Comment[GEAAccession]	E-GEAD-339
MAGE-TAB Version	1.1
Investigation Title	The effect of Reelin haplo-insufficiency on mechanism underlying learning-induced motor cortical plasticity
Experiment Description	Our molecular results that training induced upregulation of neuroplasticity-related molecules with concurrent elevation of Reelin expression prompted us to determine if there is any Reelin-mediated molecular regulation associated with cortical plasticity. To this end, we performed RNA sequence analysis on the total RNA collected from sensorimotor cortex of WT mice, heterozygous reeler mutants, and WT mice that undergone training, and heterozygous reeler mutants that undergone training.
Experimental Design	observational design	strain or line design	genotyping design	validation by real time PCR design
Experimental Factor Name	genotype	growth_condition
Experimental Factor Type	genotype	growth_condition
Person Last Name	Nishibe
Person First Name	Mariko
Person Affiliation	Graduate School of Dentistry, Osaka University
Person Roles	submitter
Public Release Date	2021-06-16
Protocol Name	P-GEAD-342	P-GEAD-343	P-GEAD-344	P-GEAD-345	P-GEAD-346	P-GEAD-347
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol	growth protocol
Protocol Description	Sensorimotor cortical sample was collected from WT mice, heterozygous reeler mutants, and WT mice that undergone training, and heterozygous reeler mutants that undergone training.	Total RNA of the sensorimotor cortex samples was isolated using Trizol reagent. Each cDNA was generated using the High Capacity cDNA Reverse Transcription Kit.	Each library was prepared using a Nextera XT DNA Library Prep Kit. DNA was simultaneously fragmented and tagged with sequencing adapters in a single tube enzymatic reaction.	Whole transcriptome sequencing was applied to the RNA samples with use of on an Illumina HiSeq 2500 platform in a 75-base single-end mode. Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat ver. 2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 1.0.	The number of fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm ver. 2.2.1.	Mice were trained to retrieve a singly-presented food pellet using reach and grasp movements for 10 days (20 pellets per training per day) using the left forelimb. Mice in the control group ate the pellets made available on the floor of the reaching box.
SDRF File	E-GEAD-339.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB9228
Comment[Last Update Date]	2021-06-16