|
| Status |
Public on Dec 30, 2008 |
| Title |
SH_AG_42928_24h_2.5uM_BP2_DF |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
sh-HepG2 24hr 2.5uM BaP B(hepg2 24h 2.5 bap)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were collected and total RNA extracted using the Qiagen RNeasy Mini Kit protocol (RNeasy Mini Handbook, Qiagen, UK). After addition of lysis buffer (RLT, Qiagen) samples were homogenized using QIAshredders (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Labelling and hybridization was carried out according to the Agilent manual for microarrays with minor modifications. Total RNA (0.5 ug) was transcribed into cDNA and labelled with either Cyanine 5 (Cy5) or Cyanine 3 (Cy3). If dye-incorporation was above 7 pmol/µg RNA, 2 µg of BaP treated-cRNA and 2 µg DMSO control-cRNA were applied on the Agilent Human 1A (V2) Oligo Microarray.
|
| |
|
| Channel 2 |
| Source name |
sh-HepG2 24h DMSO B(hepg2 24h dmso)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were collected and total RNA extracted using the Qiagen RNeasy Mini Kit protocol (RNeasy Mini Handbook, Qiagen, UK). After addition of lysis buffer (RLT, Qiagen) samples were homogenized using QIAshredders (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
Labelling and hybridization was carried out according to the Agilent manual for microarrays with minor modifications. Total RNA (0.5 ug) was transcribed into cDNA and labelled with either Cyanine 5 (Cy5) or Cyanine 3 (Cy3). If dye-incorporation was above 7 pmol/µg RNA, 2 µg of BaP treated-cRNA and 2 µg DMSO control-cRNA were applied on the Agilent Human 1A (V2) Oligo Microarray.
|
| |
|
| |
| Hybridization protocol |
Hybridization and washing were performed according to the Agilent manual.
|
| Scan protocol |
Scanner: Axon4000A. Voltage: 100%
|
| Description |
24h DMSO v 24h 2.5 BaP BP1 DF
|
| Data processing |
Regions were used for normalizing samples 1-32. To account for dye swap, the signal channel and control channel measurements for sample(s) 1, 3, 5, 7, 9-10, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32 were reversed. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.
|
| |
|
| Submission date |
Jan 12, 2007 |
| Last update date |
Nov 03, 2008 |
| Contact name |
Ian Giddings |
| E-mail(s) |
[email protected], [email protected]
|
| Phone |
+44 20 8722 4293
|
| Fax |
+44 20 8722 4141
|
| URL |
http://www.crukdmf.icr.ac.uk
|
| Organization name |
Institute of Cancer Research
|
| Department |
Section of Molecular Carcinogenesis
|
| Lab |
CANCER RESEARCH UK DNA Microarray Facility
|
| Street address |
15 Cotswold Road
|
| City |
Sutton |
| State/province |
Surrey |
| ZIP/Postal code |
SM2 5NG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL887 |
| Series (1) |
| GSE6722 |
Agilent _CRUK_platform_comparison |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
normalised log2 ratio (Treated/Control) |
| CH1_MEDIAN |
channel 1 signal intensity median - Cy3 (cyanine 3) |
| CH1_MEAN |
channel 1 signal intensity mean |
| CH1_SD |
channel 1 signal intensity standard deviation |
| CH1_AREA |
Number of pixels used to determine channel 1 signal intensity |
| CH1_BKD_MEDIAN |
channel 1 background signal intensity median |
| CH1_BKD_MEAN |
channel 1 background signal intensity mean |
| CH1_BKD_SD |
channel 1 background signal intensity standard deviation |
| CH1_BKD_AREA |
Number of pixels used to determine channel 1 background signal intensity |
| CH2_MEDIAN |
channel 2 signal intensity median - Cy5 (cyanine 5) |
| CH2_MEAN |
channel 2 signal intensity mean |
| CH2_SD |
channel 2 signal intensity standard deviation |
| CH2_AREA |
Number of pixels used to determine channel 2 signal intensity |
| CH2_BKD_MEDIAN |
channel 2 background signal intensity median |
| CH2_BKD_MEAN |
channel 2 background signal intensity mean |
| CH2_BKD_SD |
channel 2 background signal intensity standard deviation |
| CH2_BKD_AREA |
Number of pixels used to determine channel 2 background signal intensity |
| PRE_VALUE |
normalised ratio (Treated/Control) |
