|
| Status |
Public on Jun 18, 2012 |
| Title |
MYC IP_2 |
| Sample type |
RNA |
| |
|
| Source name |
MYC IP
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype/variation: wild type
developmental stage: young adult
tissue: whole worm lysate
ip antibody: anti-myc 9E10
|
| Treatment protocol |
Worm lysates were prepared in extraction buffer and subjected to IP.
|
| Growth protocol |
Worms were grown until the young adult stage, and washed and frozen in M9.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from was extracted using Trizol.
|
| Label |
biotin
|
| Label protocol |
RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix, fragmented and Biotin labeled using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization was performed overnight for 16 h in a GeneChip hybridization oven (Affymetrix).
|
| Scan protocol |
Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader.
|
| Description |
The anti-myc 9E10 antibody was used as a cell culture supernatant obtained by growing the 9E10 hybridoma cell line by the in house facility: Wright et al., 2011.
SAMPLE 2
|
| 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.
probe group file : probeId_to_tr_min10probes.tab
|
| |
|
| Submission date |
Oct 19, 2011 |
| Last update date |
Jun 18, 2012 |
| Contact name |
Dimos Gaidatzis |
| E-mail(s) |
d.gaidatzis@fmi.ch
|
| Organization name |
Friedrich Miescher Institute
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL5634 |
| Series (2) |
|
