|
| Status |
Public on Dec 30, 2014 |
| Title |
LW14 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-derived neuron sample
|
| Organism |
Homo sapiens |
| Characteristics |
age: ~ Differentiation day 45
disease: BBS (Bardet-Biedl Syndrome)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy Micro Kit (QIAGEN). Quality control of the RNA was carried out with the Agilent Bio-analyzer, Qubit 2.0 at the MPSR of Columbia University. 100 ng of RNA with RIN ≥ 9 were used for generating mRNA-focused libraries.
RNA libraries were prepared using TruSeq RNA Sample Preparation Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
B3
|
| Data processing |
Hierarchical Clustering was done in Cluster (de Hoon et al., 2004) and visualized in Treeview (Saldanha, 2004). For each experiment and every gene, the gene expression values in FPKM was median centered and normalized to have unit variance before clustering. One matrix CIM (http: //discover.nci. nih.gov/cimminer/home.do) is used to generate the cluster heatmap.
Supplementary_files_format_and_content: csv files include FPKM values for each Sample
|
| |
|
| Submission date |
Nov 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Liheng Wang |
| E-mail(s) |
lw2381@cumc.columbia.edu
|
| Organization name |
Columbia University Medical Center
|
| Department |
Department of Medicine
|
| Lab |
Domenico Accili
|
| Street address |
1150 Saint Nicholas Avenue, Room 234
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE62936 |
RNA-Seq Analysis in hES/ iPS cell-derived neuronal samples |
|
| Relations |
| BioSample |
SAMN03160337 |
| SRA |
SRX750252 |
