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Sample GSM263810 Query DataSets for GSM263810
Status Public on Sep 23, 2009
Title CBX7 overexpression in TERA2
Sample type RNA
 
Channel 1
Source name TERA2 empty vector cells
Organism Homo sapiens
Characteristics malignant embryonal carcinoma
derived from metastatic site: lung
adherent cells with epithelial morphology
Biomaterial provider ATCC
Treatment protocol Stable transfection with plasmid containing EF1 alpha promoter and puromycin resistance gene downstream from IRES.
Growth protocol Cells were maintained in McCoy's with 15% fetal bovine serum and 0.2 micrograms per ml puromycin.
Extracted molecule total RNA
Extraction protocol Trisol extraction based on manufacturer's instructions followed by RNeasy cleanup as per manufacturer's instructions.
Label Cy3
Label protocol Agilent low RNA input linear amplification kit.
 
Channel 2
Source name TERA2 CBX7 overexpressing cells
Organism Homo sapiens
Characteristics malignant embryonal carcinoma
derived from metastatic site: lung
adherent cells with epithelial morphology
Biomaterial provider ATCC
Treatment protocol Stable transfection with plasmid containing EF1 alpha promoter driving expression of CBX7 containing 3' HA tag and puromycin resistance gene downstream from IRES.
Growth protocol Cells were maintained in McCoy's with 15% fetal bovine serum and 0.2 micrograms per ml puromycin.
Extracted molecule total RNA
Extraction protocol Trisol extraction based on manufacturer's instructions followed by RNeasy cleanup as per manufacturer's instructions.
Label Cy5
Label protocol Agilent low RNA input linear amplification kit.
 
 
Hybridization protocol Agilent Gene Expression Hybridization Kit using manufacturer's protocol.
Scan protocol Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.
Description CBX7 overexpression in TERA2
Data processing Log ratio of red signal to green signal was calculated. Loess normalization as implemented in the Limma package from Bioconductor.
 
Submission date Feb 07, 2008
Last update date Sep 24, 2008
Contact name Leander Van Neste
Organization name Ghent University
Department Molecular Biotechnology
Lab Bioinformatics and Computational Genomics
Street address Coupure Links 653
City Ghent
ZIP/Postal code 9000
Country Belgium
 
Platform ID GPL4133
Series (1)
GSE10541 Polycomb CBX7 represses expression of tumor suppressor genes

Data table header descriptions
ID_REF
VALUE Normalized log ratio data: log2(CH2/CH1)
CH1_SIG_MEDIAN Median spot value of channel 1
CH1_BKD_MEDIAN Background median spot value of channel 1
CH2_SIG_MEDIAN Median spot value of channel 2
CH2_BKD_MEDIAN Background median spot value of channel 2

Data table
ID_REF VALUE CH1_SIG_MEDIAN CH1_BKD_MEDIAN CH2_SIG_MEDIAN CH2_BKD_MEDIAN
1 -0.57944884241368 85175.9 48 252700 57
2 -0.27257266791199 99 49 66 58
3 -0.0820513814402334 96 48 76 59
4 -0.142362404254518 99 49 76 60
5 -0.137390784473797 95 48 70 59
6 -0.159735163383152 98 49 73 59
7 -0.127041732146267 97 48 74 60
8 -0.112438867471261 97.5 49 76 58
9 -0.114619579274910 97 49 75 59
10 -0.154620020456632 99 50 75 58
11 -0.162060596071738 100 49 76 59
12 -0.315353259056433 1277 49 2563 59
13 0.08142534345666 153 49 222 59
14 -0.379786263793875 838 49 1460 59
15 -0.73181531686357 270 49 260 59
16 0.322080594492971 4987 49 19849.9 59
17 -0.113611626655193 299 50 495 58
18 0.153929060205076 377.5 50 818.5 60
19 0.32245526409047 18235 49 86121 60
20 0.150091493244963 317 49 656 60

Total number of rows: 45220

Table truncated, full table size 1802 Kbytes.




Supplementary file Size Download File type/resource
GSM263810.txt.gz 13.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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