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Sample GSM1519613 Query DataSets for GSM1519613
Status Public on Oct 07, 2014
Title ExVivoTCRgd_CD161-_Donor3
Sample type RNA
Source name Peripheral Blood, FACS sorted TCRgd+ T cells
Organism Homo sapiens
Characteristics cd161 subtype: negative
donor: 3
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

Data table header descriptions
VALUE vsn-normalised signal intensities

Data table
1 15.18315362
2 2.766827432
3 2.911010265
4 9.472530691
5 4.728230682
6 7.389415262
7 6.275590745
8 9.162481987
9 3.416134064
10 5.363234372
11 3.52549799
12 11.72256806
13 9.205375624
14 8.173308987
15 5.663611405
16 2.538103967
17 5.780987037
18 3.239912533
19 3.678433019
20 10.23161557

Total number of rows: 62976

Table truncated, full table size 1089 Kbytes.

Supplementary file Size Download File type/resource
GSM1519613_252800414171_S01_GE1_107_Sep09_2_2.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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