|
| Status |
Public on Jun 10, 2019 |
| Title |
septic shock patient 046 [NK cells] |
| Sample type |
RNA |
| |
|
| Source name |
peripheral NK cells from septic shock patient on ICU admission
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: septic shock
cell type: peripheral NK cells
gender: female
age: 58
|
| Treatment protocol |
For NK cells isolation, peripheral blood mononuclear cells (PBMCs) were extracted from 32 mL blood by a Ficoll gradient (GE Healthcare). PBMCs were subjected to depletion using a labeling cocktail composed of CD15, CD14, CD3 and CD19 MicroBeads on an LD column (Miltenyi Biotec) and subsequent enrichment with CD56 MicroBeads on an MS column (Miltenyi Biotec).
|
| Growth protocol |
Blood was collected in S-Monovette® K3E tubes (Sarstedt, Nümbrecht, Germany) by venipuncture with presurgical patients and from a central venous catheter with ICU patients.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from isolated NK cells stored in RNAlater® (Ambion) using a modified version of the miRVana miRNA isolation kit protocol (Applied Biosystems) (Figueiredo et al., Data Brief. 2017 Oct; 14: 77–83).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.
|
| Scan protocol |
Affymetrix GeneArray Scanner3000.
|
| Description |
S_A_046
Gene expression data from peripheral NK cells of septic shock patient on ICU admission.
|
| Data processing |
The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 18 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.
|
| |
|
| Submission date |
Dec 12, 2018 |
| Last update date |
Jun 10, 2019 |
| Contact name |
Carsten Sticht |
| Organization name |
University Heidelberg
|
| Department |
ZMF
|
| Street address |
Theodor-Kutzer-Ufer
|
| City |
Mannheim |
| ZIP/Postal code |
68169 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19803 |
| Series (2) |
| GSE123730 |
AKIRIN1 is a suitable reference gene in natural killer cells and granulocytes from patients with SIRS and septic shock [NK cells] |
| GSE123731 |
AKIRIN1 is a suitable reference gene in natural killer cells and granulocytes from patients with SIRS and septic shock |
|
