|
| Status |
Public on Jun 01, 2023 |
| Title |
InVitro_KMS-11_delta-C1orf112 |
| Sample type |
RNA |
| |
|
| Source name |
delta-C1orf112 KMS-11, 48h
|
| Organism |
Homo sapiens |
| Characteristics |
cell: MM cell line
gender: Female
age: 67y
|
| Treatment protocol |
The MM cell lines were incubated in a RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. Following 24h incubation, the cells were then incubated with either 0.1% DMSO or 10 μM of LEN of for 24 hours at 37 ºC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations. RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60℃ for 30 min according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a SurePrint G3 Human GE microarray 8x60K Ver. 3.0 for 17 h at 65 ℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37℃ GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 2 um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression in C1orf112-KO KMS-11 cells
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
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| |
|
| Submission date |
Jan 24, 2023 |
| Last update date |
Jun 01, 2023 |
| Contact name |
Akinobu Ota |
| E-mail(s) |
aota@aichi-med-u.ac.jp
|
| Organization name |
Aichi Medical University School of Medicine
|
| Department |
Biochemistry
|
| Street address |
1-1 Yazakokarimata
|
| City |
nagakute |
| State/province |
Aichi |
| ZIP/Postal code |
4801195 |
| Country |
Japan |
| |
|
| Platform ID |
GPL20844 |
| Series (1) |
| GSE223650 |
Gene expression changes between control and C1orf112-knockout (KO) human multiple myeloma (MM) cell lines |
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