|
| Status |
Public on Jun 02, 2014 |
| Title |
PAD4_1 |
| Sample type |
RNA |
| |
|
| Source name |
HEL cells transduced with shRNA against PADI4 expressing virus
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEL
proband sex: Male
treatment: transduced with shRNA against PADI4 expressing virus
|
| Treatment protocol |
HEL cells were lentivirally transduced with a virus harboring an shRNA cassette. Transduction effciency was more than 90% as measured by GFP fluorescence. Cells were harvested 6 days after transduction.
|
| Growth protocol |
Human erythroleukemia (HEL) cell were obtained from ATCC (HEL 92.1.7 (ATCC® TIB-180™). Cells were grown in RPMI-Medium supplemented with 10% fetal bovine serum, 1% peniciline/streptamycine. Cell density was at a range between 10E5 to 10E6 cell/ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was isolated from HEL cells, which were transduced with lentiviruses harboring shconstructs against the transcription factor Tal1 and PADI4 respectively, in biological triplicates. Two control samples with a control lentivirus with an shRNA against LacZ were included. RNA was prepared 6 days after transduction.. Tissue samples were transferred into trizol buffer, homogenized and mRNA was isolated in a single-step acid guanidinium thiocyanate-phenol-chloroform extraction following manufacturer´s instructions (http://tools.invitrogen.com/content/sfs/manuals/trizol_reagent.pdf)
|
| Label |
Cy3
|
| Label protocol |
For each array 200 ng RNA was processed and Cy3 labeled by the Low Input Quick Amp Labeling Kit (Agilent Technologies).
|
| |
|
| Hybridization protocol |
Hybridization was performed in the hybridization oven (Agilent Technologies, 17h, 10 rpm, 65˚C)
|
| Scan protocol |
Cy3 intensities were detected by a one-color microarray scanner (G2505C, Agilent Technologies) at 5 µm resolution
|
| Data processing |
Data were quantile normalized and log2 transformed using R and Bioconductor package limma.
|
| |
|
| Submission date |
Jan 14, 2014 |
| Last update date |
Jun 02, 2014 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
|
| Organization name |
Universitaetsmedizin Goettingen
|
| Department |
Department of Human Genetics
|
| Lab |
NGS Integrative Genomics
|
| Street address |
Justus-von-Liebig-Weg 11
|
| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37077 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13497 |
| Series (1) |
| GSE54075 |
PADI4 acts as a coactivator of Tal1 by counteracting repressive histone arginine methylation at the IL6ST (gp130) promoter |
|
