|
| Status |
Public on May 25, 2021 |
| Title |
Dermal fibroblasts CTL_TD_21_c |
| Sample type |
SRA |
| |
|
| Source name |
Dermal fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Coriell GM02171
treatment: miR-9/9*-124
treatment: TuD-miR-NS
cell type: Dermal fibroblasts
|
| Treatment protocol |
Cell treated with either TuD-miR-NS or TuD-miR-124 for 21 days
|
| 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 |
Total RNA was extracted using a combination of Trizol (Invitrogen, USA) and RNeasy plus micro kit (QIAGEN, USA).
SMARTer Ultra Low Input RNA Kit (Clontech, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were aligned to human reference genome (GRCh38) by STAR (Dobin and Gingeras, 2015).
Counts were normalized by trimmed mean of M-values (TMM) using edgeR (Robinson et al., 2010).
EdgeR (Robinson et al., 2010) was used to identify differentially expressed genes.
Bigwig files were generated using bamCoverage (RamÃrez et al., 2016).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of replicates for RNA-seq experiments
|
| |
|
| Submission date |
Nov 11, 2020 |
| Last update date |
May 25, 2021 |
| Contact name |
Ya-Lin Lu |
| E-mail(s) |
lu.y@wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Department |
Developmental Biology
|
| Lab |
Andrew Yoo
|
| Street address |
660 S. Euclide Avenue
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE161239 |
MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity [TD_RNAseq] |
| GSE161241 |
MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity |
|
| Relations |
| BioSample |
SAMN16770718 |
| SRA |
SRX9474109 |
