Y The Methodist Hospital Institutional 1516647 Animal Care and Use Committee (AUP-0811-0037). All surgery was performed under Ketamine/ Xylazine cocktail anesthesia, and all efforts were made to minimize suffering.Microarray hybridizationCells of interest were collected and genomic DNA was extracted using a Promega kit. A 250 base pair DNA fragment containing the barcode sequence was PCR amplified using the primers supplied by the vendor (Open Biosystems). The DNA was then labeled with cyanine fluorescent dyes using Agilent’s genomic DNA labeling kit. The labeled DNAs were then hybridized to microarray using the Agilent oligo aCGH hybridization kit, and the array was scanned with a Genepix scanner. The Decode RNAi 
barcode microarray was supplied by the vendor (Open Biosystems). It consists of 26105 K arrays spotted with sequences unique to each shRNA. Barcode hybridizing probes have been optimized using Agilent algorithms for assessing probe quality. Each array contains 58,498 probe sequences (most duplicated on the array).Cell lines and primary cellsAll the cell lines were purchased from the American Type Culture Collection (ATCC) and grown in DMEM with 10 fetal bovine serum (FBS) and penicillin/streptomycin at 37uC in a humidified incubator with 5 CO2. They were used within 10 passages, for less than 6 months after receipt. Cell lines were characterized by ATCC by morphology check, growth curve analysis, and short tandem repeat DNA profiling. After receipt, cells were confirmed to be free from mycoplasma contamination using a mycoplasma detection kit (Roche Applied Science). Brain tumor surgical specimen were obtained following the protocol approved by our Institutional Review Board. Briefly, fresh tumor samples obtained within 
2 hours of surgical resection were rinsed with PBS, mechanically minced with scissors, and digested for 30 minutes at 37uC with trypsin. Cells were extensively triturated and filtered through a 40 mm filter to collect single cells. They were then cultured in suspension at 105 cells/ml in serum free medium containing bFGF, EGF, and heparin. Neurospheres formed within a week and the single cells were removed using cell strainers. The cells were maintained in the neurosphere form and used for migration assay within 2 weeks. Before the assay the neurospheres were dissociated with accutase to single cells.Cell 1662274 migration assaysFor Boyden chamber assay, experiments were carried out using Matrigel invasion chambers with 8 mm pore size (BD Biosciences). To count the migrated cells, after incubation the non-invading cells were thoroughly removed from the upper surface of the membrane by scrubbing. The migrated cells attached to the lower surface of the membrane were fixed and stained with toluidine blue. The whole membrane was then imaged using a brightfield microscope with order PD-168393 montage 256373-96-3 web function. For microarray analysis or further culture, cells were separately collected from the upper chamber and lower membrane surface, trypsinized, and washed for further treatment. For wound healing assay, 56105 cells were seeded in 6-well plates. After 48 hours, a straight scratch was made in each well using a pipette tip. Time-lapse images were taken and the migrated cells were counted at different time points. All experiments were repeated at least three times, and results were presented as the mean with standard deviation. Student T test was used to evaluate the statistical significance.Cell proliferation assayTo measure the cell proliferatio.Y The Methodist Hospital Institutional 1516647 Animal Care and Use Committee (AUP-0811-0037). All surgery was performed under Ketamine/ Xylazine cocktail anesthesia, and all efforts were made to minimize suffering.Microarray hybridizationCells of interest were collected and genomic DNA was extracted using a Promega kit. A 250 base pair DNA fragment containing the barcode sequence was PCR amplified using the primers supplied by the vendor (Open Biosystems). The DNA was then labeled with cyanine fluorescent dyes using Agilent’s genomic DNA labeling kit. The labeled DNAs were then hybridized to microarray using the Agilent oligo aCGH hybridization kit, and the array was scanned with a Genepix scanner. The Decode RNAi barcode microarray was supplied by the vendor (Open Biosystems). It consists of 26105 K arrays spotted with sequences unique to each shRNA. Barcode hybridizing probes have been optimized using Agilent algorithms for assessing probe quality. Each array contains 58,498 probe sequences (most duplicated on the array).Cell lines and primary cellsAll the cell lines were purchased from the American Type Culture Collection (ATCC) and grown in DMEM with 10 fetal bovine serum (FBS) and penicillin/streptomycin at 37uC in a humidified incubator with 5 CO2. They were used within 10 passages, for less than 6 months after receipt. Cell lines were characterized by ATCC by morphology check, growth curve analysis, and short tandem repeat DNA profiling. After receipt, cells were confirmed to be free from mycoplasma contamination using a mycoplasma detection kit (Roche Applied Science). Brain tumor surgical specimen were obtained following the protocol approved by our Institutional Review Board. Briefly, fresh tumor samples obtained within 2 hours of surgical resection were rinsed with PBS, mechanically minced with scissors, and digested for 30 minutes at 37uC with trypsin. Cells were extensively triturated and filtered through a 40 mm filter to collect single cells. They were then cultured in suspension at 105 cells/ml in serum free medium containing bFGF, EGF, and heparin. Neurospheres formed within a week and the single cells were removed using cell strainers. The cells were maintained in the neurosphere form and used for migration assay within 2 weeks. Before the assay the neurospheres were dissociated with accutase to single cells.Cell 1662274 migration assaysFor Boyden chamber assay, experiments were carried out using Matrigel invasion chambers with 8 mm pore size (BD Biosciences). To count the migrated cells, after incubation the non-invading cells were thoroughly removed from the upper surface of the membrane by scrubbing. The migrated cells attached to the lower surface of the membrane were fixed and stained with toluidine blue. The whole membrane was then imaged using a brightfield microscope with montage function. For microarray analysis or further culture, cells were separately collected from the upper chamber and lower membrane surface, trypsinized, and washed for further treatment. For wound healing assay, 56105 cells were seeded in 6-well plates. After 48 hours, a straight scratch was made in each well using a pipette tip. Time-lapse images were taken and the migrated cells were counted at different time points. All experiments were repeated at least three times, and results were presented as the mean with standard deviation. Student T test was used to evaluate the statistical significance.Cell proliferation assayTo measure the cell proliferatio.
