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Series GSE1111 Query DataSets for GSE1111
Status Public on Mar 09, 2004
Title Comparison of AG and ATH1 using IAA
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary Arabidopsis seedlings (Col-0) were grown in suspension in half-strength MS medium with agitation at ~100 rpm at ~22 C under ~50 microeinsteins m-2s-1 cool white fluorescent continuous illumination as described by (Xiao et al., Plant Physiol. 2002 Dec;130(4):2118-28). Seedlings were treated at 10-12 days by addition of freshly made IAA
(0.1 or 1.0uM) to each flask, and harvested after a 1 or 3 hour incubation. Controls were not treated and harvested at 0hr. All tissue harvested. Total RNA was extracted using TRIzol (Invitrogen) as described by the manufacturer and then filtered using QIAGEN RNeasy columns. cDNA was synthesized from total RNA using a Superscript double-stranded cDNA
synthesis kit (Invitrogen) and a T7-dT24 primer. cRNA was synthesized using the Enzo BioArray HighYield RNA Transcript Labeling kit (Affymetrix p/n 900182) and fragmented by Mg2+ hydrolysis. 15ug per array was hybridized overnight at 45 C. Arrays were then
washed and scanned using the GeneChip FS400 fluidics station and Agilent GeneArray scanner.
Images were analyzed using Affymetrix Microarray Suite 5.0, scaling to a target average
intensity of 500. Spiking controls were added to the total RNA before cDNA synthesis and additional spiking samples were added to the resulting cDNA prior to cRNA synthesis.

Probe samples were recovered for use in replicate hybridizations, 2 per array for a total of 4 hybridizations. The purpose of this was the statistical comparison of the two different versions of Affymetrix Arabidopsis probe arrays, AG and ATH1, as part of the process of characterization of the newer array, ATH1.

A complete dose response assay using ATH1 and the data represented below may be found in series file GSE1110.

In comparison table below:
SIGNAL_LOG_RATIO = Mean of log to base two of the experimental divided by control signal ratios across all probe pairs in a set.
CHANGE = Qualitative measurement indicating whether the probe set signal is increased (I), marginally increased (MI), not changed (NC), marginally decreased (MD), or decreased (D) as compared to a control hybridization across all probe pairs, based on a p-value calculation.
change_p-value = Measures the probability that all probe pairs in the set indicate a change, with 0 indicating strong likelyhood for increase, 0.5 indicating little probability for difference, and 1 indicating strong probability for decrease.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Keywords = Arabidopsis
Keywords: parallel sample
 
 
Contributor(s) Redman JC, Haas BJ, Tanimoto G, Town CD
Citation(s) 15086809
Submission date Mar 05, 2004
Last update date Jun 12, 2017
Contact name Julia C Redman
E-mail(s) [email protected]
Phone 301-795-7000
URL http://www.tigr.org
Organization name The Institute for Genomic Research
Department Plant Genomics
Lab Christopher Town
Street address 9712 Medical Center Dr
City Rockville
State/province MD
ZIP/Postal code 20850
Country USA
 
Platforms (2)
GPL71 [AG] Affymetrix Arabidopsis Genome Array
GPL198 [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
Samples (12)
GSM18228 Control_1.1 (a)
GSM18229 Control_1.2 (a)
GSM18290 0.1uM_IAA_1h_1.1
Relations
BioProject PRJNA87217

GSE1111 Comparison data header descriptions
ID_REF
SLG_GSM18290vGSM18228 SIGNAL_LOG_RATIO 0.1uM_IAA_1h_1.1 (GSM18290) compared to contemporary control RNA and hybridization, control_1.1 (a) (GSM18228)
CHG_GSM18290vGSM18228 CHANGE 0.1uM_IAA_1h_1.1 (GSM18290) compared to contemporary control RNA and hybridization, control_1.1 (a) (GSM18228)
CHGP_GSM18290vGSM18228 Change_p-value 0.1uM_IAA_1h_1.1 (GSM18290) compared to contemporary control RNA and hybridization, control_1.1 (a) (GSM18228)
SLG_GSM18291vGSM18229 SIGNAL_LOG_RATIO 0.1uM_IAA_1h_1.2 (GSM18291) compared to contemporary control RNA and hybridization, control_1.2 (a) (GSM18229)
CHG_GSM18291vGSM18229 CHANGE 0.1uM_IAA_1h_1.2 (GSM18291) compared to contemporary control RNA and hybridization, control_1.2 (a) (GSM18229)
CHGP_GSM18291vGSM18229 Change_p-value 0.1uM_IAA_1h_1.2 (GSM18291) compared to contemporary control RNA and hybridization, control_1.2 (a) (GSM18229)
SLG_GSM18294vGSM18228 SIGNAL_LOG_RATIO 0.1uM_IAA_3h_1.1 (GSM18294) compared to contemporary control RNA and hybridization, control_1.1 (a) (GSM18228)
CHG_GSM18294vGSM18228 CHANGE 0.1uM_IAA_3h_1.1 (GSM18294) compared to contemporary control RNA and hybridization, control_1.1 (a) (GSM18228)
CHGP_GSM18294vGSM18228 Change_p-value 0.1uM_IAA_3h_1.1 (GSM18294) compared to contemporary control RNA and hybridization, control_1.1 (a) (GSM18228)
SLG_GSM18295vGSM18229 SIGNAL_LOG_RATIO 0.1uM_IAA_3h_1.2 (GSM18295) compared to contemporary control RNA and hybridization, control_1.2 (GSM18229)
CHG_GSM18295vGSM18229 CHANGE 0.1uM_IAA_3h_1.2 (GSM18295) compared to contemporary control RNA and hybridization, control_1.2 (GSM18229)
CHGP_GSM18295vGSM18229 Change_p-value 0.1uM_IAA_3h_1.2 (GSM18295) compared to contemporary control RNA and hybridization, control_1.2 (GSM18229)
SLG_GSM18327vGSM18325 SIGNAL_LOG_RATIO 0.1uM_IAA_1h_1.1 AG (GSM18327) compared to contemporary control RNA and hybridization, control_1.1 (a) AG (GSM18325)
CHG_GSM18327vGSM18325 CHANGE 0.1uM_IAA_1h_1.1 AG (GSM18327) compared to contemporary control RNA and hybridization, control_1.1 (a) AG (GSM18325)
CHGP_GSM18327vGSM18325 Change_p-value 0.1uM_IAA_1h_1.1 AG (GSM18327) compared to contemporary control RNA and hybridization, control_1.1 (a) AG (GSM18325)
SLG_GSM18329vGSM18325 SIGNAL_LOG_RATIO 0.1uM_IAA_3h_1.1 AG (GSM18329) compared to contemporary control RNA and hybridization, control_1.1 (a) AG (GSM18325)
CHG_GSM18329vGSM18325 CHANGE 0.1uM_IAA_3h_1.1 AG (GSM18329) compared to contemporary control RNA and hybridization, control_1.1 (a) AG (GSM18325)
CHGP_GSM18329vGSM18325 Change_p-value 0.1uM_IAA_3h_1.1 AG (GSM18329) compared to contemporary control RNA and hybridization, control_1.1 (a) AG (GSM18325)
SLG_GSM18330vGSM18326 SIGNAL_LOG_RATIO 0.1uM_IAA_3h_1.2 AG (GSM18330) compared to contemporary control RNA and hybridization, control_1.2 (a) AG (GSM18326)
CHG_GSM18330vGSM18326 CHANGE 0.1uM_IAA_3h_1.2 AG (GSM18330) compared to contemporary control RNA and hybridization, control_1.2 (a) AG (GSM18326)
CHGP_GSM18330vGSM18326 Change_p-value 0.1uM_IAA_3h_1.2 AG (GSM18330) compared to contemporary control RNA and hybridization, control_1.2 (a) AG (GSM18326)
SLG_GSM18328vGSM18326 SIGNAL_LOG_RATIO 0.1uM_IAA_1h_1.2 AG (GSM18328) compared to contemporary control RNA and hybridization, control_1.2 (a) AG (GSM18326)
CHG_GSM18328vGSM18326 CHANGE 0.1uM_IAA_1h_1.2 AG (GSM18328) compared to contemporary control RNA and hybridization, control_1.2 (a) AG (GSM18326)
CHGP_GSM18328vGSM18326 Change_p-value 0.1uM_IAA_1h_1.2 AG (GSM18328) compared to contemporary control RNA and hybridization, control_1.2 (a) AG (GSM18326)

Data table
ID_REF SLG_GSM18290vGSM18228 CHG_GSM18290vGSM18228 CHGP_GSM18290vGSM18228 SLG_GSM18291vGSM18229 CHG_GSM18291vGSM18229 CHGP_GSM18291vGSM18229 SLG_GSM18294vGSM18228 CHG_GSM18294vGSM18228 CHGP_GSM18294vGSM18228 SLG_GSM18295vGSM18229 CHG_GSM18295vGSM18229 CHGP_GSM18295vGSM18229 SLG_GSM18327vGSM18325 CHG_GSM18327vGSM18325 CHGP_GSM18327vGSM18325 SLG_GSM18329vGSM18325 CHG_GSM18329vGSM18325 CHGP_GSM18329vGSM18325 SLG_GSM18330vGSM18326 CHG_GSM18330vGSM18326 CHGP_GSM18330vGSM18326 SLG_GSM18328vGSM18326 CHG_GSM18328vGSM18326 CHGP_GSM18328vGSM18326
AFFX-BioB-5_at 0.6 NC 0.012832 0.6 I 0.000792 0.2 NC 0.5 0 NC 0.5 -0.3 NC 0.836757 0.3 NC 0.553462 0.1 NC 0.5 0 NC 0.884205
AFFX-BioB-M_at 0.8 I 0.000028 0.5 I 0.001246 0 NC 0.5 -0.2 NC 0.5 -0.1 NC 0.5 0.3 NC 0.5 0.2 NC 0.5 0 NC 0.744931
AFFX-BioB-3_at 0.8 I 0.000869 0.4 MI 0.004741 0.2 NC 0.290785 0 NC 0.5 -1.4 NC 0.878877 -1.9 NC 0.704591 0.3 NC 0.5 -1.5 NC 0.82662
AFFX-BioC-5_at 0.4 NC 0.213878 0.3 NC 0.051933 -0.1 NC 0.5 -0.2 NC 0.816091 0 NC 0.5 0.3 NC 0.5 0.6 NC 0.5 0 NC 0.5
AFFX-BioC-3_at 0.4 NC 0.093878 0.2 NC 0.314233 0 NC 0.5 -0.2 NC 0.977398 0.3 NC 0.12385 0.1 NC 0.5 0 NC 0.5 0.3 NC 0.206131
AFFX-BioDn-5_at 0.2 NC 0.5 0.3 NC 0.0873 -0.1 NC 0.631577 -0.1 NC 0.5 0.4 I 0.000028 0.2 NC 0.5 0 NC 0.5 0.5 I 0.000098
AFFX-BioDn-3_at 0.4 MI 0.005977 0.4 I 0.000008 0.1 NC 0.5 -0.1 NC 0.5 0.5 I 0.000003 0.3 NC 0.5 0.2 NC 0.5 0.4 NC 0.02189
AFFX-CreX-5_at 0.5 NC 0.011969 0.4 NC 0.009673 0.1 NC 0.5 0 NC 0.5 0.4 I 0.000001 0.2 NC 0.5 0.1 NC 0.5 0.3 NC 0.007216
AFFX-CreX-3_at 0.4 NC 0.09615 0.1 NC 0.5 0.2 NC 0.295409 0 NC 0.5 0.4 I 0.000008 0.2 NC 0.5 0.1 NC 0.5 0.3 NC 0.005977
AFFX-DapX-5_at -0.9 D 1 -0.8 D 1 -0.8 D 1 -0.8 D 1 0.3 I 0.000005 0.1 NC 0.5 0 NC 0.5 0.3 NC 0.011556
AFFX-DapX-M_at -0.6 D 0.999983 -0.4 D 0.999916 -0.5 D 1 -0.6 D 1 0.5 I 0 0.3 NC 0.5 0.2 NC 0.5 0.5 I 0
AFFX-DapX-3_at -0.2 D 0.999896 -0.3 D 0.999971 -0.4 D 1 -0.5 D 1 0.4 I 0 0.2 NC 0.5 0.2 NC 0.5 0.4 I 0
AFFX-LysX-5_at 0.2 NC 0.5 0.2 NC 0.108118 0.1 NC 0.5 0.1 NC 0.5 0.3 NC 0.008366 0.3 NC 0.309479 0.1 NC 0.5 0.4 I 0.000001
AFFX-LysX-M_at 0.3 NC 0.242292 0.3 MI 0.005125 0.2 NC 0.221792 0.1 NC 0.5 0.2 NC 0.156704 -0.9 NC 0.5 0.9 NC 0.358334 1 NC 0.09615
AFFX-LysX-3_at 0.3 NC 0.467861 0.2 NC 0.098462 0.1 NC 0.5 0.1 NC 0.5 0.4 I 0.000305 0.1 NC 0.404412 0.1 NC 0.5 0 NC 0.611131
AFFX-PheX-5_at 0.4 NC 0.024085 0.3 NC 0.009331 0.2 NC 0.009331 0.2 NC 0.225811 0.1 NC 0.085186 0.2 NC 0.605968 0.2 NC 0.5 0.1 NC 0.5
AFFX-PheX-M_at 0.4 NC 0.053377 0.3 I 0.00006 0.2 NC 0.069631 0.2 NC 0.5 0.1 NC 0.5 0.4 NC 0.129434 0.3 NC 0.5 0.1 NC 0.5
AFFX-PheX-3_at 0.5 NC 0.008999 0.4 I 0.000158 0.3 MI 0.005125 0.2 NC 0.014228 0.1 NC 0.478561 0.3 NC 0.5 0.2 NC 0.5 0.1 NC 0.5
AFFX-ThrX-5_at -2.6 D 0.998378 -0.6 NC 0.989608 -1.4 D 0.99999 -2.9 D 0.99975 0.1 NC 0.295409 -1.1 NC 0.5 1.3 NC 0.5 1.7 NC 0.018607
AFFX-ThrX-M_at -0.7 D 0.999004 -0.6 D 0.999208 -0.9 D 1 -0.6 D 0.999929 0.1 NC 0.118437 0 NC 0.5 0.2 NC 0.373502 0.3 NC 0.08311

Total number of rows: 22814

Table truncated, full table size 1921 Kbytes.




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