|
| Status |
Public on Dec 01, 2018 |
| Title |
TH17 CD161_pos 4824 medium |
| Sample type |
RNA |
| |
|
| Source name |
human blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: T Helper Lymphocyte 17
cd161 marker: positive
clone: 4824
treatment: none
|
| Treatment protocol |
Cells were analyzed either resting either after 6 hours stimulation with anti-CD2+anti-CD3+anti-CD28 coated beads.
|
| Growth protocol |
Cells were kept in culture in RPMI 1640 medium supplemented with 10% FCS and 50 IU/ml recombinanat human IL-2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy Micro Kit - QIAGEN following manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer
|
| Label |
Cy3
|
| Label protocol |
Labelling was performed with the one color (Cyanine 3-CTP) Low Input Quick Amp Labeling Kit (Agilent Technologies) accordinf to manufacturer protocol.
|
| |
|
| Hybridization protocol |
Hybridization was performed according to specifications in One-Color Microarray-Based Gene Expression Analysis Protocol
|
| Scan protocol |
The data was extracted using Agilent Feature Extraction Software version 10.7.3.1 with default parameters of protocol GE1_107_Sep09.
|
| Data processing |
Data preprocessing was performed using R/Bioconductor (version 3.6) Agi4x44PreProcess (version 1.22) package. Briefly, raw Feature Extractor data was loaded into R and further background corrected (method=”half”, offset=50), normalized (method=”quantile”) and filtered (wellaboveBG=60, isfound=60). Statistical analysis and DE extraction were peformed with limma package (version 3.34.6).
|
| |
|
| Submission date |
Feb 06, 2018 |
| Last update date |
Dec 02, 2018 |
| Contact name |
Matteo Ramazzotti |
| E-mail(s) |
matteo.ramazzotti@unifi.it
|
| Organization name |
University of Florence
|
| Department |
Experimental and Clinical Biomedical Sciences
|
| Street address |
viale Morgagni 50
|
| City |
Firenze |
| ZIP/Postal code |
50134 |
| Country |
Italy |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE110230 |
Transcriptome data from human Th17, classic Th1 and non-classic Th1 cell clones |
|
