|
| Status |
Public on May 10, 2017 |
| Title |
CD161- NK cell donor 2 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral Blood, FACS sorted CD19-CD14-CD3-CD56+ NK cells
|
| Organism |
Homo sapiens |
| Characteristics |
individual: Donor 2
tissue: Peripheral Blood
cell type: FACS sorted CD19-CD14-CD3-CD56+ NK cells
cell subtype: CD161 Negative
|
| Treatment protocol |
Live CD3-CD19-CD14-CD56+ NK 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- NK T cells
|
| Data processing |
Raw data microarray features were normalized using variance stabilizing normalization (vsn) using R and Bioconductor packages.
After data were normalized (vsn), control probes were removed and then low detected probes removed too. Negative controls were used to asses the background level and only probes having a signal above background in at least four samples were retained.
|
| |
|
| Submission date |
May 09, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Timothy Hinks |
| E-mail(s) |
timothy.hinks@ndm.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
NDM Experimental Medicine - New College
|
| Street address |
John Radcliffe Hospital, Headley Way, Oxford
|
| City |
Oxford |
| State/province |
United Kingdom |
| ZIP/Postal code |
OX3 9DU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE98702 |
CD161 defines a distinct subset of pro-inflammatory NK cells that are present in the inflamed gut |
|
