|
| Status |
Public on Jul 24, 2007 |
| Title |
Uterus_Gravid_d18_Cox-1 KO-rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Gravid day 18.0 Cox-1 KO Uterus
|
| Organism |
Mus musculus |
| Characteristics |
Strain: C57BL/6 x Sv129, Gender: female, Age 6-16 weeks, Tissue: Gravid day 18.0 Cox-1 KO Uterus
|
| Biomaterial provider |
Kathy Bethin
|
| Treatment protocol |
Rinsed in PBS in DEPC, Snap frozen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extracted, followed by RNeasy
|
| Label |
Biotinylated
|
| Label protocol |
Five micrograms of total RNA was labeled following single cycle protocols recommended in the GeneChip Expression Analysis Technical Manual. The cDNA was synthesized from RNA using a T7 promoter-dT24 oligonucleotide primer with the Invitrogen Life Technologies SuperScript Choice system. After the second strand synthesis and incubation with T4 DNA polymerase the products were purified using an Affymetrix Cleanup Module. Biotynylated cRNA was made using the Affymetrix IVT kit. The cRNA was purified with Qiagen RNeasy columns, quantitated and then fragmented at high temperature with magnesium.
|
| |
|
| Hybridization protocol |
Fifteen micrograms of biotinylated cRNA was added to a total hybridization cocktail of 300 microliters and 200 microliters was hybridized to a 430 2.0 GeneChip at 45º for 17 h with constant rotation. The GeneChips were washed, stained with phycoerythrin-labeled streptavidin, washed, incubated with biotinylated anti-streptavidin and then restained with phycoerythrin-lableled streptavidin to amplify the signals, all following the standard Affymetrix protocol.
|
| Scan protocol |
GeneChips were then scanned using a dedicated scanner controlled by Affymetrix GCOS software. The images were examined for defects and the hybridization intensity data was analyzed with the Affymetrix Microarray Suite version 5 (MAS5).
|
| Description |
The Center for Medical Genomics Core at Indiana University School of Medicine analyzed the RNA using Affymetrix 430 2.0 GeneChips.
|
| Data processing |
The images were examined for defects and the hybridization intensity data was analyzed with the Affymetrix Microarray Suite version 5 (MAS5). MAS5 calculated a set of metrics that describe probe performance. The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were imported into the MicroArray Data Portal for further analysis. All genes included in the analysis had to have a “present” call in at least 50% of the samples.
|
| |
|
| Submission date |
Jun 24, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Kathleen Bethin |
| E-mail(s) |
kbethin@iupui.edu
|
| Phone |
317-278-9329
|
| Fax |
317-274-5378
|
| Organization name |
Indiana University
|
| Department |
Pediatrics
|
| Lab |
Bethin
|
| Street address |
702 Barnhill Dr.
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE8269 |
Uterus_Gravid_d18_WT vs. Cox-1 KO |
|
| Relations |
| Reanalyzed by |
GSE119085 |
