E-GEOD-43082 - Expression data from neonatal human foreskin keratinocytes (NHKs) with NFX1-123 endogenous expression, overexpression, or knocked down expression, with or without HPV16E6 co-expression

Status
Released on 15 October 2013, last updated on 2 June 2014
Organism
Homo sapiens
Samples (24)
Array (1)
Protocols (7)
Description
GSM1056261-GSM1056272: NFX1-123 has been shown to associate with a number of RNA processing proteins, such as cytoplasmic poly(A) binding proteins (PABPC), to affect mRNA stability and translational efficiency of target genes. The high-risk human papillomavirus type 16E6 (HPV 16E6) induces telomerase activity by activation of hTERT, the catalytic subunit of telomerase. NFX1-123 can bind to hTERT mRNA and increase its stability in HPV 16E6 expressing keratinocytes (16E6 NHKs). Little is known regarding what other transcripts, and downstream signaling pathways, may be dependent on NFX1-123. In order to determine additional cellular transcripts affected by HPV 16E6 and NFX1-123, we assessed global gene expression changes in cells in which NFX1-123 was overexpressed or knocked down by short hairpin RNAs (shRNA) when compared to an isogenic scramble control, in three independently derived 16E6 NHKs GSM1212499-GSM1212510: NFX1-123 has been shown to associate with a number of RNA processing proteins, such as cytoplasmic poly(A) binding proteins (PABPC), to affect mRNA stability and translational efficiency of target genes. The high-risk human papillomavirus type 16E6 (HPV 16E6) induces telomerase activity by activation of hTERT, the catalytic subunit of telomerase. NFX1-123 can bind to hTERT mRNA and increase its stability in HPV 16E6 expressing keratinocytes (16E6 NHKs). Little is known regarding what other transcripts, and downstream signaling pathways, may be dependent on NFX1-123. In order to determine additional cellular transcripts affected solely by NFX1-123, we assessed global gene expression changes in cells in which NFX1-123 was overexpressed or knocked down by short hairpin RNAs (shRNA) when compared to an isogenic scramble control, in three independently derived NHKs. GSM1056261-GSM1056272: Three independent 16E6 expressing NHK cell lines were expanded and transduced with: short hairpin RNA (sh1) that knocked down NFX1-123 by 20%, short hairpin RNA (sh3) that knocked down NFX1-123 by 80%; a non-targeting isogenic shRNA scramble control; or a NFX1-123 overexpression construct with a FLAG-tag (FNFX1-123WT) that increased its RNA expression on average 3.5-fold. In total, twelve samples were used for the microarray, derived from the three initial NHK cell lines. GSM1212499-GSM1212510: Three independent NHK cell lines were expanded and transduced with: short hairpin RNA (sh1) that knocked down NFX1-123 by 40%, short hairpin RNA (sh3) that knocked down NFX1-123 by 83%; a non-targeting isogenic shRNA scramble control; or a NFX1-123 overexpression construct with a FLAG-tag (FNFX1-123WT) that increased its RNA expression on average 14.0-fold. In total, twelve samples were used for the microarray, derived from the three initial NHK cell lines.
Experiment type
transcription profiling by array 
Contacts
Rachel Katzenellenbogen <rachel.katzenellenbogen@seattlechildrens.org>, Jennifer R Hamiliton, Portia A Vliet-Gregg, Rachel A Katzenellenbogen
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-43082.idf.txt
Sample and data relationshipE-GEOD-43082.sdrf.txt
Processed data (1)E-GEOD-43082.processed.1.zip
Array designA-GEOD-10558.adf.txt
Links