Comment[ArrayExpressAccession]	E-GEOD-52827
MAGE-TAB Version	1.1													
Public Release Date	2015-06-17
Investigation Title	Bcl11a (Ctip1) controls migration of cortical projection neurons through regulation of Sema3c													
Comment[Submitted Name]	Bcl11a (Ctip1) controls migration of cortical projection neurons through regulation of Sema3c
Experiment Description	During neocortical development, neurons undergo polarization, oriented migration, and layer type-specific differentiation. The transcriptional programs underlying these processes are not completely understood. Here we show that the transcription factor Bcl11a regulates polarity and migration of upper layer neurons. Bcl11a-deficient late-born neurons fail to correctly switch from multipolar to bipolar morphology resulting in impaired radial migration. We show that the expression of Sema3c is increased in migrating Bcl11a-deficient neurons and that Bcl11a is a direct negative regulator of Sema3c transcription. In vivo gain-of-function and rescue experiments demonstrate that Sema3c is a major downstream effector of Bcl11a required for the cell polarity switch and for the migration of upper layer neurons. Our data uncover a novel Bcl11a/Sema3c-dependent regulatory pathway used by migrating cortical neurons. Neocortex tissue from three control (Bcl11a+/+) and three Bcl11a mutants (Bcl11aΔflox/Δflox) embryos was collected at E14.5. Total RNA was isolated from each sample separately using the RNeasy kit (Qiagen). The isolated ENA was inspected for integrity and purity using an Agilent Bioanalyzer and a NanoDrop spectrophotometer, respectively. Microarray analyses were performed using 200 ng total RNA as starting material and 5.5 µg ssDNA per hybridization in a GeneChip Fluidics Station 450 (Affymetrix). The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix). Labeled ssDNA was hybridized to Mouse Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix). The chips were scanned with a GeneChip Scanner 3000 (Affymetrix) and subsequent images analyzed using Affymetrix Expression Console Software (Affymetrix). A transcriptome analysis was performed using BRB-ArrayTools developed by Dr. Richard Simon and BRB-ArrayTools Development Team (http://linus.nci.nih.gov/BRB-ArrayTools.html).													
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl												
Person Last Name	Holzmann	Wiegreffe	Peschkes	Simon	Strehle	Cheng	Srivatsa	Liu	Jenkins	Copeland	Tarabykin	Britsch	Holzmann	Kling
Person First Name	Karlheinz	Christoph	Katharina	Ruth	Michael	Jin	Swathi	Pentao	Nancy	Neal	Victor	Stefan	Karlheinz	Carolin
Person Mid Initials									A	G				
Person Email	karlheinz.holzmann@uni-ulm.de													
Person Affiliation	Ulm University													
Person Address	Medical Faculty, Ulm University, Helmholtzstreet 8/1, Ulm, Germany													
Person Roles	submitter													
Protocol Name	P-GSE52827-1	P-GSE52827-5	P-GSE52827-6	P-GSE52827-2	P-GSE52827-3	P-GSE52827-4	P-GSE52827-7							
Protocol Description	Affymetrix® Expression Console™ Software for RMA normalization, BRB Array Tools for statistical analysis ID_REF =  VALUE = RMA normalized,  log2	Whole Transcript (WT) Sense Target Labeling Assay	according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay	Tissue was dissected in ice-cold phosphate buffer (pH7.2).	Fresh frozen dissected tissue was kept at -80°C until use.	Extraction of total RNA was performed with the Rneasy kit according to the manufacturer's instructions (Qiagen).	according to Affymetrix protocols using a GeneChip 3000 Scanner							
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol							
Experimental Factor Name	genotype													
Experimental Factor Type	genotype													
Comment[SecondaryAccession]	GSE52827													
Comment[GEOReleaseDate]	2015-06-17													
Comment[ArrayExpressSubmissionDate]	2013-11-29													
Comment[GEOLastUpdateDate]	2015-06-17													
Comment[AEExperimentType]	transcription profiling by array													
SDRF File	E-GEOD-52827.sdrf.txt