|
| Status |
Public on Dec 11, 2009 |
| Title |
Schmidt_DS-C1_Rep1_ATH1 |
| Sample type |
RNA |
| |
|
| Source name |
Col-0
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype: wildtype
developmental stage: 35 days (1.13- Boyes Key)
tissue: whole rosettes
|
| Growth protocol |
Seeds of Arabidopsis thaliana ecotype Columbia (Col-0) and PVIP1 and PVIP2 RNAi transgenic lines (pvip1/pvip2; Dunoyer et al 2004, J Virol 78: 2301) were surface-sterilised in a desiccator by chlorine gas generated with a mixture of 100 ml commercial bleach and 3 ml concentrated hydrochloric acid for 4 h. Seeds were sown on MS agar (0.8%) that contained 20 mg/l phosphinothricin (Basta) for the pvip1/pvip2 line. After stratification in the dark at 4C for 3 days, the plates with the seeds were transferred to a growth room (20C, 16 h light). 14 days after germination, Col-0 plants and Basta-resistant pvip1/pvip2 plants were transferred to soil (Scotts Levington Special Custom Mix Compost with Intercept 5GR) and grown under short-day conditions (20C, 8 h light, 70% relative air humidity) for 3 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNAeasy kit protocol
|
| Label |
biotin
|
| Label protocol |
Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling
|
| |
|
| Hybridization protocol |
Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA
|
| Scan protocol |
Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.
|
| Description |
After sowing on plates, seeds were stored in the dark at 4C for 3 days. Dry surface-sterilisation with chlorine gas generated by 100 ml household bleach and 3 ml concentrated HCl. Growth Room. Commercial soil: Scotts Levington Special Custom Mix Compost with Intercept 5GR 20C 70%.
|
| Data processing |
Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system
|
| |
|
| Submission date |
Dec 07, 2009 |
| Last update date |
Dec 10, 2009 |
| Contact name |
Nottingham Arabidopsis Stock Centre (NASC) |
| E-mail(s) |
[email protected]
|
| Phone |
+44 (0)115 951 3237
|
| Fax |
+44 (0)115 951 3297
|
| URL |
http://arabidopsis.info/
|
| Organization name |
Nottingham Arabidopsis Stock Centre (NASC)
|
| Department |
School of Biosciences, University of Nottingham
|
| Street address |
Sutton Bonington Campus
|
| City |
Loughborough |
| ZIP/Postal code |
LE12 5RD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
|
