Comment[ArrayExpressAccession]	E-MTAB-1331
Investigation Title	Depletion of HPV16 oncogenes induces autophagy and senescence in a cervical carcinogenesis model, irrespective of viral physical state
Comment[Submitted Name]	Depletion of HPV16 oncogenes induces autophagy and senescence in a cervical carcinogenesis model, irrespective of viral physical state
Experiment Description	We utilised our in vitro model of cervical neoplastic progression, W12, to investigate the effect of HPV16 viral oncogene depletion on well-defined integrant- and episome- associated series. To target HPV16 viral oncogenes we used our previously published E7-targeting siRNA sequence that caused substantial depletion of both E7 and E6 in CaSki cells. We found all E7-siRNA treated W12 series underwent widespread autophagy and senescence, with up-regulation of an innate immune response.
Experimental Design	in_vitro_design	is_expressed_design
Comment[AEExperimentDisplayName]	Transcription profiling by array of human W12 cell lines transfected with HPV16 siRNA as a model to study cervical neoplastic progression
Comment[AEExperimentType]	transcription profiling by array
Experimental Factor Name	cell line	siRNA transfection
Experimental Factor Type	cell line	rnai
Quality Control Type	technical_replicate
Public Release Date	2013-08-12
Person Last Name	Saini
Person First Name	Harpreet
Person Mid Initials	K
Person Email	hsaini@ebi.ac.uk
Person Phone	+44-1223-492676
Person Address	EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD
Person Affiliation	EMBL-EBI
Person Roles	submitter
Publication Author List	JE Hanning, HS Saini, MJ Murray, MM Caffarel, S van Dongen, DM Ward, EM Barker, CG Scarpini, IJ Groves, MA Stanley, AJ Enright, MR Pett, N Coleman
Publication Title	Depletion of HPV16 early genes induces autophagy and senescence in a cervical carcinogenesis model, regardless of viral physical state
Publication Status	submission
Protocol Name	P-MTAB-29605	P-MTAB-29606	P-MTAB-29607	P-MTAB-29608	P-MTAB-29609	P-MTAB-29610	P-MTAB-29611	P-MTAB-29612
Protocol Type	grow	siRNA transfection	RNA extraction	labeling	hybridization	image_acquisition	bioassay_data_transformation	bioassay_data_transformation
Protocol Description	All W12 cells were derived through long-term in vitro passaging of cells from an explant culture of a low-grade squamous intraepithlial legion. The W12 squamous epithelial cells used were: W12Ser4p31, W12Ser4p86, W12Ser4B and G2p13.	Cells were seeded into six-well plates at 2.4 x 105 cells per well (for protein extraction) or 12-well plates at 1x105 cells per well (for RNA extraction and growth curves) without antibiotics or feeder cells. Cells were transfected using 37nM of E7-141 siRNA or non-targeting control (NTC) siRNA.	RNA was harvested using TRIzol (Life Technologies, Grand Island, NY, USA). QuantiTect reverse transcription kit (Qiagen, Crawley, UK) was used for cDNA synthesis, and quantitative PCR was performed using SYBR Green JumpStart Taq ReadyMix (Sigma-Aldrich, Dorset, UK). Expression levels were normalised against the mean of three house-keeping genes.	Standard Illumina protocol	Standard Illumina hybridisation protocol	Standard Illumina scanning protocol	The log2-transformed data were quantile normalized	The bead level data (raw TIFF images and text files) obtained from BeadScan software were read using the Bioconductor beadarray package (version 2.2.0). The data were converted to bead-summary data using summarize function and the default logGreenChannelTransform transformation
SDRF File	E-MTAB-1331.sdrf.txt
Publication DOI	10.1002/path.4244