|
| Status |
Public on Jan 04, 2016 |
| Title |
Day 3 differentiation, QKI shRNA, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
THP cells transfected with QKI shRNA, treated with PMA for 3 days
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
phenotype: macrophage
transfected shrna: QKI shRNA
differentiation: day 3
|
| Treatment protocol |
Human THP-1 ‘monocytes’ were stably transduced using lentiviral particles that encode either a QkI-targeting shRNA (sh-QkI) or a scrambled control shRNA (sh-Cont). Stable transductants were selected using 3 µg/mL puromycin for 72h.
For differentiation, THP-1 cells were stimulated with 100 nM PMA for 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol.
|
| Label |
biotin
|
| Label protocol |
cDNA synthesis and amplification was performed using the WT Expression Kit (Ambion). Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization was performed as specified, with the GeneChip Hybridization Wash and Stain Kit (Affymetrix)
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
26_THP_D3_ko2
|
| Data processing |
Using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
|
| |
|
| Submission date |
Nov 10, 2015 |
| Last update date |
Jan 04, 2016 |
| Contact name |
Lily Shiue |
| E-mail(s) |
lshiue@ucsc.edu
|
| Phone |
831-459-2612
|
| Organization name |
UCSC
|
| Department |
MCD Biology
|
| Lab |
Ares
|
| Street address |
1156 High Street
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL15106 |
| Series (2) |
| GSE74887 |
Transcriptome-wide regulation of pre-mRNA splicing and expression by the RNA-binding protein Quaking during monocyte to macrophage differentiation [Microarray] |
| GSE74979 |
Transcriptome-wide regulation of pre-mRNA splicing and expression by the RNA-binding protein Quaking during monocyte to macrophage differentiation |
|
