|
| Status |
Public on Oct 04, 2016 |
| Title |
D398_2 |
| Sample type |
SRA |
| |
|
| Source name |
Midbrain dopaminergic neuron cultures derived from iPSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 41
subline: SG
days_differentiated: 40
genotype/variation: D398
|
| Treatment protocol |
No treatment
|
| Growth protocol |
iPSC culture and mDA differentiation protocols are described in the methods section of the article
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was prepared using a Qiagen Rneasy kit
Libraries were built using the PureLink Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base-calling performed by Illumina pipeline
Alignment to hg19 UCSC transcript map using TopHat
Comparisons between groups performed using Cuffdiff
Data analysis and visualization using Cummerbund in R
Genome_build: hg19
Supplementary_files_format_and_content: Processed data obtained using the fpkmMatrix function in Cummerbund, results are FPKM per replicate
|
| |
|
| Submission date |
Apr 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ronald P. Hart |
| E-mail(s) |
rhart@rutgers.edu
|
| Phone |
848-445-1783
|
| Organization name |
Rutgers University
|
| Department |
Cell Biology & Neuroscience
|
| Street address |
604 Allison Rd Rm B430
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE56398 |
Increased response to nicotine in human dopaminergic neurons derived from iPSC carrying the risk-associated SNP rs16969968 |
|
| Relations |
| SRA |
SRX494811 |
| BioSample |
SAMN02691602 |
