Comment[ArrayExpressAccession]	E-MTAB-1927
MAGE-TAB Version	1.1
Investigation Title	Differences between C9ORF72 iPS neuronal and Control and SOD1D90A iPS neuronal transcriptomes
Comment[Submitted Name]	Differences between C9ORF72 iPS neuronal and Control and SOD1D90A iPS neuronal transcriptomes
Experiment Description	The purpose of this experiment was to compare differences in the transcript levels between RNA samples from induced pluripotent stem cells differentiated into neurons carrying a mutation in the SOD1 gene, an expanded GGGGCC repeat mutation in the chromosome 9 open reading frame 72 gene and those without any (control).
Experimental Design	disease_state_design	in_vitro_design	co-expression_design
Comment[AEExperimentType]	transcription profiling by array
Comment[AEExperimentDisplayName]	Transcription profiling by array of neurons differentiated from induced pluripotent stem cells carrying a mutation in the SOD1 gene, an expanded GGGGCC repeat mutation in the chromosome 9 open reading frame 72 gene and those without any (control)
Experimental Factor Name	disease
Experimental Factor Type	disease
Quality Control Type	biological replicate
Quality Control Term Source REF	EFO
Public Release Date	2013-10-29
Person Last Name	Donnelly	Mistry
Person First Name	Christopher	Nipun
Person Mid Initials	J	A
Person Email	chrisdonnelly@jhmi.edu	nipunmistry@gmail.com
Person Phone	(410) 502-6476 |
Person Address	John G. Rangos Sr. Building, 855 N. Wolfe St., Rm 250.20, 2nd Floor,  Baltimore, MD 21205 USA
Person Affiliation	Johns Hopkins University School of Medicine, Department of Neurology & Brain Science Institute	Johns Hopkins University School of Medicine, Department of Neurology & Brain Science Institute
Person Roles	submitter	submitter
PubMed ID	24139042
Publication Author List	Donnelly CJ, Zhang PW, Pham JT, Heusler AR, Mistry NA, Vidensky S, Daley EL, Poth EM, Hoover B, Fines DM, Maragakis N, Tienari PJ, Petrucelli L, Traynor BJ, Wang J, Rigo F, Bennett CF, Blackshaw S, Sattler R, Rothstein JD
Publication Title	RNA Toxicity from the ALS/FTD C9ORF72 Expansion Is Mitigated by Antisense Intervention.
Publication Status	In Press at Neuron (expected online publication date 10-16-13)
Protocol Name	P-MTAB-35087	P-MTAB-35088	P-MTAB-35089
Protocol Type	growth protocol	nucleic acid extraction protocol	normalization data transformation protocol
Protocol Description	iPS cells were generated from healthy control and ALS patients and differentiated into neurons according to (Son, E.Y., Ichida, J.K., Wainger, B.J., Toma, J.S., Rafuse, V.F., Woolf, C.J., and Eggan, K. (2011). Conversion of mouse and human fibroblasts into functional spinal motor neurons. Cell stem cell 9, 205-218.)	Trizol extraction with column purification, using Qiagen Rneasy column and on-column Dnase treatment (Qiagen). 	Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
Protocol Term Source REF	EFO	EFO	EFO
Term Source Name	EFO	ArrayExpress
Term Source File	http://www.ebi.ac.uk/efo	http://www.ebi.ac.uk/arrayexpress
SDRF File	E-MTAB-1927.sdrf.txt