|
| Status |
Public on Jan 01, 2016 |
| Title |
mNPC Control siRNA #1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse neuronal progenitor cell (mNPC)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 46C mESC
protocol: mESCs were differentiated into mNPCs
treatment: siControl #1
|
| Treatment protocol |
mNPCs were reverse transfected with 10 nM of either control, Ptbp1, Ptbp2, or Ptbp1-Ptbp2 siRNA. After 48 hours, the mNPCs were harvested for total RNA.
|
| Growth protocol |
46C mNPCs were cultured on poly-ornithine and fibronectin coated plates, in mNPC media supplemented with EGF and FGF.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was collected with the Trizol reagent. Poly-A RNA was selected for using oligo-dT beads.
Libraries were constructed with the Illumina TruSeq stranded kit. A final library of 300-400 bp was size selection with an agarose gel.
The libraries were subjected to 50bp paired-end sequencing (Illumina HiSeq2000).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Transfection siRNA Control #1
mNPC_Control_splicetrap.txt
|
| Data processing |
illumina Casava software used for basecalling
Exon inclusion ratios were calculated using a splicetrap program
Genome_build: mm9
Supplementary_files_format_and_content: Text files include exon inclusion level values for each sample.
|
| |
|
| Submission date |
Jul 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chia-ho Lin |
| E-mail(s) |
[email protected]
|
| Organization name |
UCLA
|
| Lab |
BLACK LAB
|
| Street address |
6577 MRL. 675 CHARLES E YOUNG DR. SOUTH
|
| City |
LOS ANGELES |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE70985 |
Splicing analyses of 46C mNPCs following PTBP depletion |
| GSE71179 |
The splicing regulator PTBP1 controls the activity of the transcription factor Pbx1 during neuronal differentiation |
|
| Relations |
| BioSample |
SAMN03863130 |
| SRA |
SRX1098716 |
