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Sample GSM2362801 Query DataSets for GSM2362801
Status Public on Jan 01, 2017
Title U251-BMI1-shRNA
Sample type RNA
Source name whole cells
Organism Homo sapiens
Characteristics cell line: U251
phenotype: reduced BMI1 expression
Treatment protocol cells were stably transduced with a lentiviral vector containing the shRNA sequence of BMI1, USP22 and control
Growth protocol U251MG was grown in the DMEM supplemented with 10% FBS (GIBCO)
Extracted molecule total RNA
Extraction protocol RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression 8x60K v2 for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression after reducing BMI1 expression
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.
Submission date Oct 27, 2016
Last update date Apr 23, 2018
Contact name Jiangbing zhou
Organization name Yale university
Street address 310 Cedar Street, Ste LH 412A
City Newhaven
ZIP/Postal code 06510
Country USA
Platform ID GPL17077
Series (1)
GSE89239 The deubiquitinase USP22 stabilizes BMI1 polycomb ring finger oncoprotein to confer cancer stem cell traits and glioblastoma progression
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 15.297575
DarkCorner 2.207104
A_23_P117082 11.06207
A_33_P3246448 6.6668286
A_33_P3318220 2.2682385
A_33_P3236322 2.263587
A_33_P3319925 4.2249207
A_21_P0000509 16.690634
A_21_P0000744 10.173481
A_24_P215804 7.1046305
A_23_P110167 11.421924
A_33_P3211513 7.8549123
A_23_P103349 2.4220312
A_32_P61480 2.2284849
A_33_P3788124 2.2251978
A_33_P3414202 8.166623
A_33_P3316686 9.350862
A_33_P3300975 11.116635
A_33_P3263061 13.251127
A_33_P3261373 2.459458

Total number of rows: 50739

Table truncated, full table size 1145 Kbytes.

Supplementary file Size Download File type/resource
GSM2362801_U251-BMI1_shRNA.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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