|
| Status |
Public on Dec 11, 2012 |
| Title |
MEL_Ldb1KD_induced_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
MEL_Ldb1 shRNA knockdown_DMSO induced
|
| Organism |
Mus musculus |
| Characteristics |
strain background: BALB/c
cell type: Murine erythroidleukema (MEL) cells
genotype/variation: Ldb1 shRNA knockdown
induced with: 1.5-2% DMSO
|
| Treatment protocol |
Uninduced MEL cells were differentiated by incubating 2.5e5 cells/ml with 1.5-2% DMSO; cells were stably transformed with either control or Ldb1 shRNA from Open Biosystems.
|
| Growth protocol |
Cells cultured in DMEM supplemented with 10% fetal bovine serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared from 2e6 cells using the Rneasy Plus Mini Kit (Qiagen). One microgram of RNA was reverse transcribed with random hexamers using the Superscript III first-strand synthesis system as suggested by the manufacturer (Invitrogen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
kd.induced.2
|
| Data processing |
Bioconductor/R (R 2.15.2); affy (1.36.0) and limma (3.14.1) packages; Mouse430_2_Mm_ENTREZG cdf (brainarray v.16.0)
|
| |
|
| Submission date |
Dec 11, 2012 |
| Last update date |
Dec 11, 2012 |
| Contact name |
Ryan Dale |
| E-mail(s) |
dalerr@nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Child Health and Human Development
|
| Lab |
Bioinformatics and Scientific Programming Core
|
| Street address |
Rm 10D39, 10 Center Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL16368 |
| Series (1) |
| GSE42839 |
Expression changes in MEL cells upon differentiation and Ldb1 knockdown |
|
