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Sample GSM586676 Query DataSets for GSM586676
Status Public on Sep 01, 2017
Title T1-S3-R2
Sample type RNA
 
Source name liver samples from mice challenged to PCI treatment monitored after 24 hours
Organism Mus musculus
Characteristics strain: C57/BL6
sex: female
age: 8 weeks
Treatment protocol 1. faecal Peritonitis: intraperitoneal injection of 200µl of a human faeces suspension (KBE 75 x 10^6/ml), 2. Sham controls: intraperitoneal injection of 200µl of physiological sodium chloride
Growth protocol 8 weeks old female C57/BL6 Jackson mice
Extracted molecule total RNA
Extraction protocol Preparation of total RNA from lung, liver and spleen. Tissue homogenization was conducted with the tissue lyser by Qiagen (Retsch, Haan, Germany) with a 5mm steel ball for 4 minutes at 30hz and processed for total RNA isolation as described by the manufacturer using RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA-Isolation from whole blood was performed according to the protocol of PAXgene Blood RNA Kit (PreAnalytix®, Qiagen, Hilden, Germany). Additional clearing from globin RNA was used for RNA from whole blood samples according to the GLOBINclearTM Mouse/Rat Kit by Ambion® (Applied Biosystems, Darmstadt, Germany) RNA integrity and concentration analyses were performed with the Bioanalyzer 2100 (Agilent Technologies®, Palo Alto, CA, USA) according to the manufacturers protocol RNA 6000 Nano Assay using RNA 6000 Nano LabChip® Kits by Agilent Technologies®.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
 
Hybridization protocol For hybridisation, the Whole-Genome Gene Expression with IntelliHybTM Seal protocoll (Revision B) from Illumina® (San Diego, CA, USA) was used.
Scan protocol Scanning of arrays was done with the BeadArray Reader 500 X from Illumina®, San Diego, CA, USA).
Description 4338498038_D
Data processing Gene chips from 44 samples (four tissues; four replicates for 6 h and 24 h post-infection and three replicates sham) were scanned and pre-processed using BeadStudio (version 3.23). Data analysis was carried out using R statistics software (version 2.92) and BioConductor (version 2.3). A robust spline normalization, combining the features of quantile and loess normalization, was conducted for the tissue separated sample groups (liver, lung, spleen and blood) and log 2 signals were obtained.
 
Submission date Aug 24, 2010
Last update date Sep 01, 2017
Contact name S. Lambeck
Organization name JUH
Street address Erlanger Allee 101
City Jena
ZIP/Postal code 07743
Country Germany
 
Platform ID GPL6887
Series (1)
GSE23767 Tracking the molecular patterns of a common response across tissues in murine sepsis to refine treatment strategies

Data table header descriptions
ID_REF
VALUE normalized log2 signals
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1250052 7.065704021 0.30011
ILMN_1251402 6.778204848 0.95991
ILMN_3122480 6.968446198 0.57096
ILMN_1230863 6.846191044 0.88407
ILMN_2599935 8.025064703 0
ILMN_1249762 7.073022267 0.27736
ILMN_2653194 6.977523783 0.54496
ILMN_1227991 6.615544518 0.99892
ILMN_2445236 8.539361401 0
ILMN_2675543 7.089004808 0.24377
ILMN_2635314 6.562045509 1
ILMN_1212991 10.35112317 0
ILMN_2686883 7.252047449 0.04984
ILMN_1223534 6.809984462 0.93066
ILMN_2514305 7.712429219 0
ILMN_2751818 7.02419647 0.40737
ILMN_1217583 7.180218884 0.10943
ILMN_1222597 6.800916763 0.93933
ILMN_1242561 6.873313124 0.81582
ILMN_2728634 7.276521192 0.0325

Total number of rows: 45281

Table truncated, full table size 1361 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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