|
| Status |
Public on Aug 26, 2010 |
| Title |
Zhiping_KD30_1130_MoGene-1_0-st-v1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Mouse cortical neurons
|
| Organism |
Mus musculus |
| Characteristics |
strain: SV129 x C57BL/6 mixed
developmental stage: P0 pup
cell type: cortical neruons
treatment group: infected with lentiviruses expressing the CaM shRNAs
replicate date: 11/30
|
| Treatment protocol |
Cortical neuronal culture was infected on 5 DIV with CaM 1-3 shRNA mediated by lentiviruses; shRNAs with shRNA-resistant wildtype CaM; and control lentiviruses
|
| Growth protocol |
Mouse cortical culture was made as described elsewhere. Briefly, the primary cortical neurons were isolated from P0 pups of Syt1 deficient or wild-type (WT) mice, dissociated by papain digestion and plated on Matrigel coated circle glass coverslips. The neurons were cultured in vitro for 13-16 days in MEM (Gibco) supplemented with B27 (Gibco), glucose, transferrin, fetal bovine serum and Ara-C (Sigma).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultured cortical neurons (14-15 DIV) were lysed and total RNA was extracted and purified with RNAqueous-Micro kit (Ambion INC, TX) following the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Standard label protocol for the Affymetrix mouse gene ST_1.0 chip by the Protein and Nucleic Acid Facility at Stanford University.
|
| |
|
| Channel 2 |
| Source name |
Mouse cortical neurons
|
| Organism |
Mus musculus |
| Characteristics |
strain: SV129 x C57BL/6 mixed
developmental stage: P0 pup
cell type: cortical neruons
treatment group: control
replicate date: 11/30
|
| Treatment protocol |
Cortical neuronal culture was infected on 5 DIV with CaM 1-3 shRNA mediated by lentiviruses; shRNAs with shRNA-resistant wildtype CaM; and control lentiviruses
|
| Growth protocol |
Mouse cortical culture was made as described elsewhere. Briefly, the primary cortical neurons were isolated from P0 pups of Syt1 deficient or wild-type (WT) mice, dissociated by papain digestion and plated on Matrigel coated circle glass coverslips. The neurons were cultured in vitro for 13-16 days in MEM (Gibco) supplemented with B27 (Gibco), glucose, transferrin, fetal bovine serum and Ara-C (Sigma).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultured cortical neurons (14-15 DIV) were lysed and total RNA was extracted and purified with RNAqueous-Micro kit (Ambion INC, TX) following the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Standard label protocol for the Affymetrix mouse gene ST_1.0 chip by the Protein and Nucleic Acid Facility at Stanford University.
|
| |
|
| |
| Hybridization protocol |
Starndard hyb protocol for the Affymetrix mouse gene ST_1.0 chip by the Protein and Nucleic Acid Facility at Stanford University
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Data processing |
Raw data were processed with the Partex Genomic suite for background correction and quantile normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.
Single channel data was analyzed as ratios of experimental/control. Raw data (CEL files) for the two control samples (ch2) are provided as supplementary files on the Series record.
|
| |
|
| Submission date |
Aug 25, 2010 |
| Last update date |
Aug 25, 2010 |
| Contact name |
Zhiping Pang |
| E-mail(s) |
[email protected]
|
| Phone |
650-721-1421
|
| Organization name |
Stanford University School of Medicine
|
| Department |
Molecular and Cellular Physiology
|
| Lab |
Sudhof
|
| Street address |
1050 Arastradero Road
|
| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE23796 |
Calmodulin controlled gene expression profiling in mouse cortical neruons |
|
