|
| Status |
Public on May 01, 2014 |
| Title |
E13 embryo_rep4 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse embryonic cortex_E13 stage_replicate4
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E13
tissue: Brain cortex
cell type: Basal progenitors
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from FACS isolated BPs by using mirVanaTM kit (Ambion) following manufacturer's protocol
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 labeling was performed in 100ng of total RNA sample using Agilent's miRNA labeling kit following manufacturer's protocol.
|
| |
|
| Hybridization protocol |
After labeling samples were purified using MicroBioSin 6 column (Bio-Rad) according to manufacturer's protocol, then samples were completely dried using a vacuum concentrator at 45 to 55°C as per Agilent hybridization protocol, samples were then resuspended in 17 ul nuclease-free water; Agilent's miRNA Hyb Kit was used for hybridization sample preparation and manufacturer's protocol followed. Agilent microRNA spike controls were also prepared using Spike-In kit (Agilent) and 1ul Hyb Spike-In solution (3rd Dilution) was added to each sample. Samples were hybridized to Agilent mouse miRNA microarrays (V2) (G4472B) at 55°C for 20 hours in a rotating (20 rpm) Agilent Hybridization oven. After hybridization, microarrays were washed 5 min. at room temperature with GE Wash Buffer 1 (Agilent) and 5 min. with 37°C GE Wash buffer 2 (Agilent). After wasing slides were scanned immediately.
|
| Scan protocol |
Immediately after washing slides were scanned on Agilent Microarray Scanner (G2505C) and the TIFF images extracted using the Agilent Feature Extraction software (version 10.7.3.1).
|
| Description |
miRNA expression in BPs at E13
E13_67_WT
|
| Data processing |
The scanned images were analyzed by using Agilent Feature Extraction software (version 10.7.3.1) to obtain raw signal intensities. After removing control probes, background substracted signal intensity (gBGSubSignal) for the detected probes (gIsWellAboveBG=1) were used for analysis. Probes detected in one array and not in others were not considered during analysis; Further outlier probes were removed and data were quantile normalized (Bolstad BM et al., 2003).
|
| |
|
| Submission date |
Mar 24, 2013 |
| Last update date |
May 01, 2014 |
| Contact name |
Matthias Groszer |
| Organization name |
INSERM U839
|
| Department |
Developmental Neuroscience
|
| Street address |
17, rue du Fer à Moulin
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL10384 |
| Series (2) |
| GSE45449 |
Study of miRNAs function in basal progenitors during cortical neurogenesis |
| GSE45451 |
Basal progenitors during cortical neurogenesis |
|
