GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2570289 Query DataSets for GSM2570289
Status Public on Jul 19, 2017
Title MAC20_donor 2
Sample type RNA
Source name CD14 cells treated with M-CSF for 20 days
Organism Homo sapiens
Characteristics tissue: CD14 cells treated with M-CSF 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 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

Supplementary data files not provided
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap