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Sample GSM175078 Query DataSets for GSM175078
Status Public on May 02, 2007
Title C-CO-72-2-132
Sample type RNA
 
Channel 1
Source name prefrontal cortex (control)
Organism Mus musculus
Characteristics Pre-frontal Cortex from male Balb/c mice 72 h after s.c. injection of PBS
Treatment protocol Eight week old Balb/c male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 72 h
Growth protocol Mice were housed in HEPA filtered air racks (Tecniplast, Italy) with food and water ad libitum
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using TRIzol Reagent (Invitrogen). Poly A+ RNA was obtained from total RNA using the MicroPoly(A) Pure kit (Ambion)
Label Cy3
Label protocol RNA was reversed transcribed using Superscript II RT (Invitrogen) with oligo dT primers and random primers, both in the presence of aa-dUTP (Sigma). The cDNA was labeled with Cy3 or Cy5 dyes (Amersham), resuspended in DMSO, and incubated for 1 hr at room temperature in the dark. The probes were purified using the SNAP Gel Purification Kit (Invitrogen) following manufacturer instructions with the following modification: at the initial step, 500 ul of loading buffer (2.25 M guanidinium HCl in 70% isopropanol) were added to the sample, placed in a SNAP column and incubated for 4 min before the first centrifugation
 
Channel 2
Source name prefrontal cortex (72 h after injection of CT26 colon carcinoma cells)
Organism Mus musculus
Characteristics Pre-frontal cortex from male Balb/c mice 72 h after s.c. injection of CT26 colon carcinoma cells
Treatment protocol Eight week old Balb/c male mice were injected s.c. with 1E6 CT-26.WT cells in 300 ul PBS and sacrifice by decapitation after 72 h
Growth protocol Mice were housed in HEPA filtered air racks (Tecniplast, Italy) with food and water ad libitum
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using TRIzol Reagent (Invitrogen). Poly A+ RNA was obtained from total RNA using the MicroPoly(A) Pure kit (Ambion)
Label Cy5
Label protocol RNA was reversed transcribed using Superscript II RT (Invitrogen) with oligo dT primers and random primers, both in the presence of aa-dUTP (Sigma). The cDNA was labeled with Cy3 or Cy5 dyes (Amersham), resuspended in DMSO, and incubated for 1 hr at room temperature in the dark. The probes were purified using the SNAP Gel Purification Kit (Invitrogen) following manufacturer instructions with the following modification: at the initial step, 500 ul of loading buffer (2.25 M guanidinium HCl in 70% isopropanol) were added to the sample, placed in a SNAP column and incubated for 4 min before the first centrifugation
 
 
Hybridization protocol Slides were prehybridised at 42°C in 2X SSC, 0.1% SDS, 1% BSA. Labeled probes were mixed with hybridization buffer containing 30% formamide and hybridized overnight at 42°C
Scan protocol Images were obtained with a VersArray ChipReader system (BioRad) at 10 um resolution and 16bit depth. Each slide was scanned three times, each time with a 5% increment in the sensitivity of the scanner. The data integration for multipole scanning were calculated by M = log2(cy3 / cy2) and A = 0.5 * log2(cy2 * cy3) values for all the possible combinations between channels among the three scannings. Quality score for each couple of channels was calculated as QS = min(QScy2, QScy3). The resulting 9 sets of A and M values were averaged using the QS as weights to obtain the integrated A and M sets.
Description Pre-frontal cortex of male balb/c mice
Data processing Data was log2 transformed and normalizaed with an intensity- and location-dependent loess fit
 
Submission date Mar 14, 2007
Last update date May 04, 2007
Contact name Mariano Cesar Salibe
E-mail(s) msalibe@leloir.org.ar
Organization name Gentron LLC
Street address Av. Patricias Argentinas 435
City Ciudad de Buenos Aires
ZIP/Postal code 1425
Country Argentina
 
Platform ID GPL4981
Series (2)
GSE7287 profiling of prefrontal cortex from mice s.c. injected with CT-26wt colon carcinoma cells vs. PBS
GSE7565 Profiling brain and liver tissues from mice

Data table header descriptions
ID_REF
VALUE normalized log2 ratios CH2 / CH1
CH1_MEAN Channel 1 mean intensity
CH1_BG Channel 1 mean background intensity
CH2_MEAN Channel 2 mean intensity
CH2_BG Channel 2 mean background intensity
AREA Spot total area in pixels
SF Percentage of nonsaturated pixels

Data table
ID_REF VALUE CH1_MEAN CH1_BG CH2_MEAN CH2_BG AREA SF
1 -0.11718907900765 1105630 435513 0 0 169 0.1319
2 0.498027310606244 1870641 558000 1571089 376560 240 0.2475
3 0.169085154828212 3978941 1126360 3408491 870696 232 0.4174
4 0.0409529621529219 1771800 634040 1099490 300960 220 0.2485
5 2172972 1088550 0 0 205 0.1344
6 2820756 1589200 0 0 232 0.0745
7 3543446 1708974 0 0 263 0.1485
8 3193811 1117820 0 0 225 0.1936
9 -0.00632585348688716 7999511 898148 6053279 551754 302 0.3797
10 0.0570646109415319 2137609 660146 1450952 464566 254 0.1658
11 1731000 430636 0 0 201 0.1181
12 910341 157916 0 0 97 0.1958
13 -0.21380508125804 5376782 814296 3293960 539756 259 0.2714
14 -0.242234788752082 2302997 767335 1408703 603935 215 0.1100
15 0.259388555538783 1437669 548640 1110913 457962 135 0.2061
16 1924936 415290 0 0 218 0.1772
17 2249652 530160 1337257 388220 235 0.1899
18 0.0965445082107606 0 0 0 0 57 0.1098
19 867431 235145 0 0 132 0.2367
20 0 0 0 0 72 0.0520

Total number of rows: 10080

Table truncated, full table size 410 Kbytes.




Supplementary file Size Download File type/resource
GSM175078-1.txt.gz 346.8 Kb (ftp)(http) TXT
GSM175078-2.txt.gz 352.8 Kb (ftp)(http) TXT
GSM175078-3.txt.gz 358.6 Kb (ftp)(http) TXT

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