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Sample GSM2610387 Query DataSets for GSM2610387
Status Public on May 10, 2017
Title CD161- NK cell donor 4
Sample type RNA
Source name Peripheral Blood, FACS sorted CD19-CD14-CD3-CD56+ NK cells
Organism Homo sapiens
Characteristics individual: Donor 4
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
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

Data table header descriptions
VALUE vsn-normalized signal intensities

Data table
4 8.538412332
5 6.364730305
6 6.570867
7 7.953265581
8 9.808143501
10 6.05007273
12 12.59257342
13 10.03156166
14 8.47434208
15 7.097707406
17 6.874393071
20 9.734652121
21 10.12249682
24 7.421663577
25 7.973451067
26 10.48082068
28 8.051482049
29 12.39347262
32 9.163584041
35 5.708597752

Total number of rows: 36364

Table truncated, full table size 628 Kbytes.

Supplementary file Size Download File type/resource
GSM2610387_252800414384_S01_GE1_107_Sep09_2_4.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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