|
| Status |
Public on Oct 12, 2018 |
| Title |
Sox4KD1p1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse E14.5 embryonic neural stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
age: E14.5
cell type: embryonic neural stem cells
cell source: R&D Systems, Minneapolis, MN
shRNA: targeting Sox4
shRNA name and source: TRCN0000012078, Sigma Aldrich, St. Louis, MS
|
| Biomaterial provider |
Mouse Cortical Stem Cells purchased from R&D Systems, Minneapolis, MN.
|
| Treatment protocol |
Upon lentiviral transduction NSCs were grown and expanded under puromycin selection before RNA-isolation (0.5 µg/mL)
|
| Growth protocol |
NSCs were growth as monolayer in poli-L-ornithine and laminin coated plates in presence of EGF and bFGF
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
total RNA-isolation with RNAeasy kit (Qiagen)
Sample preparation was performed using Poly(A)Purist MAG Kit (Thermo Scientific) according to manufacturers’ instructions. Isolated mRNA was subsequently repurified using mRNA-ONLY Eukaryotic mRNA Isolation Kit (Epicentre (Illumina, Inc.), Madison, WI, USA). Sequencing libraries were prepared using SOLiD Total RNA-Seq Kit (Applied Biosystems Life Technologies) according to the standard protocol recommendations
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500 Genetic Analyzer |
| |
|
| Description |
gene_exp.diff.txt
|
| Data processing |
Sequencing reads were mapped against the reference genome (mm10 assembly) using TopHat v2.0.9 as previously described (Trapnell et al., 2012). Only uniquely mapped reads were selected for further analysis.
guide transcripts were assembled using CuffLinks v2.2.1. Reads were quartile normalized using the –library-norm-method quartile option.
Differential gene analysis was performed using CuffDiff. Cluster 3.0
Genome_build: mm10
Supplementary_files_format_and_content: [gene_exp.diff.txt] Tab-delimited text file containing average differential gene expression FPKM normalized values (value_1 = SCR, value_2 = Sox4KD)
|
| |
|
| Submission date |
Oct 12, 2018 |
| Last update date |
Oct 13, 2018 |
| Contact name |
Paul J Coffer |
| E-mail(s) |
p.j.coffer@umcutrecht.nl
|
| Organization name |
UMC Utrecht
|
| Department |
Regenerative Medicine Center
|
| Lab |
Coffer Lab
|
| Street address |
Uppsalalaan 6
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16790 |
| Series (2) |
| GSE121173 |
RNA-sequencing of mouse E14.5 embryonic neural stem cells transduced in vitro with a shRNA against Sox4 or a scrambled shRNA |
| GSE121174 |
Role of SOX4 in mouse embryonic neural stem cells (NSCs) |
|
| Relations |
| BioSample |
SAMN10235306 |
| SRA |
SRX4872097 |
