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Sample GSM627953 Query DataSets for GSM627953
Status Public on Feb 05, 2016
Title Germfree 28d-AC, rep4
Sample type RNA
 
Source name Mouse ascending colon, 28d, germfree control
Organism Mus musculus
Characteristics strain: C3H/HeN
gender: male
tissue: ascending colon
condition: germ-free
time: 28 days post-colonization
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.
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).
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.
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.
 
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.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.
Description GF8-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.
 
Submission date Nov 22, 2010
Last update date Feb 05, 2016
Contact name Denise Kelly
E-mail(s) D.Kelly@rri.sari.ac.uk
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
 
Platform ID GPL7440
Series (1)
GSE25544 Host/microbial cross-talk in the gut: In-depth investigation of the symbiotic effects of Roseburia hominis

Data table header descriptions
ID_REF
VALUE gcRMA-normalized signal intensity, log2 scaled

Data table
ID_REF VALUE
1415670_at 10.34
1415671_at 10.14
1415672_at 10.74
1415673_at 7.77
1415674_a_at 9.41
1415675_at 8.60
1415676_a_at 10.57
1415677_at 8.00
1415678_at 10.58
1415679_at 11.39
1415680_at 8.34
1415681_at 9.79
1415682_at 8.37
1415683_at 10.18
1415684_at 9.45
1415685_at 8.60
1415686_at 10.67
1415687_a_at 12.91
1415688_at 10.53
1415689_s_at 8.46

Total number of rows: 23865

Table truncated, full table size 409 Kbytes.




Supplementary file Size Download File type/resource
GSM627953.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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