|
| Status |
Public on Oct 05, 2022 |
| Title |
MC2_d4 vs OMM |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
primary colon epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: Germ-free (GF) C57BL/6
cell type: primary colon epithelial cells
treatment: MC2 (OMM + minimal consortium of 2 additional strains, OMM + E.coli + C. amalonaticus)
time: d4 (day 4) post colonialization
|
| Treatment protocol |
GF mice were reconstitutted with Oligo-Maus-Mikrobiota (OMM, https://pubmed.ncbi.nlm.nih.gov/27869789/) or minimal consortium (MC2, OMM + E-coli + C. amalonaticus) .
|
| Growth protocol |
Germ-free (GF) C57BL/6 mice were kept in isolators under sterile conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Primary murine eithelial cells from colon were isolated by CD45 + cell depletion followed by CD31 + ( Pecam1) positive selection. Total RNA from epithelial cells was isolated with RNeasy (Qiagen) according the supplier's instructions.
|
| Label |
Cy3
|
| Label protocol |
RNA labeling was performed with the Low Input Quick-Amp Labeling Kit (Agilent Technologies) according supplier's instructions.
|
| |
|
| Channel 2 |
| Source name |
primary colon epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: Germ-free (GF) C57BL/6
cell type: primary colon epithelial cells
treatment: OMM (Oligo-Mouse-Microbiota, community of 12 strains)
time: d4 (day 4) post colonialization
|
| Treatment protocol |
GF mice were reconstitutted with Oligo-Maus-Mikrobiota (OMM, https://pubmed.ncbi.nlm.nih.gov/27869789/) or minimal consortium (MC2, OMM + E-coli + C. amalonaticus) .
|
| Growth protocol |
Germ-free (GF) C57BL/6 mice were kept in isolators under sterile conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Primary murine eithelial cells from colon were isolated by CD45 + cell depletion followed by CD31 + ( Pecam1) positive selection. Total RNA from epithelial cells was isolated with RNeasy (Qiagen) according the supplier's instructions.
|
| Label |
Cy5
|
| Label protocol |
RNA labeling was performed with the Low Input Quick-Amp Labeling Kit (Agilent Technologies) according supplier's instructions.
|
| |
|
| |
| Hybridization protocol |
Whole mouse genome 8x60K microarrays were done according to the supplier’s protocol (Agilent Technologies).
|
| Scan protocol |
Scanning of microarrays was performed with 3 µm resolution using a DNA microarray laser scanner (Agilent Technologies)
|
| Description |
color-swap: polarity(-)
|
| Data processing |
Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA Version A.11.5.1.1 and the GE2_1200_Dec17 extraction protocol (Agilent Technologies). Interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.
|
| |
|
| Submission date |
Jul 27, 2021 |
| Last update date |
Oct 05, 2022 |
| Contact name |
Hans-Joachim Mollenkopf |
| E-mail(s) |
mollenkopf@mpiib-berlin.mpg.de
|
| Phone |
+49 30 28460 482
|
| Organization name |
Max-Planck-Institute for Infection Biology
|
| Lab |
Microarray/Genomics Core Facility
|
| Street address |
Charitéplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21810 |
| Series (1) |
| GSE180907 |
Fourteen commensals restore immunocompetence in adult germfree mice via maturation of the intestinal vascular system |
|
