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Sample GSM3816560 Query DataSets for GSM3816560
Status Public on Aug 16, 2020
Title REA15153_SS
Sample type RNA
 
Source name Peripheral Blood, septic shock
Organism Homo sapiens
Characteristics diagnosis: septic shock
tissue: whole blood
age: 70
gender: male
Treatment protocol The samples were collected in the first 24h following clinical diagnosis of septic shock and non-septic shock.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from blood samples using the PAX gene blood RNA System (Hombrechtikon, Switzerland). RNA was quantified by spectrometry (Nanodrop ND100, Nanodrop Technologies, Wilmington, Delaware). RNA was eluted with 80 µL of RNase-free H2O. RNA quality and concentration was measured by RNA Experion Bioanalyzer (BioRad, California USA) assay.
Label Cy3
Label protocol 100 ng of purified total RNA was used to produce cyanine 3-CTP-labelled cRNA using the Quick Amp Label kit (Agilent p/n 5190-0442).
 
Hybridization protocol Following “One-Colour microarray based Gene Expression Analysis protocol version 5.7” (Agilent p/n 4140-90040), 3 µg of labelled cRNA was hybridized with the Agilent Whole Human Genome Oligo Microarray Kit (Agilent p/n G2519F-014850).
Scan protocol Arrays were scanned in an Agilent Microarray Scanner Agilent G2565BA according to the manufacturer’s instructions.
Description Gene expression of peripheral blood from septic shock patient
ExVivo_Blood_SS
Data processing Raw files were read into R(limma package) by read.maimages for green only values. Background correction was performed by normexp(saddle) method, offset value=50. Then normalization between arrays was achieved by quantlile method. Repead probe names were aggregated by median values.
 
Submission date May 24, 2019
Last update date Dec 29, 2020
Contact name Pedro Martinez-Paz
E-mail(s) pjdepaz@ccia.uned.es
Organization name Facultad de Medicina
Street address C/ Ramón y Cajal 7
City Valladolid
State/province Valladolid
ZIP/Postal code 47005
Country Spain
 
Platform ID GPL13497
Series (1)
GSE131761 Gene expression patterns in septic and non-septic shock postsurgical patients

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_23_P100001 7.03576021079818
A_23_P100022 6.95883389814276
A_23_P100056 7.58073476549646
A_23_P100074 7.46634429826851
A_23_P100127 7.62598433761377
A_23_P100141 8.17592678140534
A_23_P100189 7.06278043970337
A_23_P100196 12.1062203798689
A_23_P100203 9.76170918619439
A_23_P100220 7.40455180471806
A_23_P100240 6.88413253728445
A_23_P10025 7.04921538258371
A_23_P100292 10.4472055451094
A_23_P100315 8.73511747446701
A_23_P100326 11.6502465445246
A_23_P100344 7.06013681082373
A_23_P100355 10.8758366196019
A_23_P100386 7.03044581841761
A_23_P100392 8.78058497587282
A_23_P100420 7.5247866516883

Total number of rows: 34127

Table truncated, full table size 1003 Kbytes.




Supplementary file Size Download File type/resource
GSM3816560_REA15153_SS.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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