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Sample GSM1835798 Query DataSets for GSM1835798
Status Public on Jul 18, 2017
Title MDA-MB-231_shGFP_rep1
Sample type RNA
 
Source name MDA-MB-231 shGFP
Organism Homo sapiens
Characteristics cell line: Breast cancer cell line MDA-MB-231
genotype/variation: control
Treatment protocol Lentiviral shRNA constructs were obtained from the RNAi Consortium shRNA Library at the Broad Institute. Conditioned medium containing infective lentiviral particles was generated by cotransfecting 3µg of each lentiviral vector, 3µg of pCMV d8.91 and 1µg pHCMV-G into 1×10*6 293T human embryonic kidney cells using FuGENE 6 transfection reagent (Roche Applied Science). Supernatants were collected 48 hr after transfection and filtered through a 0.45 µM membrane (Millipore). Cells were infected with each supernatants using 8µg/mL polybrene and selected with 2µg/mL puromycin. RNA was isolated 72 hr after lentiviral shRNA infection.
Growth protocol Human breast (MDA-MB-231) and lung (A549) cancer cell lines (American Type Culture Collection, Manassas, VA, USA) were grown in Dulbeccco’s modified medium, which supplemented with 10% fetal bovine serum and penicillin/streptomycin (Pen/Strep). Both cell lines were maintained in 5% CO2 at 37°C.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini kit (Qiagen, Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was isolated 72 hr after lentiviral shRNA infection.
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Arrays were scanned on Nimblegen MS200 at 2um resolution
Description This sample is of shGFP in MDA-MB-231 cells replicates 1.
Data processing Array data was background corrected and normalized as suggested using the Roche NimbleScan 2.6 software
 
Submission date Jul 29, 2015
Last update date Jul 19, 2017
Contact name Robert Morris
E-mail(s) morris.robert@mgh.harvard.edu
Phone 617-724-6552
Organization name Mass. General Hospital Cancer Center
Street address 149 13th Street
City Charlestown
State/province Massachusetts
ZIP/Postal code 02129
Country USA
 
Platform ID GPL18734
Series (1)
GSE71498 Arrayed gene expression analysis of the SETD1A depleted cancer cells

Data table header descriptions
ID_REF
VALUE RMA-normalized, probe level intensity scores

Data table
ID_REF VALUE
AB000409P01117 2206.35
AB000409P01448 3858.66
AB000409P01556 3022.8
AB000463P01737 1272.17
AB000463P01784 2080.4
AB000463P02265 2119.7
AB000781P03689 82.47
AB000781P04906 50.8
AB000781P05080 39.38
AB001328P00364 54.66
AB001328P00764 34.56
AB001328P01450 80.94
AB002294P06259 1811.56
AB002294P06304 2102.98
AB002294P06331 2911.47
AB002308P08048 7251.94
AB002308P08153 12083.45
AB002308P08407 8783.04
AB002311P05625 1301.94
AB002311P05920 1725.09

Total number of rows: 140096

Table truncated, full table size 3127 Kbytes.




Supplementary file Size Download File type/resource
GSM1835798_506681A12_532_Slot8_2013-01-11.pair.gz 2.9 Mb (ftp)(http) PAIR
GSM1835798_506681A12_532_Slot8_2013-01-11_norm_RMA.pair.gz 2.9 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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