|
| Status |
Public on Jun 14, 2013 |
| Title |
shRNA1_+DEX_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Erythroid cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: E14.5
tissue: fetal liver
cell type: early erythroid progenitors
infection: virus encoding shRNA 1 targeting RBP
culture conditions: +DEX
|
| Treatment protocol |
Early erythroid progenitors were infected with control virus or viruses encoding RBP shRNAs, and cultured in medium for 3 days before mRNA extraction.
|
| Growth protocol |
Early erythroid progenitors were enriched from mouse E14.5 fetal liver. The first step includes a negative selection for erythroid progenitors by magnetic depleting of mature blood cells (lineage positive cells), early multipotent GEMM colony forming cells (Sca-1 positive cells), and myeloid colony-forming cells (CFU-G/M/Mk) (CD16/32 positive, CD41 positive, or CD34 positive cells). The second step includes a FACS based positive selection of early erythroid progenitor process (c-kit positive and CD71 10%low cells).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted by using Qiagen RNA extraction kit following the manufacturer's instruction.
|
| Label |
Cy3
|
| Label protocol |
Label was performed following one-color microarray-based gene expression analysis low input quick amp labeling protocol (Agilent Technologies 'one-color microarray-based gene expression analysis').
|
| |
|
| Hybridization protocol |
Agilent expression arrays were hybridized according to manufacturer instructions and scanned using an Agilent DNA microarray scanner.
|
| Scan protocol |
Arrays were scanned using an Agilent DNA microarray scanner with SureScan high-resolution technology.
|
| Description |
mRNA expression in day3 cultured cells (+DEX) infected with virus encoding shRNA 1 targeting RBP repeat 1
|
| Data processing |
Data was extracted from the array images using Agilent’s Feature Extraction software, quantile normalized using limma from Bioconductor in R, and processed.
|
| |
|
| Submission date |
Apr 19, 2013 |
| Last update date |
Jun 14, 2013 |
| Contact name |
Lingbo Zhang |
| E-mail(s) |
zhanglb@wi.mit.edu
|
| Organization name |
Whitehead Institute for Biomedical Research and MIT Department of Biology
|
| Street address |
Nine Cambridge Center
|
| City |
Cambridge |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL10333 |
| Series (2) |
| GSE46215 |
Identification of genes regulated by glucocorticoids and an RNA binding protein (RBP) in early erythroid progenitor using microarray experiment |
| GSE46216 |
Role of glucocorticoids and an RNA binding protein (RBP) in early erythroid progenitors |
|
