|
| Status |
Public on Sep 10, 2016 |
| Title |
unc-4 ISOLATED GONADS 2 |
| Sample type |
RNA |
| |
|
| Source name |
unc-4 ISOLATED GONADS
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: gonad
genotype: unc-4(e120)(II)
strain used - lab list codes or cgc strain names: #860
|
| Treatment protocol |
RNA was extracted from isolated gonads of hermaphrodite worms. The age of the worms was 1,5 days after reaching adulthood.
|
| Growth protocol |
Standard procedures were used to maintain animals. Worms were grown at 25°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PicoPure RNA Isolation Kit (Applied Biosystems) according to the manufacturer’s recommendations.
|
| Label |
biotin
|
| Label protocol |
Affymetrix GeneChip WT Amplified Double Stranded cDNA Synthesis Kit according to the manufacturer’s instructions. The Affymetrix GeneChip WT Double-Stranded cDNA Terminal Labeling Kit was used for the fragmentation and labeling of 7.5 microg cDNA
|
| |
|
| Hybridization protocol |
labeled material was loaded onto Affymetrix GeneChip C. elegans Tiling 1.0R Arrays and hybridized at 65ºC for 16 h. The arrays were washed in an Affymetrix Fluidics station with the protocol FS450_0001.
|
| Scan protocol |
Affymetrix GeneChip Scanner 3000 with autoloader using Affymetrix GCC Scan Control v. 3.0.0.1214 software.
|
| Description |
RNA was purified from isolated gonads
gonadal RNA extract
|
| Data processing |
All tiling arrays were processed in R using bioconductor and the packages tilingArray and preprocessCore. The arrays were RMA background corrected and log2 transformed on the oligo level using the following command: expr <- log2(rma.background.correct(exprs(readCel2eSet(filenames,rotated=TRUE)))). We mapped the oligos from the tiling array (bpmap file from www.affymetrix.com) to the c.elegans genome assembly ce6 (www.genome.ucsc.edu) using bowtie allowing no error and unique mappig position. Expressions for individual transcripts were calculated by intersecting the genomic positions of the oligos with transcript annotation (WormBase WS190) and averaging the intensity of the respective oligos.
probeId_to_tr_min10probes, expr_RMA_TR_Notch, expr_RMA_TR_meses, Table_S1
probeId_to_tr_min10probes contains the microarray positions, expr_RMA_TR_Notch, expr_RMA_TR_meses are our annotation files with the expression data, Table_S1 contains the fold changes
|
| |
|
| Submission date |
Jul 31, 2013 |
| Last update date |
Sep 10, 2016 |
| Contact name |
Rafal Ciosk |
| E-mail(s) |
rafal.ciosk@fmi.ch
|
| Phone |
+41616975203
|
| Organization name |
Friedrich Miescher Institute
|
| Lab |
Ciosk
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| State/province |
Schweiz |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL5634 |
| Series (1) |
| GSE49395 |
Genome-wide profiling of C. elegans gonadal RNA |
|
