|
| Status |
Public on Jan 30, 2012 |
| Title |
WT vs sigI deletion mutant OD2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wild type
|
| Organism |
Mycobacterium tuberculosis CDC1551 |
| Characteristics |
genotype/variation: wild type
|
| Growth protocol |
Grown to phase (OD600 1 and 2) in roller bottles with 200-400 mL Middlebrook 7H9 media+ADC and Tween at 37℃
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pellets were bead beat in the presence of trizol. Aqueus phase isolated using phase lock gel. RNA precipitated with isopropyl alchol
|
| Label |
CY5
|
| Label protocol |
standard amino-allyl labelling protocol from TIGR. cDNA made with Superscript III using aminoallyl dUTP
|
| |
|
| Channel 2 |
| Source name |
sigma factor sigI deletion mutant
|
| Organism |
Mycobacterium tuberculosis CDC1551 |
| Characteristics |
genotype/variation: sigma factor sigI deletion mutant
|
| Growth protocol |
Grown to phase (OD600 1 and 2) in roller bottles with 200-400 mL Middlebrook 7H9 media+ADC and Tween at 37℃
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pellets were bead beat in the presence of trizol. Aqueus phase isolated using phase lock gel. RNA precipitated with isopropyl alchol
|
| Label |
CY3
|
| Label protocol |
standard amino-allyl labelling protocol from TIGR. cDNA made with Superscript III using aminoallyl dUTP
|
| |
|
| |
| Hybridization protocol |
Slides prehybed for >1 hour in prehyb buffer (5X SSC, 0.1% SDS, 1% BSA), washed 2X for 1 minute in water, 15 seconds in isopropanol, dried by centrifugation. Probes added to slides, sealed in incubation chambers and submerged in 42 degree incubator overnight. Arrays washed in increasingly stringent washes: 5 minutes at 42 degrees low stringency wash (0.2%SDS, 1XSSC), 10 minutes lower stringency wash (0.2%SDS, 0.1XSSC), 4 times 1 minute in 0.1XSSC, 10 seconds in 0.01XSSC. Slides dried by centrifugation.
|
| Scan protocol |
Arrays scanned in with a GenePix4000B using GenePix 4 scanning software.
|
| Data processing |
Data analysis conducted with Acuity 4 software
|
| |
|
| Submission date |
Jan 20, 2012 |
| Last update date |
Jan 30, 2012 |
| Contact name |
JongHee Lee |
| E-mail(s) |
jlee254@jhmi.edu
|
| Phone |
4105028230
|
| Organization name |
Johns Hopkins Medical School
|
| Department |
Medicine
|
| Lab |
TB Center
|
| Street address |
1550 Orleans St. CRB2
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
| |
|
| Platform ID |
GPL15148 |
| Series (1) |
| GSE35231 |
Mycobacterium tuberculosis CDC1551 WT/sigI mutant |
|
