|
| Status |
Public on Apr 13, 2022 |
| Title |
D1M2: Monocytes_Donor1_HD_2hr |
| Sample type |
RNA |
| |
|
| Source name |
Monocytes, Donor 1, high density culture, 2hr.
|
| Organism |
Homo sapiens |
| Characteristics |
donor: 1
cell type: Monocyte
timepoint: 2hr
initial culture density: 1x10^7 cells/mL
isolation from pbmcs: Pan Monocyte Isolation Kit, human, Miltenyi Biotech
|
| Growth protocol |
After isolation from PBMCs, cells were cultured at an initial density of 1 x 10^7 cell/mL in CTL-Test Medium ((Europe GmbH, Bonn, Germany), supplemented with glutamine (2 mM), pyruvate (1 mM), penicillin (100 IU/mL), and streptomycin (100 IU/mL)), at 37°C in 5% CO2. Cells were cultured for 0 (no culture), 2, 10 or 24 hours before RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction using RNAeasy Mini Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Standard Illumina Whole-Genome DASL HT labeling protocol
|
| |
|
| Hybridization protocol |
Standard Illumina Whole-Genome DASL HT hybridisation protocol.
|
| Scan protocol |
Arrays were scanned on a BeadArray reader
|
| Data processing |
Data was processed using the limma package (version 3.24.15) in R (version 3.3.3). Non-normalised, probe and control-probe matrices were inputed using the read.ilmn function. Data was then background-corrected and quantile normalised using the neqc function and quality checked by only including probes that were expressed in at least 3 arrays according to detection p-values of 5%. This is the data provided in the normalised matrix.
|
| |
|
| Submission date |
Jan 27, 2021 |
| Last update date |
Apr 13, 2022 |
| Contact name |
Rosanna C G Smith |
| E-mail(s) |
r.c.smith@soton.ac.uk
|
| Organization name |
University of Southampton
|
| Department |
Cancer Sciences Unit, Faculty of Medicine
|
| Lab |
Antibody and Vaccine Group
|
| Street address |
Centre for Cancer Immunology, University Hospital Southampton (MP 127), Tremona Road
|
| City |
Southampton |
| State/province |
Hampshire |
| ZIP/Postal code |
SO16 6YD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13938 |
| Series (1) |
| GSE165643 |
Microarray timecourse profiling of gene expression changes in primary human monocytes and B-cells cultured at high density to investigate FcgR2b associated gene expression changes |
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