|
| Status |
Public on Jul 31, 2023 |
| Title |
PBMCs-XCR1neg-R848-1 |
| Sample type |
RNA |
| |
|
| Source name |
isolated from PBMCs XCR1- R848
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMCs
diseasse state: healthy donor
|
| Treatment protocol |
Cells were stimulated with 5µg/ml R848 (TLR7-ligand) or control treated for 3h
|
| Growth protocol |
Blood DCs were enriched from PBMCs of healthy donors using the EasySep Pan-DC Pre-Enrichment Kit. XCR1- and XCR1+ cDC1 were sorted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were lysed using 1/3 RLT buffer and sample mRNAs were stored at -80°C
|
| Label |
N/A
|
| Label protocol |
Labeling was performed as described in the manufacturers instruction (NanoString Technologies). Briefly, samples were labeled with reporter code sets (nCounter_Hs_Myeloid_Innate_Immunity_V2 Panel) consisting of many RNA capture probes targeting specific mRNAs. Each probe is labeled with a unique combination of fluorochromes (molecular barcode).
|
| |
|
| Hybridization protocol |
Hybridization was performed as described in the manufacturers instruction. Briefly, samples were hybridized with reporter code sets (target-specific Reporter and Capture Probes) for 24h in a thermal cycler at 65°C
|
| Scan protocol |
nCounter Prep Station v4.1.0.1 was used. Scanning and image aquisition using the NanoString Digital Analyzer.
|
| Description |
reporter code sets (Nanostring Technologies, nCounter_Hs_Myeloid_Innate_Immunity_V2 Panel)
|
| Data processing |
NanoString data were analyzed and exported using nSolver software (version 4.0). RUVg method was applied to remove the batch effect and data were normalized using NanoStringNorm according to 14 control genes and 40 housekeeping spikes genes. Differential gene expression analysis were conducted using edgeR
normalized signal intensity (log2 transformed)
|
| |
|
| Submission date |
Jul 18, 2023 |
| Last update date |
Jul 31, 2023 |
| Contact name |
Chunguang Liang |
| E-mail(s) |
liang@biozentrum.uni-wuerzburg.de
|
| Phone |
09313184561
|
| Organization name |
Biozentrum
|
| Department |
Bioinformatics
|
| Lab |
Dr. Chunguang Liang
|
| Street address |
Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland
|
| City |
Würzburg 97074 |
| State/province |
Bayern |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25266 |
| Series (1) |
| GSE237715 |
XCR1 expression distinguishes human conventional dendritic cells type 1 with full effector functions from their immediate precursors |
|
