|
| Status |
Public on Jun 03, 2018 |
| Title |
685-2010--6DIV01 |
| Sample type |
RNA |
| |
|
| Source name |
Hippocampal neurons, 6DIV, replicate 2
|
| Organism |
Mus musculus |
| Characteristics |
time: 6 days
replicate: A
|
| Treatment protocol |
No treatments were performed
|
| Growth protocol |
Pregnant RjOrl:SWISS female mice were purchased from Janvier Labs. Hippocampal and cortical cell cultures were prepared from e17.5-18.5 mouse embryos. Briefly, hippocampi were dissected,treated with 0.25% trypsin (Life Technologies) during 15 min at 37ºC and dissociated into single cells by gentle trituration. Neurons were seeded on glass coverslips or plastic plates coated with 0.1 mg/ml Poly-D-lysine (Sigma) at ~105 cells/cm2 or 2x104 cells/cm2 for low-density cultures. Neurons were plated in DMEM containing 10% fetal bovine serum (FBS), penicillin/streptomycin (pen/strep), and 1-2 hours later medium was replaced by Neurobasal medium supplemented with 2% B27, pen/strep, 0.6% Glucose and Glutamax (all reagents from Life Technologies). Cytosine arabinoside (1 µM; Sigma) was added to cultures at 3 days in vitro (DIV) and 1/3 of the medium was refreshed every 4-5 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the QIAGEN Rneasy Mini Kit - Total RNA Purification kit following the manufacturers instructions
|
| Label |
biotin
|
| Label protocol |
25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.
|
| |
|
| Hybridization protocol |
cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)
|
| Scan protocol |
Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)
|
| Description |
Gene expression at 6DIV in cultured mouse hippocampal neurons
|
| Data processing |
Normalized expression signals were calculated from Affymetrix CEL files using RMA algorithm (Irizarry et al., 2003)
|
| |
|
| Submission date |
Apr 25, 2018 |
| Last update date |
Jun 03, 2018 |
| Contact name |
Camille Stephan Otto Attolini |
| Organization name |
IRB Barcelona
|
| Department |
Biostatistics and bioinformatics Unit
|
| Street address |
Baldiri Reixac 10
|
| City |
Barcelona |
| State/province |
Select a State or Province |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL10740 |
| Series (1) |
| GSE113680 |
Gene expression signatures during differentiation of mouse hippocampal neurons in primary culture |
|
