"transverse section of a cruciform church," 1530s, from Medieval Latin transeptum, from Latin trans "across, beyond" (see trans-) + saeptum "fence, partition, enclosure" (see septum). Rare before 1700. Related: Transeptal.
word-forming element meaning "across, beyond, through, on the other side of, to go beyond," from Latin trans (prep.) "across, over, beyond," perhaps originally present participle of a verb *trare-, meaning "to cross," from PIE *tra-, variant of root *tere- (2) "cross over, pass through, overcome." In chemical use indicating "a compound in which two characteristic groups are situated on opposite sides of an axis of a molecule" [Flood].
"wall separating two cavities," especially "the partition between the nostrils," 1690s, Modern Latin, from Latin saeptum "a fence, enclosure, partition," from neuter past participle of saepire "to hedge in," from saepes"a hedge, a fence," which de Vaan suggests is from a PIE *seh-i- "to tie." Related: Septal.
<a href="https://www.etymonline.com/word/transept">Etymology of transept by etymonline</a>
Harper, D. (n.d.). Etymology of transept. Online Etymology Dictionary. Retrieved $(datetime), from https://www.etymonline.com/word/transept