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Sample GSM1723406 Query DataSets for GSM1723406
Status Public on Jun 27, 2015
Title Il1b KO sipnal cord, biological rep2
Sample type RNA
 
Source name Il1b KO lesioned spinal cord, 24 hours after injury
Organism Mus musculus
Characteristics background strain: C57BL/6
genotype/variation: Il1b KO
age: 8-12 weeks
tissue: Spinal cord
Treatment protocol Spinal cord contusion of 50 kdyn was performed using the Infinite Horizon SCI device (Precision Systems & Instrumentation).
Extracted molecule total RNA
Extraction protocol Spinal cord segments of 6 mm-long centered over the lesion were rapidly dissected, frozen in liquid nitrogen, and stored at -80°C until RNA extraction. Total RNA was isolated by TRI Reagent and purified with the GenElute mammalian total RNA miniprep kit (Sigma-Aldrich Canada Ltd.).
Label biotin
Label protocol Two hundred nanograms of total RNA was labeled using the Ambion® WT Expression Kit protocol, as described by the manufacturer (Affymetrix, Santa Clara, CA). The quality of total RNA, cDNA synthesis, cRNA amplification, and cDNA fragmentation was monitored by microcapillary electrophoresis (Bioanalyzer 2100, Agilent Technologies).
 
Hybridization protocol Five µg of fragmented single-stranded cDNA was hybridized for 16 hours at 45°C with constant rotation on a GeneChip® Mouse Gene 1.0 ST Array (Affymetrix). After hybridization, were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol FS450_0007).
Scan protocol Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix)
Data processing Images were extracted with the GeneChip Operating Software (Affymetrix GCOS v1.4). Quality control of microarrays was performed using the AffyQCReport software. Background subtraction and normalization of probe set intensities was performed using the method of Robust Multiarray Analysis (RMA). Data analysis was performed using the AffylmGUI Graphical User Interface for the LIMMA microarray package (Wettenhall et al., 2006), and Partek Genomics Suite (Partek Incorporated)
 
Submission date Jun 26, 2015
Last update date Jun 27, 2015
Contact name Steve Lacroix
E-mail(s) Steve.Lacroix@crchul.ulaval.ca
Organization name Centre de recherche du Centre hospitalier universitaire (CHU) de Québec - CHUL
Department Médecine moléculaire
Street address 2705, boul. Laurier
City Québec
State/province Québec
ZIP/Postal code G1V 4G2
Country Canada
 
Platform ID GPL6246
Series (1)
GSE70302 Gene expression data of C57BL/6, Il1a-knockout and Il1b-knockout mice at 24 hours after spinal cord injury

Data table header descriptions
ID_REF
VALUE RMA normalized data (Log2)

Data table
ID_REF VALUE
10344614 7.300131
10344616 3.393902
10344620 5.733791
10344622 8.453853
10344624 9.825677
10344633 10.4286
10344637 10.11268
10344653 7.454754
10344658 9.403304
10344674 4.516881
10344679 8.913011
10344707 9.595915
10344713 9.459109
10344715 5.509388
10344717 4.048067
10344719 7.223472
10344721 3.489059
10344723 8.717988
10344725 9.278364
10344741 10.30367

Total number of rows: 35557

Table truncated, full table size 621 Kbytes.




Supplementary file Size Download File type/resource
GSM1723406_Il1b_KO-2.CEL.gz 4.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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