|
| Status |
Public on Apr 13, 2016 |
| Title |
EGFRvIII/STAT3 targets in glioblastoma pathogenesis |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Next generation sequencing platforms were used to identify STAT3 targets in the background of EGFRvIII expresssion
|
| |
|
| Overall design |
mRNA of 3 EGFRvIII positive brain tumor stem cell lines (BTSC #68, 73, and 90) were compared to an EGFRvIII negative line (#41) to identify EGFRvIII-regulated targets in human BTSC. EGFRvIII-dependent targets in mouse astrocytes were identified by mRNA-seq analyses of EGFRvIII- or MSCV-expressing astrocytes. STAT3-differentially regulated genes in EGFRvIII expressing mouse astrocytes were obtained by subjecting EGFRvIII,STAT3f/f and EGFRvIII, STAT3-/- astrocytes to mRNA-Seq analyses. Sites of STAT3 occupancy in EGFRvIII expressing astrocytes were identified by ChIP-Seq using a STAT3 antibody or IgG control. We identified OSMR as a direct target of STAT3 in both EGFRvIII-expressing human BTSC and mouse astrocytes. Therefore to identify OSMR-regulated genes, we used a lentiviral mediated RNAi system to knockdown OSMR in EGFRvIII-expressing astrocytes. OSMR-dependent differentially expressed genes were obtained by comparison of OSMR knockdown (KD1 and KD2) astrocytes to control groups (ShRNA control and Vector control)
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| |
|
| Contributor(s) |
Jahani-Asl A, Rudnicki MA, Bonni A |
| Citation(s) |
27110918 |
| Submission date |
Sep 30, 2013 |
| Last update date |
May 15, 2019 |
| Organization |
Ottawa Hospital Research Institute |
| Phone |
(613) 737-8899 -73255
|
| Department |
Cellular and Molecular Medicine
|
| Lab |
Ottawa Bioinformatics Core Facility
|
| Street address |
501 Smyth Rd.
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1H 8L6 |
| Country |
Canada |
| |
|
| Platforms (3) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (14)
|
| GSM1241815 |
OSMR-KD1_EGFRvIII expressing astrocytes |
| GSM1241816 |
OSMR-KD2 EGFRvIII expressing astrocytes |
| GSM1241817 |
Scramble control-EGFRvIII expressing astrocytes |
| GSM1241818 |
Vector-control-EGFRvIII expressing astrocytes |
| GSM1241819 |
BTSC68_EGFRvIII positive BTSC |
| GSM1241820 |
BTSC73_EGFRvIII positive BTSC |
| GSM1241821 |
BTSC90_EGFRvIII positive BTSC |
| GSM1241822 |
BTSC41_EGFRvIII negative BTSC |
| GSM1241823 |
EGFRvIII-expressing STAT3 floxed astrocytes |
| GSM1241824 |
EGFRvIII-expressing STAT3 knockout astrocytes |
| GSM1241825 |
MSCV-expressing STAT3 floxed astrocytes |
| GSM1241826 |
MSCV-expressing STAT3 knockout astrocytes |
| GSM1241827 |
STAT3-ChIP_EGFRvIII expressing astrocytes |
| GSM1241828 |
control-ChIP-Rabbit-IgG_EGFRvIII expressing astrocytes |
|
| Relations |
| BioProject |
PRJNA222297 |
| SRA |
SRP030637 |
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