|
| Status |
Public on Oct 19, 2016 |
| Title |
proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer) G154_D04_C3_PBS |
| Sample type |
RNA |
| |
|
| Source name |
proximal colon
|
| Organism |
Mus musculus |
| Characteristics |
treatment: vehicle (NaHCO3/PBS)
Sex: female
mouse strain: Ercc1-/∆7 with F1 C57Bl6J/FVB hybrid background
mouse id: C3
|
| Treatment protocol |
Lactobacillus plantarum WCFS1, Lactobacillus casei BL23, and Bifidobacterium breve DSM20213 were grown on MRS medium (Merck, Darmstadt, Germany) until stationary phase, frozen in glycerol, and stored in -80°C until use. Upon use, bacteria were thawed and 10x diluted in NaHCO3/PBS buffer. Around 2*108 CFU in 200 µL were administered to mice by gavage, three times per week. Treatment of mice started at 6 weeks of age until one day before sacrifice at 16 weeks or until death.
|
| Growth protocol |
The generation and characterization of Ercc1+/∆7 and Ercc1-/+ mice has been previously described [PMID: 9197240]. Ercc1-/∆7 mice were obtained by crossing Ercc1+/∆7 with Ercc1-/+ mice of pure C57Bl6/J and FVB backgrounds to yield Ercc1-/∆7 with an F1 C57Bl6J/FVB hybrid background. Wild-type littermates (C57Bl/6xFVB F1) were used as controls.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from proximal colon samples using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).
|
| |
|
| Hybridization protocol |
Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).
|
| Description |
proximal colon of Ercc1-/∆7 mouse treated with vehicle (NaHCO3/PBS buffer)
|
| Data processing |
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).
|
| |
|
| Submission date |
Sep 26, 2016 |
| Last update date |
Oct 19, 2016 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
[email protected]
|
| Organization name |
Wageningen University
|
| Department |
Div. Human Nutrition & Health
|
| Lab |
Nutrition, Metabolism & Genomics Group
|
| Street address |
HELIX, Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
NL-6708WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11533 |
| Series (1) |
| GSE87368 |
Supplementation with Lactobacillus plantarum WCFS1 prevents Decline of Mucus Barrier in Colon of Accelerated Aging Ercc1-/Δ7 Mice |
|
