|
| Status |
Public on Aug 13, 2018 |
| Title |
TET2 shRNA-1: MDS-L cells with shTET2-Replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
MDS-L cells with shTET2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDS-L
|
| Treatment protocol |
MDS-L cells were transduced with SIRT1 shRNA, TET2 shRNA or control shRNA
|
| Growth protocol |
RPMI 1640 medium with 10% FBS and 1% penicillin-streptomycin in the presence of 30 ng/mL human recombinant human IL-3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol Reagent (Thermo Fisher Scientific) following the manufacture`s instructions. RNA quality was assessed by spectrophotometry(NanoDrop, ND1000) and gel electrophoresis. To be considered as high-quality, the RNA had to have 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 |
0.5 µg of total RNA was reverse-transcribed and amplified using Onearray Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group). Indirect labeled the aa-UTP by NHS-Cy5 (AAT Bioquest ). Dye incorporation and aRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.1 µg Cy5-labeled aRNA of the respective sample was fragmented and hybridized onto HlncOA 1.0 using Phalanx OneArray hybridization kit (Phalanx Biotech Group). Hybridization was performed for 17h, rotating at a speed of 10rpm at 65℃ in an Agilent hybridization oven (G2545A). After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 and 1 minute with 37℃Wash buffer 2.
|
| Scan protocol |
HlncOA 1.0arrays were scanned by Agilent Microarray Scanner( G2505C ) HD_1X color protocol （Dye channel: R ; Scan resolution : 2 um; Tiff: 20-bit; Red PMT gain: 100%; XDR: No）and quantify the fluoresence intensity.
|
| Description |
MDS-L cells transduced with lentiviral vector containing interference squence targeting TET2 replicate 1
|
| Data processing |
Data processing was performed and calculated by R language (v3.4.0). The probes will filter out control probes and normalized by median scaling method between all samples. Pair-wise comparisons between samples were calculated by Bioconductor limma package and presented by log2 fold change and p-value.
|
| |
|
| Submission date |
Aug 07, 2018 |
| Last update date |
Aug 14, 2018 |
| Contact name |
Sun Jie |
| E-mail(s) |
[email protected]
|
| Organization name |
City of Hope
|
| Lab |
Li Lab
|
| Street address |
1500 East Duarte Road
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL22448 |
| Series (2) |
| GSE117272 |
SIRT1 Activation Disrupts Maintenance of Myelodysplastic Syndrome Stem and Progenitor Cells by Restoring TET2 Function [microarray expression profiling] |
| GSE117383 |
SIRT1 Activation Disrupts Maintenance of Myelodysplastic Syndrome Stem and Progenitor Cells by Restoring TET2 Function |
|
