|
| Status |
Public on Sep 17, 2019 |
| Title |
Stroma close to follicle_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
ovarian follcular thecal tissue
|
| Organism |
Bos taurus |
| Characteristics |
tissue: ovary
compartment: ovarian stroma close to follicle
|
| Treatment protocol |
For laser capture and microarray analyses of pre-theca, interstitium and tunica albuginea, strips of ovarian cortex were cut from each ovary and placed surface-side down into cryomolds containing optimal cutting temperature (OCT) compound, frozen on dry ice and stored at −80°C. 10 μm thick serial sections were placed onto room temperature PET (polyethylene terephthalate) membrane frame slides, then fixed with 70% ethanol and stained with cresyl violet. During laser-microdissection excised samples were collected into 25 μL of Ambion lysis solution for RNA isolation (Invitrogen).
|
| Growth protocol |
Bovine ovaries (one per animal) were collected at a local abattoir from non-pregnant Bos taurus cows.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from thecal samples using RNeasy mini kits (Qiagen). Total RNA was extracted from the laser-dissected samples using the RNAqueous®-Micro Kit (Cat# AM1931, Thermo Fisher Scientific) procedure for LCM. All samples were treated with DNase I. And all samples were then amplified and cDNA generated with the Ovation® Pico WTA System V2 (NuGEN, San Carlos, CA, USA) from an original amount of 5 μL each of 100–200 pg/μL per sample.
|
| Label |
biotin
|
| Label protocol |
cDNA was fragmented and labelled using the Encore Biotin Module kit (NuGEN) and used to hybridise against each array.
|
| |
|
| Hybridization protocol |
Hybridization to bovine gene 1.0 ST Arrays (Affymetrix) was performed according to Affymetrix protocols at the Ramaciotti Centre for Genomics.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from ovarian stroma
|
| Data processing |
The data were analysed in Partek Genomics Suite (v6.5) using RMA (Robust Multi Array Algorithm, Irizarry et al 2003) background corrrection with quantile normalization, mean probe set summarization and adjustment for GC content.
|
| |
|
| Submission date |
Sep 16, 2019 |
| Last update date |
Sep 17, 2019 |
| Contact name |
Katja Hummitzsch |
| E-mail(s) |
katja.hummitzsch@adelaide.edu.au
|
| Organization name |
The University of Adelaide
|
| Department |
Obstetrics& Gynaecology
|
| Lab |
Katja Hummitzsch
|
| Street address |
Level 5, North Tce/George Street
|
| City |
Adelaide |
| State/province |
SA |
| ZIP/Postal code |
5005 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16500 |
| Series (1) |
| GSE137471 |
Transcriptome analyses of ovarian stroma: tunica albuginea, interstitium and theca interna |
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