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Sample GSM1165960 Query DataSets for GSM1165960
Status Public on Jun 28, 2013
Title Mtb infected-42d-1
Sample type RNA
 
Source name Mouse lungs infected with Mtb for 42 days
Organism Mus musculus
Characteristics tissue: Lung
strain: B6D2F1
infection: Mtb
time: 42 dpi
Treatment protocol PZA, one of the first line anti-TB drugs, was used to treat one group of Mtb infected mice. The compound was used at 150mg/kg body weight, dissolved in distilled water and administered through gavage five days a weeks. Treatment was started at 28 days post infection and continued up to 63 days post infection.
Growth protocol B6D2F1 mice were infected with Mtb CDC1551 at ~2log10 (on day 0). At28 days post infection, one group of infected mice were treated with Pyrazinamide at 150mg/kg. Lung tissue from Uninfected, Untreated and PZA treated mice were isolated at Day 0, 28, 42 and 63 days post infection and used for total RNA isolation.
Extracted molecule total RNA
Extraction protocol Total RNA from the mouse lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) and purified using RNA mini prep columns (Qiagen, CA, USA) according to the instructions of the manufacturers
Label biotin
Label protocol Total RNA samples were reverse transcribed and labled with biotin as suggested by the array manufacturer (affymetrix)
 
Hybridization protocol standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute of UMDNJ was used for all the experiments
Scan protocol standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute of UMDNJ was used for all the experiments
Description Gene expression data from Mtb-infected mouse lungs
Data processing Data from the scanned images were extracted using the software from Affymetrix and processed using PARTEK Genomics Suite for further analysis
 
Submission date Jun 17, 2013
Last update date Jun 28, 2013
Contact name Selvakumar Subbian
E-mail(s) [email protected]
Phone 973-854-3226
Organization name PHRI, NJMS, Rutgers the State University of NJ
Department Medicine
Lab Laboratory of Mycobacterial Immunity and Pathogenesis
Street address 225 Warren Street
City Newark
State/province NJ
ZIP/Postal code 07103
Country USA
 
Platform ID GPL6246
Series (1)
GSE48027 Host directed activity of Pyrazinamide in Mycobacterium tuberculosis infection

Data table header descriptions
ID_REF
VALUE Partek RMA log2 signal

Data table
ID_REF VALUE
10338001 12.7895
10338002 7.51121
10338003 10.753
10338004 9.40472
10338005 2.14474
10338006 2.66897
10338007 3.58508
10338008 4.92722
10338009 9.93732
10338010 2.18779
10338011 6.86586
10338012 2.41064
10338013 1.92179
10338014 1.9771
10338015 2.0044
10338016 8.89561
10338017 13.1953
10338018 8.02126
10338019 6.26613
10338020 9.89076

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM1165960_42D_CDC1551-1.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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