|
| Status |
Public on Dec 01, 2020 |
| Title |
EcN at timepoint t1, biological repA |
| Sample type |
RNA |
| |
|
| Source name |
TLR5 overexpressing human embryonic kidney cells (HEK293) treated with flagellin of E. coli Nissle (FliCEcN, acronym=EcN) for 60min (t1)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: TLR5 overexpressing HEK293
treatment: EcN
time: 60 minutes
|
| Treatment protocol |
6.6 x106 murine TLR5 overexpressing HEK cells per flask were stimulated with isolated flagellin of E. coli Nissle (EcN) or isolated flagellin of Salmonella Typhimurium SL1344 (ST) with a concentration according to MOI 10 for 60 minutes (t1) or 120 minutes (t2).
|
| Growth protocol |
Murine TLR5 overexpressing HEK cells were cultured in custom- made SILAC-DMEM media (SILAC heavy label (Lys8Arg10), SILAC medium label (Lys4Arg6) and SILAC light label (Lys0Arg0) at 37°C and 5% CO2. At a passage number of seven the cells were highly incorporated and used for stimulation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
60 minutes or 120 minutes stimulated murine TLR5 overexpressing HEK cells were resuspended in RLT buffer containing 1% ß-mercaptoethanol for total RNA isolation with Qiagen RNeasy kit following the manufacturer’s instructions (Qiagen).
|
| Label |
biotin
|
| Label protocol |
100 ng of quality controlled (using Bioanalyzer) total RNA were used for processing of the biotinylated cRNA.
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| |
|
| Hybridization protocol |
The samples were hybridized to the Affymetrix GeneTitan:HumanGene 2.1 ST Array Plate for 16 h at 48 ºC.
|
| Scan protocol |
HT Array Plates were scanned using the HT Scanner (Affymetrix GeneChip®HT)
|
| Description |
Gene expression data from HEK293 cells treated with flagellin of E. coli Nissle for 60min
|
| Data processing |
The data was analyzed using robust multi-array average (RMA) analysis using the rma() function from the R package oligo (version 1.30.0) with default setting (target=core).
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| |
|
| Submission date |
Aug 03, 2015 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Stefan Czemmel |
| Organization name |
Quantitative Biology Center (QBiC)
|
| Department |
University of Tuebingen
|
| Street address |
Auf der Morgenstelle 10
|
| City |
Tuebingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17692 |
| Series (1) |
| GSE71660 |
Expression data from murine TLR5 overexpressing HEK293 cells treated with flagellins of E. coli Nissle (EcN) and Salmonella Typhimurium SL1344 (ST) |
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