Comment[GEAAccession]	E-GEAD-636
MAGE-TAB Version	1.1
Investigation Title	Mouse embryos of diabetic dams
Experiment Description	Pregestational diabetes increases the risk of congenital heart disease, including heterotaxy. To elucidate the underlying mechanism, mouse embryos of diabetic dams were analyzed. RNA sequencing of the embryos at embryonic day 8.0 was performed to identify the signals that affect the left-right axis related genes. Additionally, by using Wnt3a-null embryos, the regulation of Wnt signaling in embryos of diabetic dams was analyzed. This study is expected to deepen our understanding of the development of congenital abnormalities in maternal diabetes and lead to preemptive interventions.
Experimental Design	case control design	replicate design
Experimental Factor Name	disease	genotype
Experimental Factor Type	disease	genotype
Person Last Name	Meno	Matsuoka
Person First Name	Chikara	Ryohei
Person Affiliation	Department of Developmental Biology Graduate School of Medical Science, Kyushu University	
Person Roles	submitter	submitter
Public Release Date	2024-02-14
Protocol Name	P-GEAD-1937	P-GEAD-1938	P-GEAD-1939	P-GEAD-1940	P-GEAD-1941
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Streptozotocin-induced diabetic mice and Wnt3a mutant mice were subjected. Mouse embryos at embryonic day 8.0 were collected.	Total RNA was extracted from embryos with the use of a Monarch Total RNA Miniprep Kit (New England BioLabs).	RNA-seq was performed using the CEL-Seq2 protocol except that the Second Strand Synthesis Module (New England BioLabs) was used for double-stranded cDNA synthesis. Library was amplified by 10 cycles of PCR without any sample pooling.	Library was sequenced on Illumina NovaSeq6000. Quantitative analysis was conducted with 81bp of insert reads (Read2).	UMI and Cell barcode in Read1 were extracted by using UMI-tools. Adaptor sequences and low-quality sequences were eliminated, while read lengths below 20 bp were discarded by Trim Galore. Subsequently, reads were aligned to the GRCm38 reference genome using HISAT2. Read counts for each gene were acquired with featureCounts and UMI duplications were eliminated by UMI-tools.
SDRF File	E-GEAD-636.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB16464
Comment[Last Update Date]	2024-02-14