|
| Status |
Public on Aug 27, 2015 |
| Title |
3 m. endometriosis_2 |
| Sample type |
RNA |
| |
|
| Source name |
Induced endometriosis at 3 months
|
| Organism |
Papio anubis |
| Characteristics |
animal_id: 7022
Sex: female
tissue: eutopic endometrium
|
| Treatment protocol |
Eutopic endometrial tissues were harvested between days 9-11 postovulation and were snap frozen in liquid nitrogen for RNA extraction. Eutopic endometrium from the functionalis layer was consecutively harvested by endometriectomy from the same animals following experimental induction of endometriosis.
|
| Growth protocol |
Endometriosis was experimentally induced in four female baboons (Papio anubis) by intraperitoneal inoculation with menstrual endometrium on two consecutive menstrual cycles. Under laparoscopic guidance, approximately 1 g of menstrual tissue and fluid was deposited from the Pipelle at four sites: the pouch of Douglas, the uterine fundus, the cul de sac, and the ovaries. At the subsequent mense, the animals underwent a second laparoscopy and endometrial reseeding at the same ectopic sites.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Eutopic endometria were homogenized in TRI-ZOL reagent (Invitrogen, Carlsbad, CA), and RNA was extracted. Total RNA was then subjected to DNase digestion to remove genomic DNA and was purified using the RNeasy Kit (Qiagen, Valencia, CA). RNA purity was confirmed by 260/280-nm absorbance ratios and analysis on an Agilent Bioanalyzer, following which cDNA was prepared according to the Affymetrix microarray preparation protocol (Affymetrix, Santa Clara, CA)
|
| Label |
biotin
|
| Label protocol |
According to Affymetrix protocol
|
| |
|
| Hybridization protocol |
Hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays, according to Affymetrix protocol
|
| Scan protocol |
Used an HR3000 scanner. Data extraction was performed with the Affymetrix Gene-Chip Operating System V1.1, according to Affymetrix protocol
|
| Description |
unique sample, no replicate
|
| Data processing |
Probe sets were mapped to unique Entrez Gene IDs using a custom Chip Description File (CDF HGU133plus2_Hs_ENTREZG in R package “hgu133plus2hsentrezg.db” version 14.1, March 2011). Expression data were normalized and background corrected with the Robust Multichip Average method using R/Bioconductor. Genes with low variability between different time points were discarded. Differentially expressed genes were found by using the limma package in R/Bioconductor. P-values were corrected for multiple-hypothesis testing with the Benjamini-Hochberg algorithm
|
| |
|
| Submission date |
Aug 26, 2015 |
| Last update date |
Aug 27, 2015 |
| Contact name |
Damian Roqueiro |
| E-mail(s) |
damian.roqueiro@bsse.ethz.ch
|
| Phone |
+41613873282
|
| Organization name |
ETH Zurich
|
| Department |
Biosystems Science and Engineering
|
| Lab |
Machine Learning and Computational Biology
|
| Street address |
Mattenstrasse 26
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18756 |
| Series (1) |
| GSE72428 |
Changes in eutopic endometrial gene expression during the progression of experimental endometriosis in the baboon, Papio anubis |
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