|
| Status |
Public on Nov 09, 2016 |
| Title |
QK-NSC-KO_QW2-40HT_WT |
| Sample type |
SRA |
| |
|
| Source name |
neural stem cells (NSCs)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: neural stem cells
strain: C57B6/FVB
treatment: 4OHT
genotype: wild type
|
| Treatment protocol |
Cells were treated with either EtOH or 4OHT. Mice were injected with tamoxifen at P8-10.
|
| Growth protocol |
Cells were grown in neural stem cell medium with EGF/FGF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted with Rnasey kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
isolate from postnatal day one pup
processed data files: QK-NSC-KO_gene_FPKM.txt.gz and QK-NSC-KO_transcript_FPKM.txt.gz
|
| Data processing |
Sequenced reads were mapped to the mm10 genome using tophat2/2.0.8. Transcription annotation version is GENCODE vM8.
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated at both gene and transcript level using cufflinks/2.2.1. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Apr 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Hu |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Department of Cancer Biology, Division of Basic Sciences
|
| Street address |
1881 East Rd
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE79889 |
QKI's function in neural stem cells (NSCs) and pre-malignant NSCs (PM-NSCs) and transcriptome of Nestin-CreERT2 PtenLoxP/LoxP p53LoxP/LoxP QKILoxP/LoxP (QPP) mouse glioblastoma |
| GSE84134 |
QKI deficiency maintains stemness of glioma stem cells in suboptimal environment by downregulating endolysosomal degradation |
|
| Relations |
| BioSample |
SAMN04605676 |
| SRA |
SRX1678131 |
