|
| Status |
Public on Sep 02, 2010 |
| Title |
XO_hermaphrodite_L3_totalRNA_replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
L3 worms from TY2205
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: TY2205
developmental stage: L3 larval stage
|
| Growth protocol |
Worms were grown in standard S-basal media liquid culture. TY2205 (her-1(e1520) sdc-3(y126) V; xol-1(y9) X) were grown at 20C and bleached for embryos. Embryos were starved to L1, and filtered through 20uM Nitex memberane to remove dead embryos. L1s were fed and grown in 20C liquid culture until most were L3. Worms were collected and washed with M9 and PBS. Worms were resuspended in 1 pellet volume of PBS+ protease inhibitors (Calbiochem) and frozen as ÒpopcornÓ in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1V sample (frozen powdered worm) in 10V Trizol that was stored at -80C was thawed at 37C. 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 L3 XO hermaphrodites.
|
| 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 |
|
