|
| Status |
Public on Jul 01, 2020 |
| Title |
hepg2_0µg/ml_H1 |
| 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).
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| |
|
| 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.
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| |
|
| 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 |
|
