|
| Status |
Public on Feb 17, 2009 |
| Title |
Control KC vs Notch activated KC replicate 4 dye swap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
KC E
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Notch activated KC Drosophila cells [EDTA treated]
|
| Biomaterial provider |
KC cells were obtained from Dr Martin Zeidler
|
| Treatment protocol |
Notch activation was achieved by exposing cells to 2mM EDTA in PBS for 30 minutes. Control cells were pre-treated with PBS alone.
|
| Growth protocol |
KC cells were grown at 25C in Schneider's Drosophila Medium (Invitrogen) supplemented with 10% fetal calf serum, 100ug/ml streptamycin and 100 units/ml penicilin and with 10ug/ml insulin (Sigma). Cultures were split and replated in fresh medium approximately 12-18 hours prior to activation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Medium scale Trizol extraction (http://www.flychip.org.uk/protocols/gene_expression/standard_extraction.pdf).
|
| Label |
Cy3
|
| Label protocol |
Reverse transcription and direct labelling for cDNA and oligo arrays (http://www.flychip.org.uk/protocols/gene_expression/direct_labelling.pdf)
|
| |
|
| Channel 2 |
| Source name |
Kc
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Control KC Drosophila cells [no EDTA]
|
| Biomaterial provider |
KC cells were obtained from Dr Martin Zeidler
|
| Treatment protocol |
Notch activation was achieved by exposing cells to 2mM EDTA in PBS for 30 minutes. Control cells were pre-treated with PBS alone.
|
| Growth protocol |
KC were grown at 25C in Schneider's Drosophila Medium (Invitrogen) supplemented with 10% fetal calf serum, 100ug/ml streptamycin and 100 units/ml penicilin and with 10ug/ml insulin (Sigma). Cultures were split and replated in fresh medium approximately 12-18 hours prior to activation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Medium scale Trizol extraction (http://www.flychip.org.uk/protocols/gene_expression/medium_extraction.php).
|
| Label |
Cy5
|
| Label protocol |
Reverse transcription and direct labelling for cDNA and oligo arrays (http://www.flychip.org.uk/protocols/gene_expression/direct_labelling.pdf)
|
| |
|
| |
| Hybridization protocol |
Hybridisation to amino-modified long oligonucleotide microarrays using a Genomic Solutions hybridisation station with the Biosolutions hybridisation buffer (http://www.flychip.org.uk/protocols/hybridisation/hyb_oligoMWG.pdf)
|
| Scan protocol |
Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/scanning2.pdf)
|
| Description |
control KC vs Notch activated KC replicate 4 dye swap
|
| Data processing |
Spot finding and quantitation via the Dapple package.
|
| |
|
| Submission date |
Dec 19, 2007 |
| Last update date |
Feb 17, 2009 |
| Contact name |
Sarah Bray |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Cambridge
|
| Department |
PDN
|
| Street address |
Downing Street
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 3DY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL5135 |
| Series (2) |
| GSE9964 |
Notch targets in DmD8 and KC Drosophila cells |
| GSE9965 |
Notch targets in KC Drosophila cells |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
VSN normalised experiment/control ratio equivalent to log[2] ratio |
| A |
VSN normalised average intensity |
| Status1_col |
Spotfinding status channel 1; A = [A]ccepted, R =[R]ejected, S=[S]uspicious |
| fgMedian1_col |
foreground (spot) median pixel intensity of channel 1 |
| bgMedian1_col |
background (local area around spot) median pixel intensity of channel 1 |
| fgAdjMAD1_col |
foreground (spot) pixel intensity variability of channel 1 |
| bgAdjMAD1_col |
background (local area around spot) pixel intensity variability of channel 1 |
| Status2_col |
Spotfinding status channel 2; A = [A]ccepted, R =[R]ejected, S=[S]uspicious |
| fgMedian2_col |
foreground (spot) median pixel intensity of channel 2 |
| bgMedian2_col |
background (local area around spot) median pixel intensity of channel 2 |
| fgAdjMAD2_col |
foreground (spot) pixel intensity variability of channel 2 |
| bgAdjMAD2_col |
background (local area around spot) pixel intensity variability of channel 2 |
| fgN_col |
number of pixels in the foreground |
| bgN_col |
number of pixels in the background |
