|
| Status |
Public on Jun 14, 2010 |
| Title |
NUC_EXP_2_(369136) |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
amplified nuclear cDNA.
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: root (root hair zone)
cell line: Col-0
|
| Extracted molecule |
nuclear 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 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 nuclear 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 NUC_EXP_2.dat . The supplementary files NUC_EXP_2.gff and NUC_EXP_2.bedgraph contain the bi-weight mean adjusted log base 2 ratios.
|
| |
|
| 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 |
|
