|
| Status |
Public on Nov 05, 2013 |
| Title |
mes-4_3 |
| Sample type |
RNA |
| |
|
| Source name |
mes-4(ok2326) C.elegans germline
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype/variation: mes-4(ok2326)
gender: hermaphrodite
|
| Treatment protocol |
Germlines were dissected in 1X egg buffer to excise the germline including mitotic tip through meiotic late pachytene 24 hours after L4 stage.
|
| Growth protocol |
Strains for germline were cultured at 20C, using standard methods.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Germline RNA was isolated as described in Chi and Reinke (2006), and linearly amplified once using MessageAmp II aRNA Amplification Kit (Ambion).
|
| Label |
biotin
|
| Label protocol |
aRNA was labeled with biotinylated UTP using the MessageAmp II aRNA Amplification Kit (Ambion).
|
| |
|
| Hybridization protocol |
aRNA probes of three replicates were hybridized to GeneChip C. elegans genome arrays (Affymetrix). Probe-preparation, hybridization, and scanning of microarray were performed at the Genomics Core facility at University of Massachusetts Medical School.
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Description |
mes-4(ok2326) dissected germline 3
|
| Data processing |
Statistical analyses were performed using custom scripts and packages in R (http://www.r-project. org) and Bioconductor (Gentleman et al., 2004). The affy package was used to quantile normalize the data across replicates and the Robust Multichip Average (RMA) algorithm was used to obtain probe-set expression values (Irizarry et al.,2003). Log2 transformed data were used in subsequent analysis and plotting. Statistical analysis for misexpression was performed using the moderated t-test from the Bioconductor package limma (Smyth. 2004). Statistical significance of mis-expression (False Discovery Rate) was obtained with the qvalue package (Storey et at., 2003).
|
| |
|
| Submission date |
Nov 04, 2013 |
| Last update date |
Nov 05, 2013 |
| Contact name |
Susan Strome |
| E-mail(s) |
sstrome@ucsc.edu
|
| Organization name |
UC Santa Cruz
|
| Department |
MCD Biology
|
| Street address |
1156 High St
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL200 |
| Series (1) |
| GSE52064 |
DRM complex mutant lin-54 vs. H3K36 methyltransferase mutant mes-4 vs. lin-54; mes-4 double mutant vs. wild type C.elegans germline |
|
