|
| Status |
Public on Dec 30, 2008 |
| Title |
hrp48 bound RNA |
| Sample type |
RNA |
| |
|
| Source name |
hrp48 nuclear RNPs (3 replicates)
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Nuclear RNP enriched extract from SL2 cells
Nuclear extract from cell culture
|
| Treatment protocol |
The extracts used for the immunopurification come from nuclear enriched RNP fraction.
|
| Growth protocol |
Exponentiaolly growing SL2 cells in Schneider's media supplemented with 10% FBS where used to prepare nuclear RNP extract (Olson et al., 2007, NSMB. PMID: 18059285)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A description of the immuno-purification can be found in Olson et al., 2007, NSMB. PMID: 18059285. The RNA was purified using Quiagen RNAeasy kit following manufacturer protocol (Qiagen)
|
| Label |
biotin
|
| Label protocol |
GeneChip® WT Double-Stranded cDNA Synthesis Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Recommended Affymetrix protocol
|
| Scan protocol |
The microarrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to the manual
|
| Description |
Sample arrays:
H48_IP_L2-1.CEL
H48_IP_L2-2.CEL
H48_IP_L2-3.CEL
Control arrays:
Total_L2_RNP-1.CEL
Total_L2_RNP-2.CEL
FDR evaluation arrays:
IgG_IP_L2-1.CEL
IgG_IP_L2-2.CEL
IgG_IP_L2-3.CEL
|
| Data processing |
The processed sgr data files were generated from the Affymetrix cel files using the TiMAT programs developed by the Berkeley Drosophila Transcription Network Project (http://bdtnp.lbl.gov/TiMAT/TiMAT2/index.html). The probe intensities for all immunoprecipitation and control (input and/or mock) cel files in each hybridization set (each sample is a hybridization set) were normalized using median scaling and assigned to a genome position using a tpmap file based on the April 2004 release of the Drosophila melangaster genome sequence (Berkeley Drosophila Genome Project). The relative immunoprecipitation and control sample normalized intensities were used to generate scores for the microarray features.
|
| |
|
| Submission date |
Dec 14, 2008 |
| Last update date |
Dec 29, 2008 |
| Contact name |
Marco Blanchette |
| E-mail(s) |
[email protected]
|
| Phone |
415-272-4837
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Marco Blanchette
|
| Street address |
1000 E. 50th St.
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL5919 |
| Series (2) |
| GSE13940 |
Genome-wide analysis of alternative pre-mRNA splicing of the Drosophila hnRNP A/B family members |
| GSE13941 |
RIP_Chip_analysis |
|
