|
| Status |
Public on Dec 08, 2017 |
| Title |
shQk_NSC_2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse neural stem cells, Qk knockdown
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: CD1
cell type: Neural stem cells
developmental stage: E14.5
lentivirus: sh-Qk
|
| Treatment protocol |
Lentiviruses encoding sh-control or sh-Qk, which targeted all Qki proteins for knock-down (KD), were produced and infected into cultured neural stem.
|
| Growth protocol |
Neural stem cells were isolated from the E14.5 mouse cortex and cultured with KBM neural stem cell medium (KOHJIN BIO, Japan) supplemented with 10 ng/ml bFGF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Six days after infection, the cells were collected and subjected to mRNA-library generation.
TruSeq RNA Sample Prep Kit v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mRNA-seq
|
| Data processing |
Alignment with Tophat
to have BAM and Bed file.
Transcript level and alternative splicing events with Quantas.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: .txt: Tab-delimited text files; gene_id, gene_symbol, tag_number, RPKM, start and end position, strand and isoform tag_number.
|
| |
|
| Submission date |
Aug 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Masato Yano |
| E-mail(s) |
myano@med.niigata-u.ac.jp
|
| Organization name |
Niigata University
|
| Department |
Division of Neurobiology and Anatomy
|
| Street address |
757, Ichibancho, Asahimachidori, Chuo-ku, Niigata-shi,
|
| City |
Niigata |
| ZIP/Postal code |
950-0907 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE103246 |
RNAseq in control and shQk KD mouse neural stem cells |
| GSE103248 |
RNAseq in control and shQk KD mouse neural stem cells, and Qki5 CLIP in E14.5 mouse brain |
|
| Relations |
| BioSample |
SAMN07571915 |
| SRA |
SRX3144862 |
