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Sample GSM3816547 Query DataSets for GSM3816547
Status Public on Aug 16, 2020
Title SS_43exp2
Sample type RNA
 
Source name Peripheral Blood, septic shock
Organism Homo sapiens
Characteristics diagnosis: septic shock
tissue: whole blood
age: 79
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 7.10092973322187
A_23_P100022 6.92514229982801
A_23_P100056 7.04016380545238
A_23_P100074 8.55527855157408
A_23_P100127 7.83263016511769
A_23_P100141 8.51838830334478
A_23_P100189 7.0082909445689
A_23_P100196 12.1393030003054
A_23_P100203 9.03921481294643
A_23_P100220 7.25451004031691
A_23_P100240 6.90280835106244
A_23_P10025 7.1394610169123
A_23_P100292 10.719776508728
A_23_P100315 8.62792129702839
A_23_P100326 10.173906289488
A_23_P100344 7.25319937642342
A_23_P100355 11.1932593333314
A_23_P100386 6.88608098532652
A_23_P100392 8.81310683924936
A_23_P100420 7.52947667727741

Total number of rows: 34127

Table truncated, full table size 1003 Kbytes.




Supplementary file Size Download File type/resource
GSM3816547_SS_43exp2.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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