|
Status |
Public on Jun 14, 2010 |
Title |
WT_EXP_2_(369194) |
Sample type |
mixed |
|
|
Channel 1 |
Source name |
amplified root cDNA.
|
Organism |
Arabidopsis thaliana |
Characteristics |
tissue: root (root hair zone) cell line: Col-0
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA isolation was done with Qiagen RNeasy micro kit. cDNA preparation and amplification were done with the Sigma WTA2 kit.
|
Label |
Cy3
|
Label protocol |
Standard NimbleGen protocol using 5 hour labeling reaction rather than 2 hour reaction.
|
|
|
Channel 2 |
Source name |
Fragmented genomic DNA.
|
Organism |
Arabidopsis thaliana |
Characteristics |
tissue: root (root hair zone) cell line: Col-0
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was isolated with the Qiagen Plant Dneasy mini kit and fragmented by sonication.
|
Label |
Cy5
|
Label protocol |
Standard NimbleGen protocol using 5 hour labeling reaction rather than 2 hour reaction.
|
|
|
|
Hybridization protocol |
Standard NimbleGen protocol.
|
Scan protocol |
Standard NimbleGen protocol.
|
Description |
Expression profiling of total RNA from the root hair zone.
|
Data processing |
Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy3/Cy5 were computed. Then the log ratios for up to 100 exonic probes starting from the 3' ends of TAIR8 genes were averaged to give a single expression value for each gene in the supplementary file WT_EXP_2.dat . The supplementary files WT_EXP_2.gff and WT_EXP_2.bedgraph contain the bi-weight mean adjusted log base 2 ratios.
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|
|
Submission date |
Jun 08, 2010 |
Last update date |
Apr 18, 2012 |
Contact name |
Jorja Henikoff |
E-mail(s) |
jorja@fhcrc.org
|
Phone |
206-667-4850
|
Organization name |
Fred Hutchinson Cancer Research Center
|
Department |
Basic Sciences
|
Lab |
Henikoff
|
Street address |
1100 Fairview AV N, A1-162
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98109-1024 |
Country |
USA |
|
|
Platform ID |
GPL7143 |
Series (1) |
GSE19654 |
INTACT method for gene expression and chromatin profiling of individual cell types within a tissue |
|