Comment[GEAAccession]	E-GEAD-530
MAGE-TAB Version	1.1
Investigation Title	A comprehensive analysis of 124 transcriptomes from 31 tissues in developing, juvenile, and adult Japanese Black cattle
Experiment Description	Omics analyses of economically important animals, including Japanese Black cattle, are underway worldwide. Particularly, tissue and developmental stage-specific transcriptome characterization is essential for understanding the molecular mechanisms underlying phenotypic expression of genetic disorders and economical traits. Here, we conducted a comprehensive analysis of 124 transcriptomes across 31 major tissues from fetus, juvenile calf, and adult cattle using short-read sequencing. We found that genes showing high tissue-specific expression tended to gradually increase with development after 60 days of fertilization and significantly reflected the tissue-relevant biology. Based on the variation and inflection points of gene expression during development, we categorized gene expression pattern into stable, increased, decreased, temporary, or complex in each tissue. We also analyzed the expression profiles of causative genes (e.g., SLC12A1, ANXA10, MYH6) for genetic disorders in cattle, revealing disease-relevant expression patterns. Additionally, to directly analyze the structure of full-length transcripts without transcript reconstruction, we performed RNAseq analysis with 22 tissues using long-read sequencing and identified 232 novel non-RefSeq isoforms. Collectively, our comprehensive transcriptomic analysis can serve as an important resource for biological and functional interpretation of gene expression and will enable a mechanistic interpretation of genetic disorders and economical traits in Japanese Black cattle.
Experimental Design	development or differentiation design	organism part comparison design	all pairs
Experimental Factor Name	tissue
Experimental Factor Type	tissue
Person Last Name	Suzuki	wakaguri	Sasaki	Sequence
Person First Name	Yutaka	Hiroyuki	Shinji	Kashiwa
Person Affiliation	Suzuki Lab  Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences, The University of Tokyo			
Person Roles	submitter	submitter	submitter	submitter
Public Release Date	2026-08-09
Protocol Name	P-GEAD-1368	P-GEAD-1369	P-GEAD-1370	P-GEAD-1371	P-GEAD-1372
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	We collected 124 samples from seven Japanese Black cattle for RNA-seq analysis. Samples were collected in 50 mL conical tubes (Iwaki, Shizuoka, JPN, Cat. 2345-050), flash-frozen in liquid nitrogen, and stored at -80 degree Celsius until RNA extraction.	We extracted the total RNA using TRIzol (Thermo Fisher Scientific, Waltham, MA, USA, Cat. #10296010).	The extracted RNA was converted to cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara, Shiga, JPN, Cat. # Z4888N).	cDNA was sequenced using Hiseq3000 (Illumina, San Diego, CA, USA) and MinION (Oxford Nanopore Technologies, Oxford, UK), according to the manufacturer's instructions.	We determined the gene expression levels (transcripts per million [TPM] ) using StringeTie or RSEM to account for differences in sequence depth and gene length across samples.
SDRF File	E-GEAD-530.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB13733
Comment[Last Update Date]	2026-08-09