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Sample GSM140907 Query DataSets for GSM140907
Status Public on Nov 20, 2006
Title infected CT26 tumor replicate 3
Sample type RNA
 
Source name infected CT26 tumor
Organisms Mus musculus; Clostridium novyi NT
Characteristics infected CT26 tumor
Growth protocol Six- to 8-week-old BALB/c mice (Harlan, Indianapolis, IN) were inoculated subcutaneously with five million CT26 murine colon cancer cells. Three hundred million C. novyi-NT spores were administered by tail-vein injection once the tumor volumes reached ~500 mm3. Germination was generally observed to initiate within 12 hours and RNA isolated eighteen hours later, just after germination became evident.
Extracted molecule total RNA
Extraction protocol Vegetative bacteria or spores were collected by centrifugation and homogenized by vortexing in RNAwiz buffer (RiboPureTM-Bacteria kit, Ambion, Austin, TX) containing 250 µL of Zirconia beads (Biospec, Bartlesville, OK) for 10 minutes at 4°C, followed by a 5-min break. This cycle was repeated 12 times to ensure disruption of the spores (as assessed by phase contrast microscopy and RNA yield). RNA was purified with the RiboPureTM-Bacteria kit (Ambion) following the manufacturer’s instructions.
RNA was prepared from infected or uninfected tumors by homogenizing (50 strokes) the dissected tumors in a glass homogenizer containing a 10-fold volume of the RNAwiz buffer on ice. The homogenate was aliquoted into 0.5-mL RNase-free tubes. The samples were then processed exactly as described above, using a 12-cycle homogenization with Zirconia beads.
Label biotin
Label protocol total RNA was reverse transcribed with SuperScript II Reverse Transcriptase (Invitrogen). The first-strand cDNA was fragmented by DNase I (Promega, Madison WI) and labeled with biotinylated ddATP through a terminal transferase end-labeling reaction.
 
Hybridization protocol Hybridization with the end-labeled samples was carried out at 45°C for 16 hours in 100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20 and 10.5% glycerol.
Scan protocol After washing, the arrays were stained with Cy3-Streptavidin, followed by scanning with an Axon 4000B scanner.
Description The features were extracted by using the NimbleScan software.
Data processing Data was analyzed with the Bioconductor project using quantile normalization (see:Bolstad B, Irizarry R, Astrand M, Speed T (2003) A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19 (2), p185-193) and gene calls generated using the RMA algorithm (Robust multichip average described in Biostatistics 2003 Apr;4(2):249-64 ).
 
Submission date Oct 19, 2006
Last update date Nov 20, 2006
Contact name Xin Huang
E-mail(s) xhuang8@jhmi.edu
Organization name Johns Hopkins University
Department Oncology
Street address 1650 Orleans Street, CRB I, Room 520
City Baltimore
State/province MD
ZIP/Postal code 21231
Country USA
 
Platform ID GPL4463
Series (1)
GSE6087 Transcriptomes of Clostridium novyi-NT

Data table header descriptions
ID_REF
VALUE Normalized expression value

Data table
ID_REF VALUE
NT0100P0000000101 246.421684
NT0100P0000000218 81.970591
NT0100P0000000319 19.928326
NT0100P0000000530 15.280567
NT0100P0000000693 20.492401
NT0100P0000001071 171.952462
NT0100P0000001435 1041.907894
NT0100P0000001713 1476.574561
NT0100P0000001864 1315.157894
NT0100P0000002024 17.03134
NT0100P0000002085 879.241227
NT0100P0000002149 17.03134
NT0100P0000002220 13.393794
NT0100P0000002289 12.055271
NT0100P0000002361 196.549481
NT0100P0000002519 25.984756
NT0100P0000002579 169.37603
NT0100P0000002643 6565.907894
NT0100P0000002741 98.979946
NT0100P0000002872 133.055384

Total number of rows: 11630

Table truncated, full table size 329 Kbytes.




Supplementary file Size Download File type/resource
GSM140907.gpr.gz 165.6 Kb (ftp)(http) GPR

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