|
| Status |
Public on Nov 26, 2010 |
| Title |
yeast_genomic_DNA_Repl4 |
| Sample type |
genomic |
| |
|
| Source name |
wild-type genomic RNA
|
| Organism |
Saccharomyces |
| Characteristics |
strain: BY4741
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nascent RNA: Yeast cells were grown at 30C until reaching exponential phase. Cells were rapidly frozen. A chromatin fraction was generated and nascent RNA isolated by phenol-chloroform extraction. mRNA: Yeast cells were grown at 30C until reaching exponential phase. Total RNA was isolated (Ribo-Pure Yeast Kit, Ambion) and polyadenylated mRNA extracted (MicroPoly(A)Purist Kit, Ambion). Genomic DNA: Genomic DNA was extracted by phenol-chloroform digestion. Contaminating RNA was removed by enzymatic digestion.
|
| Label |
biotin
|
| Label protocol |
RNA samples were reversed transcribed (GeneChip Whole Transcript Sense Labeling Kit, Affymetrix), enzymatically fragmented and end-labeled (GeneChip Double-Stranded DNA Terminal Labeling Kit, Affymetrix). Genomic DNA samples were enzymatically fragmented and end-labeled (GeneChip Double-Stranded DNA Terminal Labeling Kit, Affymetrix).
|
| |
|
| Hybridization protocol |
For each sample 7.5µg of DNA probes were hybridized using the Affymetrix hybridization kit. Hybridization was performed for 16h at 45°C (Affymetrix GeneChip Hybridization Oven 645).
|
| Scan protocol |
Arrays were scanned on an Affymetrix Scanner 3000.
|
| Description |
Saccharomyces genomic DNA preparation Replicate 4
|
| Data processing |
Raw intensities were extracted from the CEL files. Genomic positions and sequences were allocated for each intensity using the bpmap file. Log10 Intensities for perfect match (pm) and mismatch (mm) were generated. Difference of pm and mm was calculated for each microarray spot. All analysis was performed by user-written software.
results file descriptions: For each chromosomal probe present on the array, chromosome (chrID), chromosomal position (pos), Log10 intensity of perfect match probes (logipm) and mismatch probe (logimm) is given. Furthermore the difference between perfect match and mismatch intensity (gLog(pm-mm)) as well as probe sequence is listed.
|
| |
|
| Submission date |
Sep 08, 2010 |
| Last update date |
Nov 26, 2010 |
| Contact name |
Fernando Carrillo Oesterreich |
| Organization name |
MPI-CBG
|
| Lab |
Neugebauer
|
| Street address |
Pfotenhauerstr. 108
|
| City |
Dresden |
| ZIP/Postal code |
01099 |
| Country |
Germany |
| |
|
| Platform ID |
GPL7250 |
| Series (1) |
| GSE24040 |
Genome wide analysis of Saccharomyces nascent RNA |
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