |
CH1%_OF_TOTAL |
Channel 1 % of total |
CH2%_OF_TOTAL |
Channel 2 % of total |
PRE-VALUE |
ch1 % of total / ch2 % of total |
VALUE |
log of ch1 % of total / ch2 % of total |