|
| Status |
Public on Oct 01, 2010 |
| Title |
larve 3-1 |
| Sample type |
RNA |
| |
|
| Source name |
larve 3-1
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
tissue: whole worm
developmental stage: larva 3
|
| Treatment protocol |
Dauer worms were induced by growing mixed-stage N2 worms grown in liquid medium for 7-9 days at 20ºC until dauers had become plentiful. The culture was then washed with 0.1M NaCl and floated on sucrose for several times, and dauers were purified by treating with 1% SDS for 15-30 min, followed by 3 times of sucrose floatation. Heatshock worms were obtained by subjecting 60h worms to 30ºC for 3h. All developmental stages were determined by time of culture since feeding of L1s worms at 20ºC.
|
| Growth protocol |
L1 stage, 13 hours after L1s; L2 stage, 22 hours after L1s; L3 stage, 32 hours after L1s; L4 stage, 44 hours after L1s; Heatshock stage, 60 hours after L1s.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted at each of the 6 different developmental stages and environmental conditions according to the Trizol (Invitrogen) protocol. Small RNAs (70-500nt) were isolated using a QIAGEN tip (QIAGEN), and remaining rRNAs were removed by adapting the MicrobExpress kits (Ambion). The enriched ncRNAs were dephosphorylated with CIAP (Fermentas) and then ligated to the 3’-adaptor oligonucleotide by T4 RNA ligase (Fermentas). Each RNA sample was reverse transcribed using random hexamers and a primer complementary to the 3’-adaptor.
|
| Label |
Biotin
|
| Label protocol |
Standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
Standard Affymetrix protocol
|
| Scan protocol |
Standard Affymetrix protocol
|
| Description |
larve 3-1
|
| Data processing |
The data is processed by Affymetrix Tiling Analysis Software (TAS, version 1.1.02), and the produced bed files were combined with the signal files, and mapped to UCSC ce6
Affymetrix Tiling Analysis Software (TAS, version 1.1.02) processed with windowsize=100, maxgap=30 and minrun=70 and quantile normalized.
|
| |
|
| Submission date |
Sep 08, 2010 |
| Last update date |
Sep 13, 2010 |
| Contact name |
Yunfei Wang |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Biophysics, Chinsese Academy of Sciences
|
| Street address |
Chaoyang District, Datun Road, No. 15
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL5634 |
| Series (1) |
| GSE24023 |
Expression profile analysis of C. elegans intermediate sized non-coding transcriptome |
|
