|
| Status |
Public on Apr 28, 2016 |
| Title |
Control |
| Sample type |
SRA |
| |
|
| Source name |
SK-N-SH neuronal cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: none
|
| Treatment protocol |
After differentiation for two weeks, cells were treated with a mixture composed of (MIX: FLX 10μg/l; VNX 50μg/l; CBZ 100μg/l), and Valproate (VPA: 0.035mM). Control cells were treated with DMSO (vehicle) only
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina sequencing protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
RNA-seq reads were aligned to hg19 reference genomic sequence using Tophat version 2.0.11 with default parameters
The number of reads in each sample that can map to hg19 was calculated using summarizeOverlop function in GenomicAlignments R package
Differentially expressed genes were detected using DESeq2 R package version 1.6.1
Gene set enrichment analysis was carried out using GAGE R package version 2.14.4
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample ...
|
| |
|
| Submission date |
Apr 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Thomas |
| E-mail(s) |
mthomas@isu.edu
|
| Organization name |
Idaho State University
|
| Department |
Biological Sciences Department
|
| Street address |
921 S. 8th Avenue
|
| City |
Pocatello |
| State/province |
ID |
| ZIP/Postal code |
83209 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE80635 |
Psychoactive pharmaceuticals at environmental concentrations induce in vitro gene expressions associated with neurological disorders |
|
| Relations |
| BioSample |
SAMN04893712 |
| SRA |
SRX1725366 |
