|
| Status |
Public on Dec 08, 2016 |
| Title |
glp-4(bn2); let-7(wild-type)_3 |
| Sample type |
RNA |
| |
|
| Source name |
staged L4 worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: glp-4(bn2); let-7(wild-type)
|
| Treatment protocol |
whole worms were harvested in M9 and transferred to TRI Reagent (MRC)
|
| Growth protocol |
Worms were grown until the late L4 stage (glp-4(bn2); let-7(wild-type): 33h 25°C; glp-4(bn2); let-7(mn112): 34h 25°C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRI Reagent (MRC)
|
| Label |
biotin
|
| Label protocol |
RNA was processed according to the Affymetrix GeneChip WT Amplified Double Stranded cDNA Synthesis Kit, fragmented with the Affymetrix GeneChip WT Double-Stranded DNA Terminal Labeling Kit and Biotin labeled using the GeneChip WT Genechip WT Terminal Labeling Kit
|
| |
|
| 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
|
| 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 |
Dec 09, 2014 |
| Last update date |
Dec 08, 2016 |
| 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 (1) |
| GSE64024 |
mRNA expression analysis in glp-4(bn2); let-7(wild-type) and glp-4(bn2); let-7(mn112) animals |
|
