|
| Status |
Public on Jun 14, 2012 |
| Title |
Monocytes from SLE patient number 16 (SL_16) |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood monocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Monocytes
individual: patient number 16
disease state: SLE
|
| Treatment protocol |
only for Affymetrix chips where monocytes were stimulated in vitro by TNFα, IFNα2a and IFNγ
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was collected by using the RNeasy mini kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
label protocol for 14 SLE chips (including SLE test samples), 8 RA chips (RA1 to RA 11, without RA test samples) and 12 ND chips: 3-5 µg of total RNA was amplified and labelled using the GeneChip® one-cycle target labelling and control reagents (Affymetrix)
label protocol for 3 TNF_1.5h chips, 7 IFNa2a_1.5h chips, 7 IFNg_1.5h chips, 11 Un_1.5h chips and 8 Un_0h chips: 300 ng of total RNA was amplified and labelled using the MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit according to Affymetrix instruction
label protocol for 4 RA test chips: RA_1_test, RA_18 test, RA_88_test and RA_98 test: 100 ng of total RNA was amplified and labelled using the GeneChip® one-cycle target labelling and control reagents (Affymetrix)
|
| |
|
| Hybridization protocol |
label protocol for 14 SLE chips (including SLE test samples), 8 RA chips (RA1 to RA 11, without RA test samples) and 12 ND chips: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.
label protocol for 3 TNF_1.5h chips, 7 IFNa2a_1.5h chips, 7 IFNg_1.5h chips, 11 Un_1.5h chips and 8 Un_0h chips: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v5 protocol.
label protocol for 4 RA test chips: RA_1_test, RA_18 test, RA_88_test and RA_98 test: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the FS450_0001 protocol.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
|
| Description |
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 16, labelled as SL_16
|
| Data processing |
Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database (www.bioretis.de)
|
| |
|
| Submission date |
May 30, 2012 |
| Last update date |
May 04, 2016 |
| Contact name |
Pawel Durek |
| E-mail(s) |
pawel.durek@drfz.de
|
| Organization name |
Deutsches Rheuma-Forschungszentrum
|
| Street address |
Charitéplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE38351 |
The multifaceted balance of TNF-a and type I / II interferon responses in SLE and RA: how monocytes manage the impact of cytokines |
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