|
| Status |
Public on Nov 01, 2017 |
| Title |
PTECs_N1_NT |
| Sample type |
RNA |
| |
|
| Source name |
NT-shRNA treated PTECs
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney
cell type: proximal tubular epithelial cells
|
| Treatment protocol |
Primary PTECs were transduced with PBRM1 shRNA (sh-PB1 and sh-PB2), and non-targeting shRNA (NT); PTECs without virus treatment were included as a control. Both PBRM1-WT and PBRM1-KD PTECs were transdused at high MOI and harvested at their early passages.
|
| Growth protocol |
Primary proximal tubular epithelial cells (PTECs) were cultured in DMEM/F-12 GLUTMAX-1 (Sigma-Aldrich, St. Louis, MO, USA ) containing 10% FBS, 1% P/S (100 U/ml penicillin and 100 µg/ml streptomycin), 5μg/ml ITS (Sigma-Aldrich) and 5ng/ml EGF respectively. CcRCC derived cell lines were maintained in RPMI 1640 supplemented with 10% FBS, 100 U/ml penicillin and 100μg/ml streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by using Gene JET RNA purification kit (Fermentas, Waltham, MA, USA) with the instruction offered by the manufacture.
|
| Label |
Cy5
|
| Label protocol |
First strand cDNA was synthesized from 50-100ng RNA, followed by cRNA amplification and labeling with Cy5 according to manufacturer's protocol (Agilent). Purification of Cy5 labeled cRNA was carried out with Qiagen RNeasy Mini kit.
|
| |
|
| Hybridization protocol |
Each Cy-5 sample was mixed with the same amount of a cy3-labeled sample, which was non-relevant for this study, and hybridized at 65°C overnight on Agilent-050524 SurePrint G3 Custom Human 8x60K Microarrays.
|
| Scan protocol |
On the following day, slides were washed and signals were scanned with GenePix 4000B (Agilent).
|
| Description |
NT-shRNA treated primary kidney proximl tubular epithelial cells at day 6 triplicate1
Sample name: SAMPLE 4
|
| Data processing |
Signal intensities from scanned images were processed and converted into Linear and Lowess normalized data using Agilent Feature Extraction software version 10.7.3.1. Data was analyzed by GeneSpring GX 12.5 software (Agilent Technologies). The data was subject to quantile normalization without base line transformation.
|
| |
|
| Submission date |
Oct 27, 2016 |
| Last update date |
Nov 01, 2017 |
| Contact name |
Jun Li |
| E-mail(s) |
nexusoooooo@gmail.com
|
| Phone |
+31641112670
|
| Organization name |
University Medical Center Groningen
|
| Department |
Genetics
|
| Lab |
Klaas Kok
|
| Street address |
Esdoornlaan
|
| City |
GRONINGEN |
| State/province |
Netherlands |
| ZIP/Postal code |
9741MG |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18641 |
| Series (1) |
| GSE89214 |
Gene expression analysis of kidney primary tubular epithelial cells (PTECs), SETD2-KD PTECs, PBRM1-KD PTECs and ccRCC derived cell lines |
|
