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Sample GSM1446156 Query DataSets for GSM1446156
Status Public on Jul 14, 2016
Title Uninfected HeLa cells
Sample type RNA
 
Source name Unifected HeLa cells transduced with shRNA library and cultured for 17 days
Organism Homo sapiens
Characteristics cell type: Human epithelial carcinoma cell line
cell line: HeLa
infection: Uninfected
Treatment protocol Latently infected and unifected HeLa cells were transduced with the lentiviral shRNA library for 6 hours at an MOI of approximately 0.4. Transduced cells were selected with Puromycin and cultured for a total of 17 days, which was experimentally determined to provide ample time for shRNA expression and knockdown of the target gene, as well as viral reactivation and viral protein-mediated cell death in the experimental sample. In other words, a negative selection protocol was used to identify shRNAs that activated latent virus by taking advantage of the cytotoxic effects of the HIV-1 viral protein Vpr.
Growth protocol HeLa cells transduced with the shRNA library were cultured for 17 days in standard conditions (37 degrees celsius with 5% CO2) in MEM GlutaMAX medium (Life Technologies, Grand Island, NY) supplemented with 10% FetalClone III Serum (Thermo Scientific Hyclone, Logan, UT), 2X MEM Non-essential amino acids solution (Life Technologies, Grand Island, NY), 100U/mL penicillin-100μg/mL streptomycin solution (Life Technologies, Grand Island, NY), and 0.75μg/mL Puromycin (Sigma-Aldrich, St. Louis, MO).
Extracted molecule total RNA
Extraction protocol System Biosciences isolated total RNA, reverse transcribed the RNA into cDNA, and amplified the cDNA as a fee for service according to GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 3): Chapter 2
Label Biotin
Label protocol System Biosciences amplified the cDNA using Biotin-conjugated primers as a fee for service according to GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 3): Chapter 2
 
Hybridization protocol System Biosciences hybridized the labeled cDNA to the Affymetrix GeneChip Array (HG-U133+ 2.0) using GeneChip Hybridization Oven 640 and washed and stained using GeneChip Fluidics Station 450 as a fee for service according to GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 3): Chapter 3
Scan protocol GeneChips were scanned using GeneChip Scanner 3000 7G
Description Uninfected
Data processing The data were analyzed with GeneChip Operating Software v1.4 using default analysis and normalization settings
GeneChip Operating Software v1.4 signal intensities per probeset ID were averaged for each individual microarray. In other words, probeset signal intensities were averaged for the experimental sample microarray and probeset signal intensities were averaged for the reference control sample microarray). Averages per probeset ID are reported in two separate columns in the matrix file according to which array they were obtained from.
 
Submission date Jul 25, 2014
Last update date Jul 14, 2016
Contact name Joseph Dougherty
E-mail(s) doughejp@rwjms.rutgers.edu
Phone 732-235-4588
Organization name Rutgers University - Robert Wood Johnson Medical School
Department Department of Pharmacology
Lab Research Towers Rm. 813
Street address 675 Hoes Lane West
City Piscataway
State/province NJ
ZIP/Postal code 08854
Country USA
 
Platform ID GPL570
Series (1)
GSE59758 Genome-wide shRNA screen to identify cellular regulators of the maintenance of HIV-1 latency

Data table header descriptions
ID_REF
VALUE GeneChip Operating Software v1.4 signal intensities

Data table
ID_REF VALUE
1552504_a_at 127
1552899_at 405
1552972_at 178
1553878_at 59
1553894_at 62
1554176_a_at 78
1554314_at 94
1554354_at 70
1554649_at 66
1554986_a_at 244
1555585_a_at 66
1555889_a_at 59
1556354_s_at 77
1557236_at 260
1557257_at 64
1557813_at 64
1558233_s_at 72
1559256_at 507
1559289_at 2387
1559901_s_at 85

Total number of rows: 54569

Table truncated, full table size 892 Kbytes.




Supplementary file Size Download File type/resource
GSM1446156_SBI_Ref.control_HG-U133_Plus_2_.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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