Comment[ArrayExpressAccession]	E-MEXP-3921
Investigation Title	Photoreceptor precursors derived from 3D cultures of embryonic stem cells mature and integrate in degenerate retina
Comment[Submitted Name]	Photoreceptor precursors derived from 3D cultures of embryonic stem cells mature and integrate in degenerate retina
Comment[AEExperimentDisplayName]	Transcription profiling by array of photoreceptor precursors derived from 3D cultures of embryonic stem cells mature and integrated in degenerate retina
Comment[MIAMExpressLogin]	mhubank
Comment[MIAMExpressSubmissionID]	8792
Experiment Description	To isolate photoreceptor precursors fit for transplantation, we adapted a 3D differentiation protocol that generates neuroretina from mouse ES cells. We used an adeno-associated viral vector (pseudotype2/9)carrying a GFP reporter under the control of a Rhodopsin promoter (AAV2/9.Rhop.GFP)to select rod precursors. AAV2/9.Rhop.GFP+ rods were sorted at days 26 and 34 and post natal day P12.
Experimental Design	in_vitro_design	co-expression_design	cell type comparison design
Comment[AEExperimentType]	transcription profiling by array
Experimental Factor Name	cell type	developmental stage
Experimental Factor Type	cell type	developmental stage
Person Last Name	hubank
Person First Name	mike
Person Mid Initials	j
Person Email	m.hubank@ich.ucl.ac.uk
Person Phone	2079052266
Person Affiliation	Institute of Child Health
Person Address	ICH Gene Microarray Centre, 30, Guilford St, London, London, WC1N1EH, United Kingdom
Person Roles	submitter
Person Roles Term Source REF	EFO
Quality Control Type
Public Release Date	2013-07-17
Comment[ArrayExpressSubmissionDate]	2013-06-07 11:37:47
Publication Title	Photoreceptor precursors derived from three-dimensional embryonic stem cell cultures integrate and mature within adult degenerate retina.
Publication Author List	Gonzalez-Cordero A, West EL, Pearson RA, Duran Y, Carvalho LS, Chu CJ, Naeem A, Blackford SJ, Georgiadis A, Lakowski J, Hubank M, Smith AJ, Bainbridge JW, Sowden JC, Ali RR.
Publication Status	submitted
Protocol Name	P-MTAB-33229	P-MTAB-33240
Protocol Description	MirVana miRNA isolation Kit Ambion (Parameters: Extracted product = total_RNA, Amplification = none)	3x10^4 dissociated ES cells (mouse EK CCE ES cell line) were resuspended per millilitre of differentiation medium (GMEM containing 1.5% KSR, 0.1mM NEAA, 1mM pyruvate, 0.1mM 2-mercaptoethanol), plated into 96 well low-binding (Corning) plates and incubated at 37oC, 5% CO2. Embryoid body cell aggregates (EBs) formed within 24 hrs. On day 1 of culture, growth factor reduced Matrigel (BD Bioscience) was added to each well to give a final concentration of 2%. For whole EB retinal differentiation, EBs were transferred into retinal maturation medium (DMEM/F12 Glutamax containing N2 supplement and Pen/strep) at day 9, plated in low-binding plates at a density of 6 EBs/cm2 and incubated at 37oC, 5% CO2. The media was changed every 2-3 days, with the addition of 1mM Taurine (Sigma) and 500nM retinoic acid (Sigma) from day 14 of culture onwards. For further retinal differentiation EBs were transferred to fresh low-binding plates at day 27 of culture, at a density of 3 EBs/cm2, with 50% media changes every 2-3 days.
Protocol Type	nucleic acid extraction protocol	growth protocol
Protocol Term Source REF	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-MEXP-3921.sdrf.txt
PubMed ID	23873086
Publication DOI	10.1038/nbt.2643