|
| Status |
Public on Jun 12, 2013 |
| Title |
V6.5 ZERT2 clone #18 (Tmx-) rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
V6.5 ZERT2 clone #18 (Tmx-) rep1
|
| Organism |
Mus musculus |
| Characteristics |
clone: #18
cell line: ES cell line V6.5
strain: hybrid from C57Bl/6 x 129
gender: male
transfection: pCAG-Zscan4-ERT2
tamoxifen induction: no
individual identifier: v6.5 ERT2 ES#1a; 251508710802A4
|
| Treatment protocol |
ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in ES standard medium with LIF for 2 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol according to Invitrogen's protocol. Cells were pelleted and 1mL Trizol reagent was added to the cell pellet.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.
|
| |
|
| Channel 2 |
| Source name |
Universal Mouse Reference 129ES Cell
|
| Organism |
Mus musculus |
| Characteristics |
reference: Universal Mouse Reference (total RNA from 11 cultured cell lines) plus 129ES cell RNA (Lif+)
|
| Biomaterial provider |
Stratagene
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube
|
| Label |
Cy5
|
| Label protocol |
Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.
|
| |
|
| |
| Hybridization protocol |
Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol, Product # G4140-90050, Version 5.0.1, August 2006)
|
| Scan protocol |
Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.
|
| Description |
v6.5 ERT2 ES
|
| Data processing |
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 9 arrays in the series: AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin
|
| |
|
| Submission date |
Dec 17, 2010 |
| Last update date |
Jun 12, 2013 |
| Contact name |
Minoru S.H. Ko |
| E-mail(s) |
[email protected]
|
| Phone |
410-558-8359
|
| Organization name |
NIH
|
| Department |
National Institute on Aging
|
| Lab |
Lab of Genetics
|
| Street address |
251 Bayview Blvd, Suite 100, 10C
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL6867 |
| Series (2) |
| GSE26162 |
Rejuvenation of pluripotent stem cells by frequent activation of Zscan4, Part B |
| GSE26278 |
Rejuvenation of pluripotent stem cells by frequent activation of Zscan4 |
|
