|
| Status |
Public on Sep 21, 2010 |
| Title |
GLD-2 gld-2(RNAi)-IP, biological replicate 4 |
| Sample type |
RNA |
| |
|
| Source name |
C. elegans gld-2(RNAi) adult extracts used to immunoprecipitate GLD-2
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: gld-2(RNAi)
developmental stage: adult
gender: hermaphrodite
tissue: whole animal
sample type: RNA from GLD-2 immunoprecipitation
antibody: anti-GLD-2
|
| Treatment protocol |
Adults were washed extensively and used to prepare extracts
|
| Growth protocol |
Synchronized adults were grown at 20C until 15 hours after L4 stage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol followed by RNeasy MinElute columns (Qiagen), following the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNAs were prepared using the MessageAmp Biotin-II Enhanced kit (Ambion) according the manufacturer's instructions from 1ug total RNA or up to 200 ng coimmunoprecipitated RNA
|
| |
|
| Hybridization protocol |
Following fragmentation, 100% or up to 10 µg of amplified RNA (aRNA) were hybridized in the GeneChip 640 Hybridization Oven (Affymetrix). GeneChips were washed and stained in GeneChip Fluidics Station 450 (Affymetrix) .
|
| Scan protocol |
Arrays were scanned using GC3000 G7 scanner (Affymetrix)
|
| Description |
mRNA associated with GLD-2
|
| Data processing |
The data were analyzed with GeneChip Operating Software (GCOS) v.1.4. For IP samples, the data were scaled based on the control AFFX probe sets and the trimmed mean target intensity of each array was arbitrarily set to 5000. For total RNA samples, global scaling was applied and the trimmed mean target intensity of each array was arbitrarily set to 1000.
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| |
|
| Submission date |
Aug 27, 2010 |
| Last update date |
Sep 21, 2010 |
| Contact name |
Judith Kimble |
| E-mail(s) |
jekimble@wisc.edu
|
| Phone |
608-262-6188
|
| Fax |
608-265-5820
|
| Organization name |
University of Wisconsin-Madison
|
| Department |
HHMI / Biochemistry
|
| Street address |
433 Babcock Drive
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706-1544 |
| Country |
USA |
| |
|
| Platform ID |
GPL200 |
| Series (1) |
| GSE23843 |
RIP-chip analysis of the C. elegans GLD-2 and RNP-8 protein |
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