Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 36
Release date: Jan 6 2014
Last update date: Aug 9 2018
Access: Public
Diseases: Eye Infections, Viral
Dataset link T helper lymphocyte- and monocyte-specific type I interferon (IFN) signatures in autoimmunity and viral infection.

Experimental Protocol


Collection of cells from Systemic Lupus Erythematosus (SLE) patients: For CD4pos T cells, six patients with SLE (average age: 29.0 +/- 7.6) and four normal healthy donors (ND; 24.8 +/- 0.5) were recruited. For CD16neg monocytes, four patients with SLE (26.5 +/- 1.7) and four NDs (24.8 +/- 0.5) were recruited. For CD16pos monocytes, four patients with SLE (26.5 +/- 1.7) and three NDs (24.7 +/- 0.6) were recruited. All patients and NDs were female. The same NDs were examined before and after immunisation with yellow fever vaccine (YFV). Collection of cells from yellow-fever vaccinated individuals: ND were immunised with a vaccine against the wild-type YF virus, which is a single-stranded RNA virus without adjuvants. This vaccine consists of a live but attenuated strain of the yellow fever virus (YFV-17D). Based on its vaccination-associated clinical and serological manifestations, this immunisation can be regarded as a real viral infection. A total of 50 ml peripheral blood was taken 7 days after immunisation, when sufficient numbers of CD19pos/CD27high plasmablasts were detected by flow cytometry. Cell sorting: A total of 50 ml peripheral blood was collected in Vacutainer heparin tubes and erythrocytes were lysed in EL buffer. Subsequently, granulocytes were depleted using CD15-conjugated microbeads (MACS). The CD15-depleted fraction was stained with a CD14-fluorescein isothiocyanate (FITC) antibody, a CD16-APC-Cy7 antibody, a CD3-Vioblue antibody and a CD4-FITC antibody. Using a FACSAria cell sorter, CD4pos T cells, CD16neg monocytes and CD16pos monocytes were isolated with purities and viabilities of >97%. After sorting, the cells were immediately lysed with RLT buffer and frozen at -70 °C. Total RNA was isolated using an RNeasy mini kit, and quality control was ensured by Bioanalyser measurements.Total RNA was extracted using the RNeasy Mini kit. The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer and a NanoDrop ND-1000 spectrophotometer. Biotinylated complementary RNA (cRNA) was synthesized from 100 ng total RNA, using reagents as recommended in the technical manual from Affymetrix. Fifteen micrograms of fragmented cRNA of each sample were hybridized to HG-U133 plus 2.0 arrays. Hybridization was performed according to procedure 2 as described in the technical manual. Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software. All relevant GCOS data of quality checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA, unpublished), using the BioRetis database (www.bioretis-analysis.de), as described and validated previously.

Repositories


GEO

GSE51997

ArrayExpress

E-GEOD-51997

BioProject

PRJNA226024

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Contact


Pawel Durek
Joachim R. Grün

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