|
| Status |
Public on May 17, 2016 |
| Title |
olig2cKOtumor_3 |
| Sample type |
SRA |
| |
|
| Source name |
brain tumor
|
| Organism |
Mus musculus |
| Characteristics |
background strain: mixed C57Bl/6;129Sv;CD-1
tissue: brain tumor
genotype: Pten lox/lox : P53lox/lox : Olig2lox/lox
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were isolated from the brain tumor tissue of the control tumor mice and Olig2cKO tumor mice with trizol as recommended by the manufacturer.RNA-seq libraries were prepared using Illumina RNA-seq preparation Kit (Illumina)
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 |
| |
|
| Data processing |
RNA-seq reads were mapped using TopHat with default settings.(http://tophat.cbcb.umd.edu)
TopHat output data were then analyzed by Cufflinks to (1) calculate FPKM values for known transcripts in mouse genome reference mm9; (2) test the changes of gene expression between Olig2cKO and control tumors..
Genome_build: All sequencing data were mapped to mm9
Supplementary_files_format_and_content: txt files of gene expression FPKM values
|
| |
|
| Submission date |
Jul 29, 2015 |
| 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) |
| GSE71493 |
Gene expression profiling of retrovirus PDGFB induced Glioma in control and Olig2cKO tumor |
| GSE80089 |
Gene expression profiling and genome-wide maps in PDGFB-induced glioma |
|
| Relations |
| BioSample |
SAMN03943683 |
| SRA |
SRX1123505 |
