Comment[ArrayExpressAccession]	E-MTAB-2682
MAGE-TAB Version	1.1						
Investigation Title	Isoform-specific depletion of U2AF1						
Comment[Submitted Name]	Isoform-specific depletion of U2AF1
Experiment Description	RNA-Seq data of U2AF1 isoform depletion experiments.						
Experimental Factor Name	transfection	library selection					
Experimental Factor Type	genetic modification	protocol					
Experimental Factor Term Source REF							
Experimental Factor Term Accession Number							
Person Last Name	Vorechovsky	Knut					
Person First Name	Igor	Marcin					
Person Mid Initials							
Person Email	igvo@soton.ac.uk	m.knut@soton.ac.uk					
Person Phone							
Person Fax							
Person Address	Duthie Building, Southampton General Hospital, Tremona Rd, Southampton, Hampshire SO16 6YD, UK	Duthie Building, Southampton General Hospital, Tremona Rd, Southampton, Hampshire SO16 6YD, UK					
Person Affiliation	University of Southampton	University of Southampton					
Person Roles	data analyst;experiment performer;investigator;submitter	data analyst;data coder;investigator;submitter					
Public Release Date	2015-01-31						
Protocol Name	P-MTAB-39843	P-MTAB-39844	P-MTAB-39845	P-MTAB-39846	P-MTAB-39847	P-MTAB-39848	P-MTAB-39849
Protocol Type	growth protocol	treatment protocol	treatment protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	high throughput sequence alignment protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Term Accession Number	EFO_0003789	EFO_0003969	EFO_0003969	EFO_0004184	EFO_0004184	EFO_0004170	EFO_0004917
Protocol Description	Cell lines were grown under standard conditions in DMEM supplemented with 10% (v/v) bovine calf serum (Gibco BRL)	Transfections of small interfering RNAs (siRNAs) were carried out in 6- or 12- well plates using jetPRIME (Polyplus) according to manufacturer's recommendations. The cells received treatment with siRNA twice - 24h post seeding, and 48h post seeding when splitting into a new plate.	Transfections of  splice-switching oligonucletides (SSOs) targeting mutually exclusive U2AF1 exons were carried out in 6- or 12- well plates using jetPRIME (Polyplus) according to manufacturer's recommendations. The cells received treatment with SSO twice - 24h post seeding, and 48h post seeding when splitting into a new plate.	PolyA library selection was performed using NEBNext poly(A) mRNA magnetic isolation module (E7490L) according to the manufacturer's specifications.	A human/mouse/rat Ribo-Zero rRNA Removal Kit (Cambio/Epicentre) was used according to the manufacturer's specifications.	Size-selected and multiplexed libraries were sequenced using Illumina HiSeq 2500 using paired-end sequencing.	Sequence alignment was performed using Bowtie 2 and TopHat 2 against genome and transcriptome references (hg19, UCSC). The transcriptome reference was altered to include U2AF1 isoform s. Following alignment, sequences recognised as originating from mtRNA, rRNA, and tRNA were removed.
Protocol Hardware						Illumina HiSeq 2500	IRIDIS 4 High Performance Computing Cluster
Protocol Software							Bowtie (v. 2.1.0), TopHat (v. 2.0.9)
Term Source Name	EFO
Term Source File	http://www.ebi.ac.uk/efo/						
Term Source Version							
Comment[AEExperimentType]	RNA-seq of coding RNA						
Comment[AEExperimentDisplayName]	RNA-Seq data of U2AF1 isoform depletion experiments						
Comment[SecondaryAccession]	ERP006200
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/ERR553454-ERR553469
SDRF File	E-MTAB-2682.sdrf.txt