|
| Status |
Public on Mar 26, 2015 |
| Title |
control siRNA 4h sample3 |
| Sample type |
RNA |
| |
|
| Source name |
N1E-115 cells
|
| Organism |
Mus musculus |
| Characteristics |
sirna: control siRNA
differentiation time: 4h
|
| Biomaterial provider |
American Tissue Culture Collection
|
| Treatment protocol |
For KD cells were transfected with 80 nM either control or Hmgn5 siRNA (Dharmacon siRNA smartpool Plus)
|
| Growth protocol |
Mouse N1E-115 cells (American Tissue Culture Collection) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 2% L-glutamine and 1% penicillin/streptomycin (all reagents from Sigma Aldrich). For differentiation, cells were starved overnight in Neurobasal medium (Invitrogen) with 2% L-glutamine and 1% penicillin/streptomycin. After starvation, cells were replated on 10 μg/ml laminin (Millipore)- coated coverlisps.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from whole cell preparations was isolated with the Nucleospin RNA II kit (Macherey-Nagel).
|
| Label |
biotin
|
| Label protocol |
270ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h.
|
| Scan protocol |
Scanning was performed with Affymetrix GCC Scan Control on a GeneChip Scanner 3000 with autoloader
|
| Description |
gene expression data from N1E-115 cells
|
| Data processing |
Arrays were normalized by RMA (oligo package from Bioconductor).
|
| |
|
| Submission date |
Apr 30, 2014 |
| Last update date |
Nov 17, 2021 |
| Contact name |
DBM Bioinformatics Core Facility |
| Phone |
+41612073541
|
| Organization name |
University of Basel
|
| Department |
Departement of Biomedicine
|
| Street address |
Hebelstrasse 20
|
| City |
Basel |
| State/province |
BS |
| ZIP/Postal code |
4053 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE57185 |
Growth cone localization of the mRNA encoding a chromatin regulator modulates neurite outgrowth |
|
