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Sample GSM2700945 Query DataSets for GSM2700945
Status Public on Jul 01, 2020
Title hepg2_16µg/ml_H3
Sample type RNA
 
Source name liver cancer cells
Organism Homo sapiens
Characteristics tissue: liver cancer cells
tissue: hepatocellular carcinoma
Treatment protocol Two samples were treated with polaprezinc at 0 or 16 µg/ml
Growth protocol Human hepatic cancer cell lines cultured in RPMI 1640 medium (Gibco; Thermo Fisher Scientific, Inc., Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS, Gibco;Thermo Fisher Scientific, Inc.). The cells were maintained at 37˚C in 5% CO2.
Extracted molecule total RNA
Extraction protocol RNA extraction by Trizol Reagent ( Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).
Label cy5
Label protocol 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion). Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).
 
Hybridization protocol HOA 7.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.
Scan protocol HOA 7.1 The arrays were scanned by Agilent Microarray Scanner (G2505C) 0.1 XDR protocol and quantify the fluoresence intensity.
Description After 7 days of treatment with polaprezinc at 0 or 16 µg/ml, total RNA from hepG2 cells was extracted using theTRIzol(Invitrogen; Thermo Fisher Scientific, Inc.)method.A NanoDrop ND-1000 spectrophotometer (NanoDropTechnologies; Thermo Fisher Scientific, Inc.) was used to determine RNA concentration. The criteria for absorbance ratios was established as A260/A280Z1.8 and A260/A230Z1.5. The criteria for the RNA integrity numbervalue was set at 46. Genomic DNA contamination was evaluated by gel electrophoresis. Microarray analysis was performed using Human OneArray(®) Annotation HOA v7 release 1.0(Phalanx Biotech Group, Inc. ) , which contains 31,741 mRNA probes, detecting 20,672 genes in the human genome.
Data processing Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that flag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.
Rosetta Resolvers computed normalized intensities, average of technical replicates.
 
Submission date Jul 12, 2017
Last update date Jul 01, 2020
Contact name jingjing wang
Organization name NA
Street address WENYI WEST road
City hangzhou
ZIP/Postal code 310000
Country China
 
Platform ID GPL21282
Series (1)
GSE101305 Polaprezinc inhibits liver fibrosis and proliferation in hepatocellular carcinoma

Data table header descriptions
ID_REF
VALUE Normalized Intensity

Data table
ID_REF VALUE
PH_hs_0000002 371.929199
PH_hs_0000003 102.939217
PH_hs_0000004 14273.625
PH_hs_0000005 72.302544
PH_hs_0000006 626.213562
PH_hs_0000007 5298.91846
PH_hs_0000008 6522.54736
PH_hs_0000009 6299.51221
PH_hs_0000010 64252.4531
PH_hs_0000011 1640.28735
PH_hs_0000012 1213.21216
PH_hs_0000013 3075.92188
PH_hs_0000014 517.147034
PH_hs_0000015 209.554825
PH_hs_0000016 113.355682
PH_hs_0000017 77.817146
PH_hs_0000018 1310.63684
PH_hs_0000019 97.424614
PH_hs_0000021 727.314575
PH_hs_0000022 124.99762

Total number of rows: 28264

Table truncated, full table size 682 Kbytes.




Supplementary file Size Download File type/resource
GSM2700945_H004-3140903233.gpr.gz 1.6 Mb (ftp)(http) GPR
Processed data included within Sample table

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