|
| Status |
Public on Mar 08, 2019 |
| Title |
cNSC-BAC_Cre_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
cultured cortical NSCs
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: cultured cortical neural stem cells (NSCs)
treatment: Ad:Cre
developmental stage: Derived from embryonic day 12.5
genotype/variation: Pnky(fl/fl);BAC-Pnky +Ad:Cre
|
| Growth protocol |
Acutely dissected cortical NSCs cultured with media containing EGF/FGF.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated by Trizol (Life Technologies), purified using Direct-zol (Zymo) kit with on-column DNAse treatment.
Strand-specific, poly(A) selected cDNA libraries were generated using TruSeq Stranded mRNA kit (Illumina, #20020594).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Pnky(fl/fl);BAC-Pnky +Ad:Cre Rep3
|
| Data processing |
For NSC culture RNA-seq, reads were psuedoaligned to Genocde GRCm38.p5 mouse transriptome with kallisto v0.43.0 using 100 bootstrap replications. DESeq2 was used to perform differential expression analysis.
Genome_build: mouse mm10, Gencode GRCm38.p5 mouse transriptome
|
| |
|
| Submission date |
Mar 07, 2019 |
| Last update date |
Mar 08, 2019 |
| Contact name |
Tomasz Nowakowski |
| E-mail(s) |
[email protected]
|
| Organization name |
UCSF
|
| Street address |
1550 4th St
|
| City |
San Francisco |
| State/province |
Ca |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE127987 |
The long noncoding RNA Pnky is a trans-acting regulator of cortical development in vivo |
|
| Relations |
| BioSample |
SAMN11082130 |
| SRA |
SRX5491741 |
