|
| Status |
Public on Jun 10, 2015 |
| Title |
Adult with Sepsis 6 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Adult with Sepsis 6
|
| Organism |
Homo sapiens |
| Characteristics |
age: 38
cell type: neutrophil granulocytes
|
| Growth protocol |
Neutrophils were isolated from blood samples immediately after the collection using a Ficoll gradient and stored at −80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol reagent (Life Technologies, Carlsbad, CA, USA) following the manufacturer’s protocol.
|
| Label |
Cy3
|
| Label protocol |
200 ng of total RNA were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit following manufacturer's instructions
|
| |
|
| Channel 2 |
| Source name |
common reference RNA pool
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: cyanine-5 labeled reference RNA (Universal Human Reference RNA, Agilent, cat #740000)
|
| Growth protocol |
Neutrophils were isolated from blood samples immediately after the collection using a Ficoll gradient and stored at −80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol reagent (Life Technologies, Carlsbad, CA, USA) following the manufacturer’s protocol.
|
| Label |
Cy5
|
| Label protocol |
200 ng of total RNA were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit following manufacturer's instructions
|
| |
|
| |
| Hybridization protocol |
Agilent Gene Expression Hybridization Kit were used and samples were applied to microarrays enclosed in Agilent Microarray Hybridization Chamber. After hybridization, slides were washed sequentially.
|
| Scan protocol |
Slides were read on a SureScan Microarray Scanner (Agilent, USA).
|
| Description |
Biological replicate 6 of 6: Adult with sepsis vs. common reference
|
| Data processing |
Images were processed using the Feature Extraction Software v12 (Agilent, USA) for quality control, determination of feature intensities and ratios, and for background correction. The flag 'IsWellAboveBG' in the FE output was used to select probes whose intensity were within a 99% confidence interval of being well above the background levels. 16698 out of 58717 probes with valid 'Well Above Background' flag in both Cy3 and Cy5 channels in at least 5 out of 6 replicates of at least one group (elderly sepsis, elderly healthy, adult sepsis, adult healthy) were further analyzed.
|
| |
|
| Submission date |
Apr 07, 2015 |
| Last update date |
Nov 01, 2016 |
| Contact name |
Eduardo Moraes Reis |
| E-mail(s) |
emreis@iq.usp.br
|
| Phone |
+55-11-30912173
|
| Organization name |
University of São Paulo
|
| Department |
Biochemistry
|
| Street address |
Av. Prof. Lineu Prestes, 748
|
| City |
São Paulo |
| State/province |
SP |
| ZIP/Postal code |
05508-900 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL16699 |
| Series (1) |
| GSE67652 |
Septic shock in advanced age: Transcriptome analysis reveals altered molecular signatures in neutrophil granulocytes |
|
| Relations |
| Reanalyzed by |
GSM2367541 |
