|
| Status |
Public on Aug 24, 2015 |
| Title |
mA2.lox.Cre_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Neural progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ES-derived neural progenitor cells
strain: 129/Ola
transgene: TRE_Cre
|
| Treatment protocol |
To activate transgene, neural progenitors were induced for 12hr with 1ug/ml doxycycline
|
| Growth protocol |
mESCs were maintained in a serum free condition with CHIR99021, PD184352, and LIF on sparse feeder cells. Neural progenitors were derived by depleting feeder cells and culturing cells in suspension in neural differentiation basal medium (DFNB) for 2 days followed by 500nM all-trans retinoic acid treatment in DFNB.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NucleoSpin RNA column (Clontech)
Library was constructed with TruSeq kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
mA2.lox.Cre parental cell line reference rep4
232-mA2-t60
|
| Data processing |
Basecall was performed with the default pipeline for Illumina NextSeq
Sequence tags were aligned with the mm10 genome with STAR aligner
Differentially expressed genes were identified with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Expression values for all replicates and all analyzed genes (tab1) and fold repression values for genes repressed by at least one transgene by 2 fold
|
| |
|
| Submission date |
Jan 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuichi Nishi |
| E-mail(s) |
[email protected]
|
| Phone |
323-442-8077
|
| Organization name |
University of Southern California
|
| Department |
Eli and Edythe Broad-CIRM Center for Regenerative Medicine
|
| Lab |
Andrew McMahon
|
| Street address |
1425 San Pablo St.
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE65457 |
mRNAseq analysis of Nkx2.2, Nkx6.1, and Olig2 overexpression in neural progenitors |
| GSE65462 |
Nkx2.2, Nkx6.1, Olig2, and Gli3 genomic binding regions and overexpression in neural progenitors |
|
| Relations |
| BioSample |
SAMN03322520 |
| SRA |
SRX860876 |
