|
| Status |
Public on Oct 10, 2023 |
| Title |
AG4456_FB_1 |
| Sample type |
SRA |
| |
|
| Source name |
Dermal fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
subject: Individual III
age group: Young
cell line: Coriell AG4456
|
| Growth protocol |
Direct neuronal reprogramming of human fibroblasts to neurons was performed as previously described (Abernathy et al., 2017; Richner et al., 2015).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At 4 weeks, total RNA from reprogramming cells was extracted using the RNeasy Micro Kit (Qiagen).
Samples were prepared according to the library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw data obtained was aligned, quantified and analyzed by usingPartek Flow® Software Analysis Pipeline.
Trim bases (from 3’ end with minimum quality score (Phred) of 20)
RNA-seq reads were mapped to the human reference genome (GRCh38) using STAR STAR version 2.7.3a.
Differential gene expression (GSA) analysis was done using CPM normalization
Assembly: hg38
|
| |
|
| Submission date |
Aug 22, 2023 |
| Last update date |
Oct 10, 2023 |
| Contact name |
Youngmi Oh |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University in St. Louis
|
| Department |
Development department
|
| Lab |
Andrew Yoo
|
| Street address |
660 S. Euclid Avenue
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE241430 |
Longitudinal modeling of human neuronal aging reveals the contribution of the RCAN1-TFEB pathway to Huntington's disease neurodegeneration |
|
| Relations |
| BioSample |
SAMN37112328 |
| SRA |
SRX21453649 |
