Dataset reporting Glycerol dialkyl glycerol tetraether (GDGT) lipid counts of 36 sediment samples from IODP Expedition 342 Sites U1405, U1406, U1407, U1409, and U1410 in the Northwest Atlantic (including five samples with three repeat measurements each). All samples were pre-processed and analysed at MARUM, Bremen on a Dionex Ultimate 3000RS ultra high performance liquid chromatography instrument coupled to a Bruker maXis ultra-high resolution quadrupole time-of-flight mass spectrometer, equipped with an APCI II ion source. The reported data includes sample ID, age (sample midpoints), the amount of total lipid extract injection and integrated peak areas of GDGT-0, GDGT-1, GDGT-2, GDGT-3, crenarchaeol and the crenarchaeol regioisomer.