|
| Status |
Public on Oct 07, 2014 |
| Title |
ExVivoTCRgd_CD161+_Donor2 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral Blood, FACS sorted TCRgd+ T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cd161 subtype: positive
donor: 2
cell type: TCRgd T cells
|
| Treatment protocol |
TCRgd+ T cell subsets were sorted using a FACS sorter
|
| Growth protocol |
Cells taken ex vivo from healthy donors and separated using Ficoll centrifugation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rneasy® Mini Kit, Qiagen following manufacturer's protocol. RNA samples were quality checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies)
|
| Label |
Cy3
|
| Label protocol |
10ng of each total RNA sample was used to produce Cy3-labeled cRNA using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and dye-incorporation rate were measured with the ND-100 Spectrophotometer (NanoDrop Technologies).
|
| |
|
| Hybridization protocol |
The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17hrs, 65degrees celsius) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.
|
| Scan protocol |
Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.
|
| Description |
Gene expression in FACS sorted CD161+ TCRgd T cells
|
| Data processing |
Raw data microarray features were normalised using variance stabilising normalisation (vsn) using R and Bioconductor packages.
|
| |
|
| Submission date |
Oct 06, 2014 |
| Last update date |
Oct 07, 2014 |
| Contact name |
Joannah R Fergusson |
| Organization name |
University of Oxford
|
| Department |
Peter Medawar Building for Pathogen Research
|
| Street address |
South Parks Road
|
| City |
Oxford |
| State/province |
select a state |
| ZIP/Postal code |
OX1 3SY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13607 |
| Series (2) |
| GSE62097 |
CD161 defines a transcriptional and functional phenotype shared across distinct human T cell lineages (TCRgd) |
| GSE62099 |
CD161 defines a transcriptional and functional phenotype shared across distinct human T cell lineages |
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