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Sample GSM3510347 Query DataSets for GSM3510347
Status Public on Jun 10, 2019
Title SIRS patient 044 [NK cells]
Sample type RNA
 
Source name peripheral NK cells from SIRS patient on ICU admission
Organism Homo sapiens
Characteristics diagnosis: SIRS
cell type: peripheral NK cells
gender: male
age: 60
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_C_044
Gene expression data from peripheral NK cells of SIRS 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

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
100009613_at 3.556152344
100009676_at 5.623046875
10000_at 9.474609375
10001_at 7.484375
10002_at 3.619140625
100033413_at 7.913085938
100033422_at 3.258789063
100033423_at 2.828125
100033424_at 3.346679688
100033425_at 2.849609375
100033426_at 11.88671875
100033427_at 13.02929688
100033428_at 3.8515625
100033430_at 2.776855469
100033431_at 8.744140625
100033432_at 6.147460938
100033434_at 4.159179688
100033435_at 12.89648438
100033436_at 3.965332031
100033437_at 2.723632813

Total number of rows: 25088

Table truncated, full table size 517 Kbytes.




Supplementary file Size Download File type/resource
GSM3510347_Lindner_030614_S-C-044_HuGene-2_0-st_.CEL.gz 8.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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