|
| Status |
Public on Jul 19, 2017 |
| Title |
OC20_donor 1 |
| Sample type |
RNA |
| |
|
| Source name |
CD14 cells treated with M-CSF/RANKL for 20 days
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: CD14 cells treated with M-CSF/RANKL for 20 days
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Human monocytes were isolated using MACS CD14 microbeads (Milteny) from peripheral blood mononuclear cells using the manufacturer's protocol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Not provided
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).
|
| Scan protocol |
Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
|
| Description |
CD14 cells treated with M-CSF/RANKL for 20 days
|
| Data processing |
Expression data has been normalized using functions from the R package limma. In detail the data was background corrected using the function "normexp" and then normalized between arrays using quantile normalization. Normalized array feature values were grouped by gene name and summarized by mean. The "patient effect" was substracted from the genewise data by a linear model using "patient" as predictor.
Given are the luminescense values (Cy3) from the Agilent array; as raw data for all array features and as normalized and summarized genewise expression values as described above.
|
| |
|
| Submission date |
Apr 07, 2017 |
| Last update date |
Jul 19, 2017 |
| Contact name |
Esteban Ballestar |
| Organization name |
Josep Carreras Research Institute (IJC)
|
| Lab |
Epigenetics and Immune Disease
|
| Street address |
Ctra de Can Ruti, Camí de les Escoles s/n
|
| City |
Badalona, Barcelona |
| State/province |
N/A = Not Applicable |
| ZIP/Postal code |
08916 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE97498 |
Comparison of the RNA expression profiles of CD14+ monocytes from human peripheral blood with derived macrophages (MACs) and osteoclasts (OCs) obtained by exposure with M-CSF and M-CSF/RANKL, respectively, during 5 and 20 days |
|
