|
| Status |
Public on Aug 11, 2010 |
| Title |
LDmuscle_96_G |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
LDmuscle_1798
|
| Organism |
Sus scrofa |
| Characteristics |
selectioncriteria_status: bf_L
litter number: 96
gender: female
phenotype: back fat depth at the 10th rib
|
| Growth protocol |
detailed growth protocol can be found in J. Anim Sci. 2008. 86:241-253.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 1.0 g of tissue was extracted using TRIzol reagent (Invitrogen Corp., Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA concentration and quality were determined with an RNA 6000 Pico LabChip® kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Palo Alto, CA, USA).
|
| Label |
cy3
|
| Label protocol |
Five µg of total RNA were reverse transcribed with a T7 oligo(dT) primer using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer’s instructions. Following first-strand and second-strand synthesis and purification, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs. After purification, aRNAs were labeled with N-hydroxysuccinate (NHS) ester Cy3 or Cy5 (GE Healthcare, UK).
|
| |
|
| Channel 2 |
| Source name |
LDmuscle_1800
|
| Organism |
Sus scrofa |
| Characteristics |
selectioncriteria_status: bf_H
litter number: 96
gender: female
phenotype: back fat depth at the 10th rib
|
| Growth protocol |
detailed growth protocol can be found in J. Anim Sci. 2008. 86:241-253.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 1.0 g of tissue was extracted using TRIzol reagent (Invitrogen Corp., Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA concentration and quality were determined with an RNA 6000 Pico LabChip® kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Palo Alto, CA, USA).
|
| Label |
cy5
|
| Label protocol |
Five µg of total RNA were reverse transcribed with a T7 oligo(dT) primer using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer’s instructions. Following first-strand and second-strand synthesis and purification, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs. After purification, aRNAs were labeled with N-hydroxysuccinate (NHS) ester Cy3 or Cy5 (GE Healthcare, UK).
|
| |
|
| |
| Hybridization protocol |
Labeled aRNAs were purified and combined with 65 µl of Slide Hyb #1 solution (Ambion, Inc.) and denatured at 70C for 5 min. Hybridizations were performed in sealed hybridization cassettes (ArrayIt, TeleChem International, Inc., Sunnyvale, CA, USA) for 18 h at a humid 54C. Following hybridization, slides were washed in 2X SSC/0.5% SDS and 0.1X SSC/0.1% SDS solutions for 10 min each. The slides were rinsed in a 0.1X SSC solution and nuclease-free water and dried by centrifugation.
|
| Scan protocol |
Fluorescent images were detected by a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) and fluorescence intensity data were collected using GenePix software (Molecular Devices) after spot alignment. Median intensity values for each dye channel were stored as comma-separated values data files.
|
| Description |
LD MUSCLE EXPRESSION PRP title indicates litter (number) and sex (G=female, B=male)
|
| Data processing |
Bioconductor package Marray was used for pre-processing. Values are log2 ratio Cy3/Cy5.
|
| |
|
| Submission date |
Jul 30, 2010 |
| Last update date |
Aug 10, 2010 |
| Contact name |
juan p steibel |
| E-mail(s) |
[email protected]
|
| Organization name |
Michigan State University
|
| Street address |
1205 I Anthony Hall
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48842 |
| Country |
USA |
| |
|
| Platform ID |
GPL7435 |
| Series (1) |
| GSE23351 |
Genome-wide linkage analysis of global gene expression of loin muscle tissue identifies putatively cis-acting candidate genes in pigs |
|
