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Sample GSM5111578 Query DataSets for GSM5111578
Status Public on Feb 27, 2021
Title PCI 10 weeks 4
Sample type RNA
 
Source name 10 weeks after PCI_whole brain
Organism Mus musculus
Characteristics strain: C57Bl/6J
gender: male
age: 12-14 weeks
sepsis: 10 weeks after PCI
meropenem: s.c. 10 days
enrofloxacin: trinking water 9 weeks
tissue: mouse whole brain
Treatment protocol Experimental sepsis was induced by the standardized and established PCI model as described previously . In brief, PCI mice received an intraperitoneal injection of human fecal slurry (diluted 1:4 in saline solution, 3 µl/g B.W.) with a 21-gauge cannula. Control mice were injected with 100µl of 0.9 M saline solution. Mice were closely monitored and the Clinical Severity Score (CSS) was assessed as described previously. To avoid premature death due to acute severe peritonitis, mice were systemically treated with antibiotics. PCI mice received the first subcutaneous (s.c.) injection of the beta-lactam antibiotic meropenem (650µl, 1mg/ml) when the CSS reached a point value of 3. To increase long-time survival after PCI, meropenem was s.c. injected b.i.d. for 7 days and one time per day at the following three days. Thereafter, enrofloxacin (Baytril 2,5%, Bayer AG, Germany) was added to the sugared drinking water (saccharose solution 2,5%) in a final concentration of 2 mg/ml until the end of the experiment. Both, PCI and control animals received equal amounts of antibiotic treatment
Growth protocol All animal experiments were approved by the state authorities of Thuringia (UKJ-02-085-14) and were performed in accordance with animal welfare and the ARRIVE guidelines for reporting animal research. All efforts were made to minimize animal suffering and to reduce the number of animals used. Adult male C57BL6/J mice were kept in a 12 h light-/dark cycle in standard cages with free access to food and water.
Extracted molecule total RNA
Extraction protocol Total cellular RNA from murine brain biopsies were isolated according to standard totalRNA extraction procedures using QIAzol lysis reagent and RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer instructions.
Label Biotin
Label protocol Label incorporation metho: Hybridized arrays were stained with 1 µg/µl Alexa Fluor 555 Streptavidin (Invitrogen, Karlsruhe, Germany), washed dried and scanned immediately on a Illumina iScan array Reader.
Label used: Alexa Fluor 555 Streptavidin (Invitrogen, Karlsruhe, German).
 
Hybridization protocol 250ng of total RNA of each sample were reversely transcribed and amplified using the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChips (Epicentre, Biozym, Hessisch Oldendorf, Germany) a Biorad MJ Thermal Cycler (Biorad, München, Germany). All cRNA samples were quantified with a NanoDrop spectrophotometer (Nanodrop-Technologies) before proceeding to sample hybridization. Samples were prepared for hybridization according to the Illumina WGGEX Direct Hybridization Assay Guide (Illumina, San Diego, USA).
Hybridization is performed according to the Illumina WGGEX Direct Hybridization Assay Guide (Illumina).
Quantity of target used: 0.75 µg cRNA of each sample was hybridized on a Mouse-Ref-8 v2.0 Expression BeadChip (Illumina, San Diego, USA/Eindhoven, The Netherlands) containing 25,697 probes for murine genome-wide expression analysis and several control probes for sample- preparation, hybridisation, washing and staining quality
Hybridization time: 20 h
Volume: 15 µl
Temperature: 58° C
Scan protocol Scanning hardware : Illumina iScan array scanner; scanning software: iScan control software; spatial resolution (pixel space) 0.53 µm.
Description recoverd, no obviouse disease
Data processing Data processing was performed using Genome Studio Software V2011.1 and R Package “lumi”. Raw data was subjected to average normalization (RSN, log2 signal transformation), quality control and background correction.
Bead types with detection values p < 0.01 in at least one sample (sham 3 d, sham 10 w, PCI 3 d, or PCI 10 w) were called ‘present’ and analyzed. Hierarchical clustering identified sample 9298740075_G as an outlier and was removed from further processing. Differentially expressed genes (DEG) with LFC=log2FC >1 for PCI vs. Sham at same time point for False Discovery Rate adjustment (FDR-adj.) were filtered. False Discovery Rate was adjusted at p-value <0.05 using the Welch-modified t-test.
 
Submission date Feb 26, 2021
Last update date Feb 27, 2021
Contact name Markus Blaess
E-mail(s) markus.blaess@web.de
Organization name Furtwangen University
Department Institute of Precision Medicine
Street address Jakob-Kienzle-Strasse 17
City Villingen-Schwenningen
ZIP/Postal code 78054
Country Germany
 
Platform ID GPL6885
Series (1)
GSE167610 Brain Genexpession of a mouse modle of Sepsis-associated encephalopathy (SAE)

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
ILMN_2599935 9.32767159894036
ILMN_2751818 7.9494784870592
ILMN_1232875 7.62120995087937
ILMN_1258507 7.71063257138105
ILMN_1231129 12.9971296760902
ILMN_2707099 7.78962730110929
ILMN_2942000 8.24028373331405
ILMN_2642403 13.4170972871949
ILMN_1242024 8.11693378369396
ILMN_2465874 7.87461674353648
ILMN_2908874 11.0929908622725
ILMN_1222991 7.77078269987511
ILMN_1230413 10.2331788940595
ILMN_3163481 9.23849532201485
ILMN_2611510 9.77156611815595
ILMN_2756157 7.88181552884221
ILMN_1253269 10.8805716124949
ILMN_2763951 8.36142264841745
ILMN_2719266 7.72516836214022
ILMN_1227266 9.26350883333147

Total number of rows: 12903

Table truncated, full table size 376 Kbytes.




Supplementary file Size Download File type/resource
GSM5111578_9298740088_D_Grn.idat.gz 1.2 Mb (ftp)(http) IDAT
Raw data provided as supplementary file
Processed data included within Sample table
Raw data are available on Series record

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