|
| Status |
Public on Sep 02, 2010 |
| Title |
N2_embryo_totalRNA_replicate2 |
| Sample type |
RNA |
| |
|
| Source name |
mixed stage embryos from N2
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
developmental stage: mixed embryos
|
| Growth protocol |
Embryos were prepared by bleaching from gravid adults grown in standard S-basal media liquid culture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1V sample in 10V Trizol that was stored at -80C was thawed at 37C, vortexed 30 seconds and re-frozen in liquid nitrogen. Freeze-cracking was repeated a total of four times. 1/5 V chloroform was added and vortexed for 30 seconds. After centrifugation at 13000 rpm for 5 minutes, aqueous phase containing RNA was recovered. RNA was precipitated by mixing with 0.8V isopropanol and incubation on ice, followed by centrifugation at 13000 rpm at 4C for 20 minutes. RNA was washed with 75% ethanol, dissolved in DEPC H2O and cleaned up using Qiagen RNeasy kit.
|
| Label |
Cy3
|
| Label protocol |
Cy3 Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.http://www.nimblegen.com/products/lit/index.html
|
| Description |
Gene expression data from mixed stage embryos isolated from N2 strain.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Sep 02, 2010 |
| Last update date |
Sep 02, 2010 |
| Contact name |
Jason D Lieb |
| E-mail(s) |
jlieb@bio.unc.edu
|
| Phone |
919-843-3228
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Biology
|
| Lab |
Jason Lieb
|
| Street address |
408 Fordham Hall, CB# 3280
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-3280 |
| Country |
USA |
| |
|
| Platform ID |
GPL8673 |
| Series (1) |
| GSE20136 |
Genome-wide nucleosome occupancy profiling by high throughput sequencing, and microarray analysis of RNA abundance |
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