|
| Status |
Public on Oct 01, 2017 |
| Title |
SW480_TSA_rep5 |
| Sample type |
RNA |
| |
|
| Source name |
SW480 Dukes' type B, colorectal adenocarcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SW480
cell type: colorectal adenocarcinoma cell line
tsa treated: 160 nM TSA for 24 hours
|
| Treatment protocol |
Cells were seeded 24h prior to treatment in a 96-well flat clear bottom black plate (Corning, Corning NY, USA), after which they were treated with 160 nM Trichostatin A (TSA) (Sigma-Aldrich, St. Louis, MO) for 24 hours. DMSO (Sigma-Aldrich) was used as vehicle control.
|
| Growth protocol |
Human colon adenocarcinoma cell lines DLD-1 and SW480 were purchased from the American Type Culture Collection (ATCC, Manassas, VA) and cultured in 10% fetal bovine serum (FBS) (Gibco, Thermofisher Scientific, Waltham, MA. USA) supplemented RPMI (Gibco) or DMEM (Gibco) medium, respectively. DLD-1 cells harboring an extra copy of chromosome 7 (DLD-1+7) were previously described (Upender et al. 2004) and maintained in 10% FBS supplemented RPMI medium with 100 µg/ml geneticin (G418) (Thermofisher).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the cells using the RNeasy Mini Kit (Qiagen, Hilden, Germany) and RNA integrity (RIN) was assessed with an RNA 6000 Nano LabChip Kit using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only samples with a RIN number >8.0 were included, and five replicates per condition were used.
|
| Label |
Cy3
|
| Label protocol |
One µg RNA from each cell line was amplified and labeled with Cy3 using the Quick Amp Labeling Kit, one-color (Agilent), according to manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Hybridization was performed over night on Human GE 4x44K v2 Microarrays (Agilent) according to the manufacturer’s protocol version 6.5.
|
| Scan protocol |
Slides were scanned with a microarray scanner G2565BA (Agilent) at 5-micron resolution.
|
| Data processing |
Raw data were log2 transformed and normalized to 75 percentile according to Agilent protocol. Probes with intensity no less than 50 in at least one sample were kept for analysis.
|
| |
|
| Submission date |
Jun 30, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Yue Hu |
| E-mail(s) |
yue.hu@nih.gov
|
| Organization name |
NCI
|
| Department |
Genetic
|
| Lab |
Thomas Ried
|
| Street address |
50 South Drive, Bldg. 50, Rm. 1408
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL13497 |
| Series (1) |
| GSE100705 |
Trichostatin A preferentially reverses the upregulation of gene expression levels induced by gain of chromosome 7 in colorectal cancer cell lines |
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