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Sample GSM1347027 Query DataSets for GSM1347027
Status Public on Aug 26, 2014
Title Gammadelta_LoIncidence_Unstim_rep1
Sample type RNA
 
Source name Gammadelta T cells, low incidence, unstimulated, replicate 1
Organism Homo sapiens
Characteristics cells: Vdelta2+ gammadelta T cells
treatment: Unstimulated
incidence: low
Treatment protocol PBMCs were thawed, rested overnight, and co-incubated with P. falciparum-infected red blood cells for 6 hours, followed by FACS isolation of the Vdelta2+ subset of gammadelta T cells.
Growth protocol PBMCs were isolated from Ugandan children over Ficoll-Histopaque and cryopreserved in liquid nitrogen.
Extracted molecule total RNA
Extraction protocol RNA was isolated with the RNAqueous Micro kit (Life Technologies). Isolated RNA was amplified using the Aminoallyl MessageAmp II kit (Life Technologies).
Label Cy3
Label protocol Aminoallyl-incorporated aRNA was conjugated to Cy3 dye (Life Technologies) for 1 h in sodium bicarbonate buffer and cleaned up on a spin column.
 
Hybridization protocol 1.5 ug of Cy3-labeled aRNA was fragmented and hybridized to Agilent 8x60k mouse gene expression microarrays as per manufacturer instructions.
Scan protocol Arrays were scanned on an Agilent scanner at 3 um resolution as 20-bit TIFF images.
Description Gene expression in Vdelta2+ gammadelta T cells after incubation without stimulation
Data processing Features were extracted using Agilent Feature Extraction software. Non-background subtracted raw Cy3 intensities were taken as gene expression values and quantile normalized.
 
Submission date Mar 12, 2014
Last update date Aug 26, 2014
Contact name Charlie Kim
E-mail(s) cckim47@gmail.com
Organization name University of California, San Francisco
Department Medicine
Lab Kim
Street address 1001 Potrero Ave
City San Francisco
State/province CA
ZIP/Postal code 94110
Country USA
 
Platform ID GPL16699
Series (1)
GSE55843 Loss and dysfunction of Vdelta2+ gammadelta-low T cells is associated with clinical tolerance to malaria

Data table header descriptions
ID_REF
VALUE Normalized log2 Cy3 intensity

Data table
ID_REF VALUE
4 10.8277049
5 5.26364153
6 5.404132556
7 5.990905073
8 6.038910882
9 9.443742969
10 11.18431991
11 11.27351353
12 11.61085069
13 9.047678937
14 5.603003762
15 5.525506694
16 5.678433573
17 6.695313934
18 6.678458743
19 11.48801702
20 12.88979555
21 5.445438573
22 10.39438682
23 5.354174912

Total number of rows: 58717

Table truncated, full table size 1017 Kbytes.




Supplementary file Size Download File type/resource
GSM1347027_US45102938_253949419805_S01_GE1-v1_95_Feb07_1_1.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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