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Sample GSM5111568 Query DataSets for GSM5111568
Status Public on Feb 27, 2021
Title PCI 3 days 1
Sample type RNA
Source name 3 days after PCI_whole brain
Organism Mus musculus
Characteristics strain: C57Bl/6J
gender: male
age: 12-14 weeks
sepsis: 3 days after PCI
meropenem: s.c. 3 days
enrofloxacin: no
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 acute Sepsis
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
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
VALUE normalized

Data table
ILMN_2599935 9.22440416175644
ILMN_2751818 7.65241998282734
ILMN_1232875 8.06992364711518
ILMN_1258507 7.86547279057606
ILMN_1231129 12.8880575174057
ILMN_2707099 7.91940523960781
ILMN_2942000 8.56551941095628
ILMN_2642403 13.4931027488407
ILMN_1242024 8.07043082905403
ILMN_2465874 7.88098978706647
ILMN_2908874 11.113305729515
ILMN_1222991 7.89068186629416
ILMN_1230413 9.6072261164374
ILMN_3163481 9.2097916728709
ILMN_2611510 9.9112089592914
ILMN_2756157 7.80002299542188
ILMN_1253269 10.6909506187502
ILMN_2763951 8.70875665494639
ILMN_2719266 7.78063767174822
ILMN_1227266 9.35535578813169

Total number of rows: 12903

Table truncated, full table size 376 Kbytes.

Supplementary file Size Download File type/resource
GSM5111568_9298740075_B_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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