|
| Status |
Public on Jul 10, 2019 |
| Title |
HCC 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
sorted CSCs
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: Hepatocellular carcinoma (HCC) patient
gender: male
tissue: liver tumor
cell type: cell stem cell (CSC); CD13+CD133+
|
| Treatment protocol |
Hepatocytes were isoloated from liver tumor tissues. Cells were incubated with the following commercial antibodies: phycoerythrin (PE)-anti-human CD133 (Miltenyi Biotec) and fluorescein isothiocyanate (FITC)- anti-human CD13 (eBioscience) on ice for 30 minutes. Then, cells were washed with phosphate buffered saline (PBS) for three times, followed by sorting with FACS Aria III (BD Immunocytometry Systems, San Jose, CA, USA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Trizol from cells according to the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.
|
| |
|
| Channel 2 |
| Source name |
soted non-CSCs
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: Hepatocellular carcinoma (HCC) patient
gender: male
tissue: liver tumor
cell type: non cell stem cell (non-CSC):CD13-CD133-
|
| Treatment protocol |
Hepatocytes were isoloated from liver tumor tissues. Cells were incubated with the following commercial antibodies: phycoerythrin (PE)-anti-human CD133 (Miltenyi Biotec) and fluorescein isothiocyanate (FITC)- anti-human CD13 (eBioscience) on ice for 30 minutes. Then, cells were washed with phosphate buffered saline (PBS) for three times, followed by sorting with FACS Aria III (BD Immunocytometry Systems, San Jose, CA, USA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Trizol from cells according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.
|
| |
|
| |
| Hybridization protocol |
Labelled cDNA hybridised using the MWG Gene-Frame system. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning.
|
| Scan protocol |
Arrays scanned using an Affymetrix 428 scanner and Imagene version 4 software.
|
| Description |
Gene expression data from CSCs and non-CSC of HCC 2
|
| Data processing |
Data analysis was carried out using Imagene, version 5.1 and Genesight version 4 (Biodiscovery Inc). The mean values from each channel were log2 transformed and normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the Cy5/Cy3 fluorescence ratios from each patient.
|
| |
|
| Submission date |
Nov 12, 2018 |
| Last update date |
Jul 10, 2019 |
| Contact name |
Yanying Wang |
| E-mail(s) |
wangyanying@moon.ibp.ac.cn
|
| Organization name |
Institute of Biophysics, Chinese Academy of Sciences
|
| Street address |
15 Datun Road, Chaoyang District,Beijing 100101, China
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL20115 |
| Series (1) |
| GSE122420 |
Expression data from CSC and Non-CSC of three primary HCC samples |
|
