|
| Status |
Public on Oct 10, 2020 |
| Title |
Mammary gland cow Nuisette_Control |
| Sample type |
RNA |
| |
|
| Source name |
Mammary gland before restriction
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein cow
animal id: Nuisette
diet: CONT
tissue: Mammary gland biopsy
|
| Treatment protocol |
During the control period (CONT) before restriction, all cows were allowed ad libitum intake of a lactation diet. During the restriction period (REST), feed allowance was reduced to meet 50% of NEL requirements calculated from body weight, feed intake and milk production and composition recorded before restriction. Mammary gland (MG) samples were collected by biopsies on day 0 and day 6 relative to initiation of feed restriction. Mammary biopsies were performed after the selection of the biopsy site at a midpoint on a rear quarter. Approximately 600–650 mg of tissue was collected, rinsed in sterile 0.9% saline solution, snap-frozen in liquid nitrogen, and stored at −80 °C until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from approximately 50 mg of MG biopsies using the miRVana kit (Thermo Fisher Scientific, USA). The concentration and quality of the RNAs were estimated by spectrophotometry Nanodrop TH (ND-1000, NanoDrop Technologies LLC, Wilmington, DE, USA) and using the Bioanalyzer 2100 (Agilent Technologies Inc., Santa Clara, CA, USA), respectively.
|
| Label |
Cy3
|
| Label protocol |
50 ng of total RNA extracted were amplified and fluorescently labelled to produce Cy3 cRNA using the Low Input Quick Amp Labeling one color Kit (Agilent, USA) in the presence of spike-in one color control.
|
| |
|
| Hybridization protocol |
After purification (Qiagen RNeasy Mini Kit), 1,65 µg of Cy3 labeled cRNA were hybridized onto G2519F-023647 Bovine (V2) Gene Expression Microarray, 4x44K (Agilent, USA) with hybridization buffer (Agilent Gene Expression Hybridization Kit) according to the manufacturer’s instructions. After 17h of hybridization, slides were washed with the Gene Expression Wash Pack.
|
| Scan protocol |
Microarrays were scanned using the Agilent Microarray Scanner G2505 version B (Agilent Technologies, Inc. Santa Clara, CA, USA).
|
| Description |
Nuisette CONT
Gene expression before restriction
|
| Data processing |
The resulting TIFF images (Tagged Image File Format) were processed using Feature Extraction software Version 11. Microarrays were analyzed to determine differential gene expression (DEG) at the mRNA level using GeneSpring software, and data were normalized with 75th percentile shift followed by t-tests moderated with the Benjamini-Hochberg (FDR) correction, Significance was considered at Padj < 0.10.
|
| |
|
| Submission date |
Oct 09, 2020 |
| Last update date |
Oct 10, 2020 |
| Contact name |
Christine LEROUX |
| E-mail(s) |
christine.leroux@inrae.fr
|
| Organization name |
INRAE
|
| Lab |
Christine LEROUX
|
| Street address |
Route de Theix
|
| City |
St Genès-Champanelle |
| ZIP/Postal code |
63122 |
| Country |
France |
| |
|
| Platform ID |
GPL11648 |
| Series (1) |
| GSE159302 |
Effects of restriction on mammary gland transcriptome |
|
