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Sample GSM3816550 Query DataSets for GSM3816550
Status Public on Aug 16, 2020
Title REA17264
Sample type RNA
 
Source name Peripheral Blood, septic shock
Organism Homo sapiens
Characteristics diagnosis: septic shock
tissue: whole blood
age: 80
gender: female
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 7.19162943215574
A_23_P100022 6.92300116749787
A_23_P100056 7.22197563669095
A_23_P100074 7.89827010814198
A_23_P100127 7.80680165025001
A_23_P100141 8.93459605923135
A_23_P100189 7.10898912243695
A_23_P100196 12.4607401714621
A_23_P100203 9.23112091213555
A_23_P100220 7.41908909307232
A_23_P100240 6.8814299268276
A_23_P10025 7.15658248010143
A_23_P100292 10.342300745938
A_23_P100315 8.50296235671394
A_23_P100326 10.9504922242733
A_23_P100344 7.05049460668524
A_23_P100355 10.9857462368846
A_23_P100386 6.93479120737313
A_23_P100392 9.25534006237549
A_23_P100420 7.56354428476141

Total number of rows: 34127

Table truncated, full table size 1004 Kbytes.




Supplementary file Size Download File type/resource
GSM3816550_REA17264.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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