|
| Status |
Public on Jun 11, 2011 |
| Title |
RR2_CRHydplushydrogen03_Cy3_ch1_CRHyd03_Cy5_ch2_7DE13915856 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Transcription profile from 14028s grown anaerobically to log phase in CRHyd in presence of 20% hydrogen, replicate 3, dye swapped
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S |
| Characteristics |
growth: anaerobically to log phase after presence of 20% hydrogen for 15 min
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After immediate treatment with 0.15 volumes of ethanol: phenol (95 %: 5 % vol/vol) cells were pelleted, resuspended in lysis buffer (10 mM Tris, 1 mM EDTA, 0.5 mg/ml lysozyme) and treated with 1 ml of 10 % SDS for 2 min at 64°C. The suspensions were treated with sodium acetate, pH 5.2, then nucleic acids were phenol/chloroform extracted and subsequently precipitated with 0.1 vol 3M sodium acetate and 1.0 vol of cold isopropanol. Finally, DNAse treatment at 37°C for 30min degraded present DNA, leaving clean ribonucleic acid after a second round of phenol/chloroform extraction and precipitation.
|
| Label |
Cy3
|
| Label protocol |
Standard labeling using Cy3-dUTP with reverse transcriptase and random hexamers
|
| |
|
| Channel 2 |
| Source name |
Transcription profile from 14028s grown anaerobically to log phase in CRHyd without hydrogen, replicate 3, dye swapped
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S |
| Characteristics |
growth: anaerobically to log phase without hydrogen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After immediate treatment with 0.15 volumes of ethanol: phenol (95 %: 5 % vol/vol) cells were pelleted, resuspended in lysis buffer (10 mM Tris, 1 mM EDTA, 0.5 mg/ml lysozyme) and treated with 1 ml of 10 % SDS for 2 min at 64°C. The suspensions were treated with sodium acetate, pH 5.2, then nucleic acids were phenol/chloroform extracted and subsequently precipitated with 0.1 vol 3M sodium acetate and 1.0 vol of cold isopropanol. Finally, DNAse treatment at 37°C for 30min degraded present DNA, leaving clean ribonucleic acid after a second round of phenol/chloroform extraction and precipitation.
|
| Label |
Cy5
|
| Label protocol |
Standard labeling using Cy5-dUTP with reverse transcriptase and random hexamers
|
| |
|
| |
| 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 STv5_SP040504_adapforsmallpins_040817
|
| Description |
biological replicate, Date of Scan Thu Jun 24 15:55:43 2010
|
| 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 |
Jun 03, 2011 |
| Last update date |
Jun 11, 2011 |
| Contact name |
Michael McClelland |
| E-mail(s) |
[email protected]
|
| Phone |
858-336-9554
|
| Organization name |
University of California, Irvine
|
| Department |
Microbiology & Molecular Genetics
|
| Street address |
132 Med Surge I
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL11279 |
| Series (1) |
| GSE29739 |
Transcriptional profiles of anaerobically grown Typhimurium 14028 with and without hydrogen in CRHyd |
|
| 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 |
