|
| Status |
Public on May 10, 2019 |
| Title |
HeLa_6hr_THZ1 0.1μM_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
HeLa, 6hr, THZ1 100nM, replicate 3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
treatment: 100nM THZ1 or DMSO for 6 hours.
|
| Treatment protocol |
HeLa were seeded in 6-well plates at a density of 1ⅹ106 cells each well, and then treated with 100nM THZ1 or DMSO for 6 hours.
|
| Growth protocol |
HeLa were maintained in DMEM/high glucose medium containing 10% fetal bovine serum and 1% penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIZOL (Invitrogen) after treatment with THZ1 or DMSO for 6 hours. RNA was quantified using a NanoDrop ND-2000 (Thermo Scientific).
|
| Label |
Cy3
|
| Label protocol |
Total RNA were transcribed to double strand cDNA, then synthesized into cRNA. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug cRNA using One-Color (24×） low input Quick-Amp Labeling Kit（Agilent） according to the manufacturer's instructions. The labeled cRNAs were purified by RNAeasy column(QIAGEN RNAeasy Mini kit) . Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2545A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression after 100nM THZ1 treatment for 6 hours in HeLa
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1_QCM_Feb07) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Jan 23, 2019 |
| Last update date |
May 10, 2019 |
| Contact name |
Shanshan Zhong |
| E-mail(s) |
zhongshanshan1128@163.com
|
| Phone |
8617521199484
|
| Organization name |
Ren Ji hospital
|
| Street address |
NO.160 Road, Pudong New District
|
| City |
Shanghai |
| ZIP/Postal code |
200127 |
| Country |
China |
| |
|
| Platform ID |
GPL21185 |
| Series (1) |
| GSE125543 |
Inhibition of gene transcription after THZ1 treatment in HeLa |
|
