|
| Status |
Public on Jun 16, 2007 |
| Title |
RTS II cell line stimulation 9 (SsamcellINF9a) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RTS II cells stimulated with recombinant interferon gamma
|
| Organism |
Oncorhynchus mykiss |
| Characteristics |
RTS II cells stimulated with recombinant interferon gamma
|
| Biomaterial provider |
University of Aberdeen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAstat (TEL_TEST INC.) According to manufacturers instructions.
|
| Label |
CY5
|
| Label protocol |
Labelled cDNA was generated using Amersham Pharmacia post labelling kit. Total RNA (20mg) was used as template for each labelling.
|
| |
|
| Channel 2 |
| Source name |
RTS II cells Non stimulated
|
| Organism |
Oncorhynchus mykiss |
| Characteristics |
RTS II cells Non stimulated
|
| Biomaterial provider |
University of Aberdeen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAstat (TEL_TEST INC.) According to manufacturers instructions.
|
| Label |
CY3
|
| Label protocol |
Labelled cDNA was generated using Amersham Pharmacia post labelling kit. Total RNA (20mg) was used as template for each labelling.
|
| |
|
| |
| Hybridization protocol |
Prior to hybridization 1.5mL d(A)80 (1mg ml-1), 110mL formamide, 55ul hybridization buffer (Amersham Biosciences) and water was added to give a final volume of 220 ml. The cDNA was heated to 95°C for 2 min before being added to the hybridization chamber. The hybridization was performed for 16 h at 42°C on an Amersham Lucidea hybridization station. Prior to hybridization slides were pretreated by heating in water at 95°C for 5 min, then washed with isopropanol and air dried. Washes were as follows: 1X SSC 10 min, 1X SSC +0.2% SDS 10 min, 0.1 X SSC + 0.2% SDS 10 min. Slides were then dried before being scanned.
|
| Scan protocol |
Images were scanned using Axon 4100B scanner. Resolution was at 10mM. Gel images were edited using GenePix Version 5.1.
|
| Description |
Rainbow trout cell line RTS II stimulated with recombinant Interleukin 1 beta for 6 hours
|
| Data processing |
Initial image analysis was performed with the GenPix (version 5.1, Axon instruments) program; the array images were edited to ensure that the GAL (Gene Associated List) file was correctly orientated and that any abnormal hybridization signals were flagged as bad. Edited images were imported into Acuity (version 5.1, Axon instruments) and analysis performed. All arrays were background corrected using local background correction and normalized using Lowess normalization. The data was filtered to remove bad signal and signal that did not reach a predetermined threshold (signal to noise ratio >1.5 for either Cy3 or Cy5). Data in VALUE column is RAW data and not normalized
|
| |
|
| Submission date |
Jun 16, 2006 |
| Last update date |
Apr 24, 2013 |
| Contact name |
Sam A Martin |
| E-mail(s) |
sam.martin@abdn.ac.uk
|
| Phone |
+44 1224 272867
|
| Fax |
+44 1224 272396
|
| Organization name |
University of Aberdeen
|
| Department |
Zoology
|
| Lab |
Scottish Fish Immunology Research Centre
|
| Street address |
Tillydrone Avenue
|
| City |
Aberdeen |
| State/province |
Scotland |
| ZIP/Postal code |
AB24 2TZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL2899 |
| Series (1) |
| GSE5091 |
Cell line stimulated with recombinant cytokines interleukin-1b and interferon gamma. |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
Log2 ratio (CH_1 Median-CH1_B/CH2_Median-CH2_B) |
| CH1_ Median |
Median pixel intensity for CH_1 |
| CH1_ Mean |
Mean pixel intensity for CH_1 |
| CH1_B |
Local Background used to correct feature |
| CH1_B Median |
Local background median for CH_1 |
| CH1_B Mean |
Local Background mean for CH_1 |
| CH2_ Median |
Median pixel intensity for CH_1 |
| CH2_ Mean |
Mean pixel intensity for CH_1 |
| CH2_B |
Local Background used to correct feature |
| CH2_B Median |
Local background median for CH_1 |
| CH2_B Mean |
Local Background mean for CH_1 |
| CH1_ Median - CH1_B |
CH_1 median pixel - CH_1 local background median |
| CH2_ Median - CH2_B |
CH_2 median pixel - CH_2 local background median |
| CH1_ Total Intensity |
Total pixel intensity for CH_1 |
| CH2_ Total Intensity |
Total pixel intensity for CH_2 |
| SNR 635 |
signal to noise ratio as determined by GenePix for CH_1 |
| SNR 532 |
signal to noise ratio as determined by GenePix for CH_2 |
| Flags |
Flags are: bad -100, not found -50, absent -75, good 100, unflagged 0. Determined from GenePix. |
