|
| Status |
Public on Apr 01, 2014 |
| Title |
579_254451610098 |
| Sample type |
RNA |
| |
|
| Source name |
M. longissimus dorsi_LO
|
| Organism |
Sus scrofa |
| Characteristics |
drip loss phenotype: low (LO)
Sex: male
batch: 18
tissue: muscle sample of M. longissimus dorsi
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the miRNeasy Kit (Qiagen, 217004) following the manufacturer's recommendations. The protocol includes on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies)
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared using Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v6.5, May 2010), followed by ? RNAeasy column purification (Qiagen, 4106)
|
| |
|
| Hybridization protocol |
Hybridization were made in house using Tecan HS400 Pro (Tecan Group Ltd., Switzerland) according to Agilent's protocol.
|
| Scan protocol |
Processed arrays were scanned using Tecan PowerScanner (Tecan Group Ltd., Switzerland). Array signal intensities and local backgrounds were then summarized using Array-Pro Analyzer 6.3 (Meida Cybernetics Inc., USA), with potentially unreliable spots marked for removal.
|
| Description |
254451610098-532-Area1-B18-2013-05-29
|
| Data processing |
Previously marked spots were first removed across samples. Then local background were subtracted before vsn normalization using spike-in controls. As the last step, signals are corrected for batch effect using ComBat.
|
| |
|
| Submission date |
Nov 14, 2013 |
| Last update date |
Apr 01, 2014 |
| Contact name |
Klaus Wimmers |
| Organization name |
Leibniz Institute for Farm Animal Biology
|
| Street address |
Wilhelm-Stahl-Allee 2
|
| City |
Dummerstorf |
| State/province |
Mecklenburg-Vorpommern |
| ZIP/Postal code |
18196 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17683 |
| Series (2) |
| GSE52383 |
Transcriptome profiling of pig chromosomes regions associated with water holding capacity [PiF1]. |
| GSE52384 |
Transcriptome profiling of pig chromosomes regions associated with water holding capacity |
|
