|
| Status |
Public on Jan 01, 2016 |
| Title |
D2 MN Pbx1 I6 +/- clone #1 |
| Sample type |
SRA |
| |
|
| Source name |
Day 2 mouse motor neuron cultures (D2 MN)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: HB9-GFP mESC
genotype/variation: Pbx1 I6 +/- CRISPR deletion
protocol: mESC clones were harvested after Day 2 of differentiation in MN media
|
| Treatment protocol |
I6 +/- clones were treated with transiently transfected with Cas9 and guide RNA sequences to generate heterozygous deletions at the Pbx1 intron 6 locus.
|
| Growth protocol |
HB9 mESCs were grown in aggregate culture in the presence of RA and SAG.
|
| 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.
The libraries were subjected to 50bp single-end sequencing (Illumina HiSeq2000).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were mapped to mm9 genome using TopHat. FPKM values were calculated using the Cufflinks package.
Genome_build: mm9
Supplementary_files_format_and_content: Text files include exon inclusion level values for each sample.
|
| |
|
| Submission date |
Jul 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chia-ho Lin |
| E-mail(s) |
CHIAHOLI@g.UCLA.EDU
|
| 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) |
| GSE70883 |
Gene expression analyses of HB9-GFP D2 mMN cultures following Pbx1 exon 7 inclusion |
| GSE71179 |
The splicing regulator PTBP1 controls the activity of the transcription factor Pbx1 during neuronal differentiation |
|
| Relations |
| BioSample |
SAMN03857790 |
| SRA |
SRX1096568 |
