|
| Status |
Public on Feb 19, 2016 |
| Title |
MbnlsiRNASoma3 |
| Sample type |
SRA |
| |
|
| Source name |
CAD cells Mbnl1/2 siRNA soma
|
| Organism |
Mus musculus |
| Characteristics |
cell line: CAD cells
compartment: soma
knockdown: Mbnl siRNA
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were fractionated using porous membranes into soma and neurite fractions.
For all N2A and CAD samples, libraries were prepared using the standard "dUTP" strand-specific method. For cortical neuron samples, libraries were prepared using the Clontech Low Input Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Mbnl siRNA Soma Rep3
|
| Data processing |
Reads were aligned to the mm9 genome using either Tophat version 2.0.12 or STAR 2.0.4d
Expression values were calculated using Cufflinks version 2.1.1
Alternative isoform abundances were calculated using MISO
Genome_build: mm9 supplemented with alternative isoforms identified in Merkin et al (Science) 2012
|
| |
|
| Submission date |
Apr 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew Taliaferro |
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Biology
|
| Street address |
12801 E 17th Ave, RC1 South Room 10403D
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE67828 |
Profiling of soma and neurite transcriptomes |
|
| Relations |
| BioSample |
SAMN03481293 |
| SRA |
SRX993473 |
