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Sample GSM477889 Query DataSets for GSM477889
Status Public on Dec 05, 2009
Title Weise_1-6_ptpks_Rep3_ATH1
Sample type RNA
 
Source name Salk_053285
Organism Arabidopsis thaliana
Characteristics genotype: ptpkis2 mutation
developmental stage: 3.70
tissue: leaves
stock code: N553285
Growth protocol Plants were sewn in flats of modified commercial soil and grown in a growth chamber with a 12 hour photoperiod, quantum flux of 100 micromol m-2s-1, relative humidity was at least 75%, and a constant temperature of 20 degrees Celsius
Extracted molecule total RNA
Extraction protocol Leaf material was powered using a mortar and pestle and RNA was extracted using a Purescript RNA isolation kit (Gentra Systems, MN, USA)according to kit directions. Samples were then treated with DNaseI (Invitrogen, CA, USA) according to manufactures directions
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 Growth chamber Levington F2 (Fine peat/with intercept an insecticide) with extra grit 4mm at 40%. 75% 20oC. Three leaves from 8 different plants of each genotype were harvested using a green safe lamp 0.5 hours before the lights came on in the morning and immediately frozen in LN2.
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 02, 2009
Last update date Aug 15, 2018
Contact name Nottingham Arabidopsis Stock Centre (NASC)
E-mail(s) affy@arabidopsis.info
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)
GSE19260 Transcript inhibition from limited starch degradation
Relations
Reanalyzed by GSE118579

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-r2-P1-cre-5_at 3202.0009765625 P 0.000244141003349796
AFFX-r2-P1-cre-3_at 5276.50732421875 P 0.000244141003349796
AFFX-r2-Ec-bioD-5_at 699.941040039063 P 0.000244141003349796
AFFX-r2-Ec-bioD-3_at 1013.28137207031 P 0.000244141003349796
AFFX-r2-Ec-bioC-5_at 235.637954711914 P 0.000244141003349796
AFFX-r2-Ec-bioC-3_at 262.8994140625 P 0.000244141003349796
AFFX-r2-Ec-bioB-M_at 67.1442642211914 P 0.000244141003349796
AFFX-r2-Ec-bioB-5_at 105.36548614502 P 0.00415039015933871
AFFX-r2-Ec-bioB-3_at 42.2852935791016 P 0.000244141003349796
AFFX-r2-Bs-thr-M_s_at 1.93470585346222 A 0.334473013877869
AFFX-r2-Bs-thr-5_s_at 0.614478647708893 A 0.916015625
AFFX-r2-Bs-thr-3_s_at 5.34880828857422 A 0.753906011581421
AFFX-r2-Bs-phe-M_at 7.90843868255615 A 0.533936023712158
AFFX-r2-Bs-phe-5_at 3.95135021209717 A 0.59228515625
AFFX-r2-Bs-phe-3_at 7.15989351272583 A 0.398925989866257
AFFX-r2-Bs-lys-M_at 4.06617641448975 A 0.753906011581421
AFFX-r2-Bs-lys-5_at 0.350171893835068 A 0.997070014476776
AFFX-r2-Bs-lys-3_at 1.03443586826324 A 0.533936023712158
AFFX-r2-Bs-dap-M_at 0.381893903017044 A 0.985840022563934
AFFX-r2-Bs-dap-5_at 0.252233266830444 A 0.998778998851776

Total number of rows: 22810

Table truncated, full table size 1070 Kbytes.




Supplementary file Size Download File type/resource
GSM477889.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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