|
| Status |
Public on Oct 15, 2013 |
| Title |
Ediff 20h rep1 |
| Sample type |
RNA |
| |
|
| Source name |
FDCPmix_Ediff 20h
|
| Organism |
Mus musculus |
| Characteristics |
cell line: FDCPmix
cytokine condition: Epo+hemin
differentiation stage: Erythroid
|
| Treatment protocol |
For differentiation, cells were washed and then triplicate samples were cultured in IMDM plus 10% FCS and low IL-3 supplemented with either Epo and hemin (erythroid output) or G-CSF and SCF (neutrophil output).
|
| Growth protocol |
FDCPmix were routinely maintained in Fischer's medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from triplicates using TRIzol reagent, and RNA concentration and integrity were determined using RNA 6000 Nano RNA kit (Agilent) on BioAnalyzer 2100 (Agilent).
|
| Label |
Cy3
|
| Label protocol |
Total RNA (150ng) and Agilent One-Color RNA Spike-In were reverse-transcribed and linearly amplified in the presence of Cy3-labeled CTP using Low RNA Input One-Color Kit (Agilent) following Agilent protocols, to generate Cy3-labeled cRNA for hybridisation to high-density microarrays. Quality and yield/specific activity of cRNA were determined using RNA 6000 Nano kit and spectrophotometer (NanoDrop ND- 1000). All samples generated comparable quality cRNA profiles, with specific activities in the range of 10.3 to 12.2 pmol Cy3/mg cRNA.
|
| |
|
| Hybridization protocol |
Each Cy3-labeled cRNA sample (1.6ug as per NanoDrop reading) was hybridised to an individual 44K subarray of 4x44K high-density microarray slide (Whole Mouse Gene Expression Microarrays, Agilent), washed, scanned and feature-extracted as per Agilent protocols.
|
| Scan protocol |
Scanning and feature extraction was performed as per Agilent protocols
|
| Description |
Ediff_28
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software (Agilent v10.1.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
|
| |
|
| Submission date |
Aug 19, 2013 |
| Last update date |
Oct 15, 2013 |
| Contact name |
Shamit Soneji |
| E-mail(s) |
shamit.soneji@med.lu.se
|
| Organization name |
BMC
|
| Street address |
Sölvegatan 19
|
| City |
Lund |
| ZIP/Postal code |
221 84 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL7202 |
| Series (2) |
| GSE49987 |
Dynamic analysis of gene expression and genome wide transcription factor binding during lineage-specification of multipotent progenitors [TC] |
| GSE49991 |
Dynamic analysis of gene expression and genome wide transcription factor binding during lineage-specification of multipotent progenitors |
|
