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Sample GSM1347024 Query DataSets for GSM1347024
Status Public on Aug 26, 2014
Title Gammadelta_LoIncidence_Stim_rep3
Sample type RNA
 
Source name Gammadelta T cells, low incidence, iRBCs, replicate 3
Organism Homo sapiens
Characteristics cells: Vdelta2+ gammadelta T cells
treatment: P. falciparum-infected red blood cells
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 Pf iRBC 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 10.75785122
5 5.306028875
6 4.905305599
7 5.082230793
8 5.473324579
9 7.255824731
10 10.93306898
11 10.37973509
12 9.982621739
13 9.579883909
14 5.099961815
15 4.843098561
16 5.524455539
17 6.982645754
18 7.825110917
19 10.67848555
20 12.46087788
21 4.886513568
22 9.137112894
23 4.612735699

Total number of rows: 58717

Table truncated, full table size 1016 Kbytes.




Supplementary file Size Download File type/resource
GSM1347024_US45102938_253949419804_S01_GE1-v1_95_Feb07_2_2.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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