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Sample GSM942972 Query DataSets for GSM942972
Status Public on Jun 05, 2012
Title peritumor derived γδT_rep5
Sample type RNA
 
Source name Human paired peritumor-derived γδT cells, replicated 5
Organism Homo sapiens
Characteristics tissue: Peritumor liver tissue
gender: male
Treatment protocol Freshly acquired HCC tissue and paired peritumor liver tissue were minced into small pieces of ~1mm3, then digested in an enzyme cocktail (1mg/ml collagenase type IV, 0.02mg/ml DNase in HBSS with 10% FBS) for 1 hour at 37°C. After filtration and extensive wash, the cells were subjected to discontinous density gradient centrifugation in Percoll. After removal of dead cells and incubation with components of TCRγ/δ isolation kit (Mitenyi Biotec), γδ T cells were positively selected from the single-cell suspension using autoMACS Separator (Miltenyi Biotec) with recommended programs.
Extracted molecule total RNA
Extraction protocol Total RNA were extracted from freshly purified γδ T cells using Trizol reagent (Invitrogen) following the manufacturer's recommendation. Sample RNA Quality Control was performed with using Bioanalyzer 2100 to evaluate the RNA integrity from all samples. The NanoDrop ND-1000 was used for accurately measuring RNA concentrations (OD260), protein contamination (ratio of OD260/OD280) and organic compound contamination (ratio of OD260/OD230).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol the arrays were scanned by the Agilent Scanner G2505B.
Description Gene expression of peritumor-derived γδT cells
Data processing Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).
 
Submission date Jun 04, 2012
Last update date Jun 05, 2012
Contact name Yong Yi
E-mail(s) yiyong1984@gmail.com
Phone 15821328520
Organization name Liver Cancer Institute
Street address 180 Fenglin Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL13497
Series (1)
GSE38476 Investigation of the gene expression pattern of human hepatocellular carcinoma (HCC) infiltrating γδT cells

Data table header descriptions
ID_REF
VALUE quantile normalized signal intensity

Data table
ID_REF VALUE
A_23_P42935 8.396611514
A_23_P117082 11.04838908
A_23_P2683 6.819166049
A_33_P3367647 5.836871819
A_23_P157316 6.885131908
A_32_P14850 14.45160185
A_23_P158596 7.034559896
A_23_P350107 9.485016952
A_23_P388190 8.30806109
A_23_P106544 11.7622604
A_23_P94998 8.471034088
A_23_P103905 9.459522202
A_24_P497186 7.367891088
A_23_P118536 8.193252811
A_23_P434289 6.218712284
A_33_P3326898 4.125793758
A_24_P67898 10.61523879
A_24_P28657 9.981446625
A_33_P3344292 4.783514359
A_23_P2873 8.32971131

Total number of rows: 22736

Table truncated, full table size 556 Kbytes.




Supplementary file Size Download File type/resource
GSM942972_846P_gdT.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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