|
| Status |
Public on Mar 24, 2020 |
| Title |
SPM, LPS, patient 2 |
| Sample type |
RNA |
| |
|
| Source name |
Small Peritoneal Macrophages treated with LPS 20 ng/ml for 3h, BioSample 2
|
| Organism |
Homo sapiens |
| Characteristics |
patient: 2
cell type: peritoneal macrophages
pm subset: SPM
treatment: LPS
|
| Treatment protocol |
Cells were treated with 10 ng/mL lipopolysaccharide (LPS) from E. coli K12 (InvivoGen) or left untreated (control)
|
| Growth protocol |
Sorted PM subsets were seeded in cell culture plates at a density of about 100k cell per cm2 (0.75 – 1.0 mio cells per well) in RPMI supplemented with 10% FCS and 1% L-glutamine-penicillin-streptomycinand for 3h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using NucleoSpin RNA Kit (Macherey-Nagel) according to manufactures protocol. The RNA concentration and purity were determined spectrophotometrically. RNA integrity was determinded using the Agilent RNA Screen Tape System on a TapeStation 2200 instrument (Agilent Technologies).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT PLUS Reagent Kit).
|
| |
|
| Hybridization protocol |
According to manufacture protocol (GeneChip® WT PLUS Reagent Kit, ThermoFisher Scientific). Complentary DNA was hybridized for 16 hr at 45C and 60 rpm on a Clariom S HT 24 array plate.
|
| Scan protocol |
Clariom S HT 24 array plate was scanned using an Affymetrix GeneTitan Scanner.
|
| Description |
Gene expression data from small peritoneal macrophages of patient with liver cirrhosis isolated from ascitic fluid after treatment with 10 ng/ml LPS
|
| Data processing |
CHP files were created using Transcriptome analysis concole (TAC, ThermoFisher Scientific). GC Correction, SST (Signal Space Transformation), RMA background and quantile normalization were applied. Differential gene expression between SPMs and LPMs was analyzed in steady state or following LPS stimulation. Before extracting differentially expressed genes, patient dependent differences were eliminated using repeated measure option (pairwise analysis or batch effect removal) of TAC software package.
|
| |
|
| Submission date |
Jan 09, 2019 |
| Last update date |
Mar 24, 2020 |
| Contact name |
Sven Stengel |
| E-mail(s) |
[email protected]
|
| Organization name |
Jena University Hospital
|
| Department |
Clinic for Internal Medicine IV
|
| Lab |
Gastroenterology, Hepatology and Infectiology
|
| Street address |
Am Klinikum 1
|
| City |
Jena |
| ZIP/Postal code |
07747 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24324 |
| Series (1) |
| GSE124878 |
Peritoneal macrophage heterogeneity in decompensated liver cirrhosis |
|
