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Sample GSM1341099 Query DataSets for GSM1341099
Status Public on Apr 07, 2014
Title hip mutant HT1170, biological rep2
Sample type RNA
 
Source name hip mutant HT1170
Organism Mycobacterium tuberculosis
Characteristics genotype/variation: hip mutant
growth stage: stationary phase cells
Treatment protocol Stationary phase cultures were treated with two volumes RNA protect (Qiagen) prior to total RNA extraction.
Growth protocol M. tuberculosis wild type strain (mc[2]6020) and hip mutants were grown in Middlebrook 7H9 broth (with supplements) at 37°C in a shaking incubator (200 rpm) to stationary phase (two weeks).
Extracted molecule total RNA
Extraction protocol Cells were resuspended in RNA Pro (MP Biochemicals) and lysed by bead beating. 2. Total RNA was extracted with chloroform and preciptated with isopropanol.
Label biotin
Label protocol At room temp, prepared an IVT Master Mix in a nuclease-free tube. Master mix consisted of: IVT Biotin Label, IVT Labeling Buffer and IVT Enzyme Mix. 2. Mixed well by pipetting up and down several times. 3. Transfered 30 µL of IVT Master Mix to each (30 µL) double-stranded cDNA sample. Mixed thoroughly. 4. Incubated the IVT reaction for 4 or 16 hours at 40 °C in a thermal cycler
 
Hybridization protocol Mixed fragmented and labeled RNA with Control Oligonucleotide B2, 20X Hybridization Controls, 2X Hybridization Mix DMSO and Nuclease-free Water. 2. Hyb on thermocycler for 5 mins at 99 degrees. 3. Incubateed the probe array filled with Pre-Hybridization Mix at 45 °C for 10 minutes with rotation. 4. Transfered the hybridization cocktail that has been heated at 99 °C, in Step 3, to a 45 °C heat block for 5 minutes. 5. Spun the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture. 6. Removed the array from the hybridization oven. Vented the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refiledl the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube. 7. Placed probe array into the hybridization oven, set to 45°C. 8. Rotated array at 60 rpm. 9. Hybridize for 16 hours
Scan protocol Equipment and Consumables Required for Washing and Staining Arrays: GeneChip® Fluidics Station 450, GeneChip Scanner 3000 series, Affymetrix GeneChip® Command Console AGCC v1.1.
Description Gene expression data from hip mutant strain stationary phase cells
Data processing Statistical analysis of the data was performed using R/Bioconductor with the oneChannelGUI package and comparing the twelve hip mutant strains to the wild type strain.
 
Submission date Mar 06, 2014
Last update date Apr 07, 2014
Contact name Kim Lewis
Organization name Northeastern University
Street address 360 Huntington Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL17082
Series (1)
GSE55647 Gene expression analysis of Mycobacterium tuberculosis high-persister (hip) mutants.

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
AFFX-BioB-3_at 10.50094354
AFFX-BioB-5_at 10.45660952
AFFX-BioB-M_at 10.60963904
AFFX-BioC-3_at 11.60179347
AFFX-BioC-5_at 11.87733419
AFFX-BioDn-3_at 13.2942181
AFFX-BioDn-5_at 11.94061422
AFFX-CreX-3_at 14.39557127
AFFX-CreX-5_at 14.25002576
AFFX-DapX-3_at 2.867959152
AFFX-DapX-5_at 2.496024304
AFFX-DapX-M_at 2.429563525
AFFX-HXB2_3_at 2.488380513
AFFX-HXB2_5_at 2.778382364
AFFX-HXB2_M_at 2.643456754
AFFX-LysX-3_at 2.38400178
AFFX-LysX-5_at 2.383490824
AFFX-LysX-M_at 2.689904312
AFFX-PheX-3_at 3.331292457
AFFX-PheX-5_at 2.362339663

Total number of rows: 13284

Table truncated, full table size 349 Kbytes.




Supplementary file Size Download File type/resource
GSM1341099_TURPS_p_MtbHipMutants_MTbH37Rva520730F_E04_758562.CEL.gz 665.1 Kb (ftp)(http) CEL
Processed data included within Sample table

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