|
| Status |
Public on Oct 30, 2015 |
| Title |
BD patient, Li-non-responder (N3) |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-derived hippocampal dentate gyrus granule neurons
|
| Organism |
Homo sapiens |
| Characteristics |
lithium treated: no
bd patient: yes
cell type: Hippocampal dentate gyrus (DG) granule neurons
|
| Treatment protocol |
Lithium Cloride was added to the culture media as described in the manuscript
|
| Growth protocol |
Hippocampal dentate gyrus (DG) granule neurons were derived according to Yu et al, Stem Cell Reports 2014
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA by RNAbee extraction
total RNA, ribosomal depletion, stranded, according to Illumina protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Paired end reads from all libraries were mapped to the human reference genome (GRCh37) using STAR version 2.3.0. The assignment of reads to gene regions was performed by htseq-count, version 0.5.4 p5. The raw counts are taken as input for edgeR pacakage for differential gene expression analysis.
Genome_build: GRCh37
Supplementary_files_format_and_content: edgeR.txt: tab-delimitted text file containg cpm of genes in different samples and p-values, logFC for multiple comparisons
|
| |
|
| Submission date |
Jun 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Son Pham |
| E-mail(s) |
spham@salk.edu
|
| Organization name |
Salk Institute
|
| Department |
LOG
|
| Lab |
Gage
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE58933 |
Hyper-excitability of Neurons generated from Patients with Bipolar Disorder |
|
| Relations |
| BioSample |
SAMN02898147 |
| SRA |
SRX641460 |
