|
| Status |
Public on Jun 23, 2020 |
| Title |
CD163- d6, donor 1 |
| Sample type |
RNA |
| |
|
| Source name |
In vitro, GM-CSF+IFNg+IL23, day 6
|
| Organism |
Homo sapiens |
| Characteristics |
cytokine cocktail: GM-CSF+IFNg+IL23
cd163 expression: CD163-
timepoint: day 6
cell type: Inflammatory monocyte-like cells
donor: 1
donor diagnosis: Healthy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Machery-Nagel Nucleospin kit as per manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
Sense-strand cDNA was synthesized from 9 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the GeneChip® WT PicoTerminal Labeling Kit according to manufacturer’s instructions (Thermo Fisher Scientific).
|
| |
|
| Hybridization protocol |
5 µg DNA target was hybridized on GeneChip® Clariom™ D human (Thermo Fisher Scientific) and incubated at 45°C in the GeneChip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (ThermoFisher) using GeneChip Hybridization Wash and Stain kit according to the manufacturer’s instructions (ThermoFisher).
|
| Scan protocol |
The microarrays were scanned on a GeneChip® scanner 3000 (ThermoFisher).
|
| Data processing |
The preprocessing of the microarray data was done in R and its derived library for genomic data analysis, Bioconductor. We used the Bioconductor package oligo to load the CEL files in R environment and the rma function implemented in oligo for background subtraction, normalization and log2 transformation.
|
| |
|
| Submission date |
May 01, 2020 |
| Last update date |
Jun 26, 2020 |
| Contact name |
Marika Sarfati |
| E-mail(s) |
m.sarfati@umontreal.ca
|
| Organization name |
CRCHUM
|
| Street address |
900 Rue St Denis
|
| City |
Montreal |
| State/province |
Qc |
| ZIP/Postal code |
H2X 0A9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL23126 |
| Series (1) |
| GSE149722 |
A two-step human culture system replicates intestinal monocyte maturation cascade: conversion of tissue-like inflammatory monocytes into macrophages |
|
