|
| Status |
Public on May 17, 2016 |
| Title |
Ctrl tumor cell_5 |
| Sample type |
SRA |
| |
|
| Source name |
brain tumor cells, control
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: mixed C57Bl/6;129Sv;CD-1
genotype/variation: Ptenfl/fl;Trp53fl/fl:PDGFB-Cre (control)
cell type: brain tumor (glioma)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were isolated from the tumor cells, OPCs, astrocytes and normal cortex with Trizol as recommended by the manufacturer.
RNA libraries were prepared for sequencing using the Illumina RNA-seq preparation Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq reads were mapped using TopHat with default settings (http://ccb.jhu.edu/software/tophat/index.shtml).
TopHat output data were then analyzed by Cufflinks to calculate FPKM values for known transcripts in mouse genome reference mm9.
Differential gene expression analysis was performed using Cuffdiff.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Apr 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard Lu |
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
CBDI
|
| Lab |
Lu Lab,T6.525
|
| Street address |
3333 Burnet Ave
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE80087 |
Gene expression profiling of retrovirus PDGFB-induced glioma |
| GSE80089 |
Gene expression profiling and genome-wide maps in PDGFB-induced glioma |
|
| Relations |
| BioSample |
SAMN04625843 |
| SRA |
SRX1688474 |
