|
| Status |
Public on Mar 02, 2013 |
| Title |
RIL TK175, wet treatment |
| Sample type |
RNA |
| |
|
| Source name |
Leaf_wet treatment
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
recombinant inbred line (ril) from: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)
tissue: leaf
|
| Treatment protocol |
Wet treatment was well watered to 100% field capacity. Dry treatment experienced 6 day drydown to 40% of field capacity.
|
| Growth protocol |
Grown in 2.5-inch pots in fritted clay. Daylength: 12 hours. Light period: 23°C and 40% humidity. Dark period: 20°C and 50% humidity. Light intensity: 330 µmol m-2 s-1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue preserved in RNAlater (Ambion, Inc.) and stored at -80°C. Extraction by RNeasy Plant Mini Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
7ug of RNA was converted without amplification to cDNA using GeneChip Whole Transcript (WT) Double-Stranded cDNA Synthesis Kit (Affymetrix). Fragmentation and end labeling with biotin were carried out using the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization to atSNPTILE array (Affymetrix) by proprietary Asuragen protocols using a GeneChip Fluidics Station 450 (Affymetrix)
|
| Scan protocol |
Scan by proprietary Asuragen protocols using a GeneChip Scanner 3000 7G
|
| Description |
TK175_wet
|
| Data processing |
CEL file data were processed in JMP Genomics using log2 transformation and quantile normalization of probe intensities. Mean summary of probesets (defined by a custom CDF file based on TAIR version 9) were calculated for genes with three or more nonpolymorphic probes.
|
| |
|
| Submission date |
Nov 20, 2012 |
| Last update date |
Mar 02, 2013 |
| Contact name |
David Bryant Lowry |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Texas at Austin
|
| Department |
Integrative Biology
|
| Lab |
Thomas Juenger
|
| Street address |
1 University Station #C0930
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL16303 |
| Series (1) |
| GSE42408 |
EXPRESSION QTL MAPPING ACROSS SOIL MOISTURE ENVIRONMENTS REVEALS CONTRASTING ASSOCIATIONS WITH GENOMIC FEATURES IN ARABIDOPSIS THALIANA |
|
