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Sample GSM2411190 Query DataSets for GSM2411190
Status Public on Nov 28, 2018
Title Cynomolgus monkey PBMCs treated with PHA (10 μg.ml-1) replicate 1
Sample type RNA
 
Channel 1
Source name The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with PHA ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 1
Organism Macaca fascicularis
Characteristics tissue: peripheral blood
cell type: mononuclear
process: test
stimulation: PHA
Treatment protocol The PBMCs (1×10^6 cells/ml) obtained from the cynomolgus monkeys or the human donors were treated with PHA (2 μg.ml-1 or 10 μg.ml-1) or LPS (2 μg.ml-1 or 10 μg.ml-1) and incubated at 37 °C for 3 days. Cells cultured under similar conditions without any stimulation served as the negative control.
Growth protocol Whole heparinized cynomolgus monkey blood was obtained from 3 apparently healthy 2.5-year-old cynomolgus monkeys. The monkey PBMCs were isolated by Ficoll-Hypaque density centrifugation (Histopaque LTS1079, Sigma, USA). All procedures were performed in accordance with the Guide for the Care and Use of Laboratory Animals of NCSED, China. A relative centrifugal force of 2000 rpm was used for 30 minutes to separate the PBMCs. The PBMCs were washed twice in Hank’s and re-suspended at a final concentration of 1×10^6 cells/ml in culture medium (RPMI1640, GIBCO, USA) supplemented with 10% fetal calf serum. All experiments using the cultured cells were set up in triplicate.
Extracted molecule total RNA
Extraction protocol The total RNA was extracted from the PBMCs using Trizol reagent (Invitrogen Company) according to the manufacturer’s instructions. The purity of the RNA in each sample was assessed spectrophotometerically at 260 and 280 nm (NanoDrop Technologies), and the RNA integrity was assessed using formaldehyde agarose gel electrophoresis.
Label Cy5
Label protocol not provided
 
Channel 2
Source name The PBMCs cultured under similar conditions without any stimulation served as the negative control, replicate 1
Organism Macaca fascicularis
Characteristics tissue: peripheral blood
cell type: mononuclear
process: control
Treatment protocol The PBMCs (1×10^6 cells/ml) obtained from the cynomolgus monkeys or the human donors were treated with PHA (2 μg.ml-1 or 10 μg.ml-1) or LPS (2 μg.ml-1 or 10 μg.ml-1) and incubated at 37 °C for 3 days. Cells cultured under similar conditions without any stimulation served as the negative control.
Growth protocol Whole heparinized cynomolgus monkey blood was obtained from 3 apparently healthy 2.5-year-old cynomolgus monkeys. The monkey PBMCs were isolated by Ficoll-Hypaque density centrifugation (Histopaque LTS1079, Sigma, USA). All procedures were performed in accordance with the Guide for the Care and Use of Laboratory Animals of NCSED, China. A relative centrifugal force of 2000 rpm was used for 30 minutes to separate the PBMCs. The PBMCs were washed twice in Hank’s and re-suspended at a final concentration of 1×10^6 cells/ml in culture medium (RPMI1640, GIBCO, USA) supplemented with 10% fetal calf serum. All experiments using the cultured cells were set up in triplicate.
Extracted molecule total RNA
Extraction protocol The total RNA was extracted from the PBMCs using Trizol reagent (Invitrogen Company) according to the manufacturer’s instructions. The purity of the RNA in each sample was assessed spectrophotometerically at 260 and 280 nm (NanoDrop Technologies), and the RNA integrity was assessed using formaldehyde agarose gel electrophoresis.
Label Cy3
Label protocol not provided
 
 
Hybridization protocol The purified total RNA was amplified and labeled, and the microarray analysis was then performed overnight using Agilent Human and Monkey Whole Genome GeneChips (Agilent, Palo Alto, CA).
Scan protocol not provided
the array data were analyzed using Agilent Feature Extraction software.
Description Cy5/Cy3
Data processing After normalization of the raw data, probes with intensities <400 were removed from the subsequent analysis using Significance Analysis of Microarray (SAM) software. The differentially expressed genes (DEGs) were identified as those having an adjusted q-value of <0.05 and an average fold-change difference of >1.5.
 
Submission date Nov 30, 2016
Last update date Nov 28, 2018
Contact name wang liang
E-mail(s) wangliangkexue@163.com
Organization name BioChainBJ
Street address 7A North Yongchang Road BDA
City Beijing
ZIP/Postal code 100176
Country China
 
Platform ID GPL22725
Series (2)
GSE90722 The morphological and functional differences and similarities of immune cells between non-human primates and humans [monkey]
GSE90723 The morphological and functional differences and similarities of immune cells between non-human primates and humans

Data table header descriptions
ID_REF
VALUE ratio representing test/control (cy5/cy3)

Data table
ID_REF VALUE
A_01_P000001 1.329098531
A_01_P000003 0.505441317
A_01_P000012 1.146841693
A_01_P000013 1.034832694
A_01_P000018 1.556680047
A_01_P000038 1.041180318
A_01_P000039 1.33180642
A_01_P000041 1.050008596
A_01_P000043 1.011532318
A_01_P000061 1.216514836
A_01_P000063 1.046723824
A_01_P000068 0.932772534
A_01_P000072 0.647444528
A_01_P000077 0.3008129
A_01_P000079 0.882101945
A_01_P000080 0.995807876
A_01_P000085 0.759717334
A_01_P000090 1.3187595
A_01_P000095 0.967370743
A_01_P000105 1.285985952

Total number of rows: 15268

Table truncated, full table size 381 Kbytes.




Supplementary file Size Download File type/resource
GSM2411190_SG12154191_253804010004_S001_GE2_1100_Jul11_1_3.txt.gz 4.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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