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Status |
Public on Feb 05, 2016 |
Title |
R. hominis 28d-AC, rep3 |
Sample type |
RNA |
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Source name |
Mouse ascending colon, 28d after colonization, R. hominis
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Organism |
Mus musculus |
Characteristics |
strain: C3H/HeN gender: male tissue: ascending colon condition: Roseburia hominis colonization time: 28 days post-colonization
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Treatment protocol |
GF male mice were gavaged at 0d with 100 uL of R. hominis culture. All mice were sacrificed on 14d and 28d post-colonization in parallel to age-matched GF controls.
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Growth protocol |
C3H/HeN mice were bred at the INRA facilities in Jouy-en-Josas. Germ-free (GF) mice were maintained in plastic isolators and fed ad libitum on a commercial diet (R03-40; UAR) sterilized by γ-irradiation (40 kGy).
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Extracted molecule |
total RNA |
Extraction protocol |
Ileal and ascending colon tissue was excised, processed in ice-cold PBS, transferred to RNAlater (Ambion) and stored at -20 °C. Tissue was removed from RNAlater, lyzed in Trizol (Invitrogen), and RNA was extracted using chloroform/isopropanol steps. Total RNA was further treated with the RNeasy kit (Qiagen) according to the manufacturer’s instructions, including an RNase-free DNase I (Qiagen) digestion step.
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Label |
biotin
|
Label protocol |
Fragmented and biotin-labelled cRNA was synthesized from 8 ug purified RNA using the One-Cycle Target Labeling Kit (Affymetrix) according to the manufacturer's protocol.
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Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip NuGO Mouse Array (NuGO_Mm1a520177). GeneChips were washed and stained in the Affymetrix Fluidics Station.
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Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.
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Description |
Rh8-AC
|
Data processing |
Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA. The moderated t-test provided by the Bioconductor package limma was used to test for differential expression. Data was considered significant when P<0.05 using the Benjamini and Hochberg false discovery method.
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Submission date |
Nov 22, 2010 |
Last update date |
Feb 05, 2016 |
Contact name |
Denise Kelly |
E-mail(s) |
D.Kelly@rri.sari.ac.uk
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Phone |
+44 1224 716648
|
Organization name |
University of Aberdeen
|
Lab |
Gut Immunology Group
|
Street address |
Institute of Medical Sciences
|
City |
Aberdeen |
ZIP/Postal code |
AB25 2ZD |
Country |
United Kingdom |
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|
Platform ID |
GPL7440 |
Series (1) |
GSE25544 |
Host/microbial cross-talk in the gut: In-depth investigation of the symbiotic effects of Roseburia hominis |
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