|
| Status |
Public on May 21, 2014 |
| Title |
RPE1-BAZ1B-D5-2 |
| Sample type |
RNA |
| |
|
| Source name |
hTERT-RPE1 (retinal pigment epithelial cells), BAZ1B knockout
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hTERT-RPE1
genotype/variation: BAZ1B knockout
gender: female
clone: D5
|
| Treatment protocol |
The BAZ1B gene was knocked out by targeting both copies of exon-7 using zinc finger nucleases (D5, F3 and M1 - all independent clones). Clone A6 is targeted at one allele only and is a heterozygous mutant clone.
|
| Growth protocol |
Cells were grown in DMEM/F12, supplemented with 10% FBS, Pen/Strep, 2mM L-Glutamine, 0.348% NaBicarbonate. Cells were maintained at 37C in 5% CO2, humidified.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Qiagen RNeasy Spin Kit. RNA was treated with DNaseI, before cleaning on an RNeasy spin column. Confirmation of DNA absence was performed by PCR to the repeat element DXZ4, and RNA quality was determined by agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed at a NimbleGen Systems certified core facility at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed at a NimbleGen Systems certified core facility at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed at a NimbleGen Systems certified core facilty at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.
|
| Description |
RPE1 BAZ1B homozygous mutant.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
May 26, 2013 |
| Last update date |
May 21, 2014 |
| Contact name |
Brian P Chadwick |
| E-mail(s) |
chadwick@bio.fsu.edu
|
| Phone |
850-645-9279
|
| Organization name |
Florida State University
|
| Department |
Biological Science
|
| Street address |
319 Stadium Drive, King 3076
|
| City |
Tallahassee |
| State/province |
FL |
| ZIP/Postal code |
32306 |
| Country |
USA |
| |
|
| Platform ID |
GPL16025 |
| Series (1) |
| GSE47390 |
Changes in gene expression in BAZ1B knockout and heterozygous targeted clones |
|
