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Sample GSM4199180 Query DataSets for GSM4199180
Status Public on Dec 03, 2019
Title U87MG, 4 hr, MOI=0.01, replicate 1
Sample type RNA
 
Source name U87MG, 4 hr, MOI=0.01, replicate 1
Organism Homo sapiens
Characteristics cell line: U87MG
Treatment protocol SH-SY5Y and U87MG cells were seeded at a density of 3×105 cells/well in 12-well plate overnight to adhere. Cells were washed twice with phosphate buffer saline (PBS) and infected with HSV-1 strains of 17syn+、Kos and Mckrae at an MOI of 0.01, respectively.
Growth protocol Human neuroblastoma cells SH-SY5Y and human glioblastoma cells U87MG were purchased from American Type Culture Collection (ATCC, VA, USA) and stored in Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences (Kunming, China). The above tow types of cells were cultured in Dulbecco′s modified Eagle′s medium (DMEM, Thermo Fisher Scientific, MA, USA), supplied with 10% (V/V) fetal bovine serum (FBS, Gibco, MA, USA) and penicillin–streptomycin (100 U/mL and 100 μg/mL). The cells were maintained at 37C in a humidified atmosphere containing 5% CO2.
Extracted molecule total RNA
Extraction protocol The total RNA of infected cells was extracted and purified using miRNeasy Mini Kit (QIAGEN, GmbH, Germany) according to the manufacturer’s instructions at the time point of 0, 4 and 10 hpi. The RNA concentration was measured by NanoDrop ND-2000 spectrophotometer (Thermo, MA, USA) and RNA integrity number (RIN) was determined by 2100 Bioanalyzer (Agilent technologies, CA, USA) and agarose gel electrophoresis.
Label Cy3
Label protocol miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat #5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.
 
Hybridization protocol Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C,20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).
Scan protocol Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.
Description miRNAs expression profile infected by HSV-1 in U87MG cells
Data processing Raw data were normalized by Quantile algorithm
 
Submission date Dec 02, 2019
Last update date Dec 05, 2019
Contact name yongzhong duan
E-mail(s) duanyongzhong@imbcams.com.cn
Phone +8613888329604
Organization name kunming medical university
Street address chongrong west road, chenggong new district
City kunming
State/province Yunnan
ZIP/Postal code 650500
Country China
 
Platform ID GPL25134
Series (1)
GSE141241 HSV-1 infection of neural system-derived cells, including SH-SY5Y and U87MG cells at 0, 4 and 10 hour post infection with an MOI of 0.01,to identify the differentially expressed miRNAs and perform pathway enrichment analysis using KEGG.

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
Blank 2.237393725
dmr_285 10.58057935
dmr_3 14.02484971
dmr_308 2.938039258
dmr_316 3.332842768
dmr_31a 9.262474775
dmr_6 13.80302768
hsa-let-7a-3p 3.217693749
hsa-let-7a-5p 12.20854515
hsa-let-7b-3p 4.231663429
hsa-let-7b-5p 11.31359572
hsa-let-7c-3p 3.100384784
hsa-let-7c-5p 9.69215415
hsa-let-7d-3p 3.005835452
hsa-let-7d-5p 7.570906381
hsa-let-7e-3p 3.01628005
hsa-let-7e-5p 8.705791248
hsa-let-7f-1-3p 4.599750218
hsa-let-7f-2-3p 3.202946722
hsa-let-7f-5p 11.24200169

Total number of rows: 2556

Table truncated, full table size 66 Kbytes.




Supplementary file Size Download File type/resource
GSM4199180_U87MG-4hpi.txt.gz 6.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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