Among the smaller but still important casualties of Hurricane Sandy were thousands of laboratory rodents, genetically altered for use in the study of heart disease, cancer and mental disorders like autism and schizophrenia, that drowned in basement rooms at a New York University research center in Kips Bay.

The collection of carefully-bred rodents was considered one of the largest and most valuable of its kind in the country. The animals lived in colonies in the cellar of the Smilow Research Center, on 1st Avenue near 30th Street.

New York University medical and research staff worked furiously to protect their human patients — and others threatened by the storm — in all three of its facilities in Kips Bay. Though most of the animals at the center were unharmed, the center staff could not rescue the animals in one of the facilities, despite hours of work amid the flooding that started at the institute on Monday night.

"The combined tide and wind resulted in extensive flooding in the building, and unfortunately, my mouse colonies were wiped out," said Gordon J. Fishell, associate director of the N.Y.U. Neuroscience Institute. "These animals were the culmination of 10 years of work, and it will take time to replace them."

N.Y.U. officials said that, storm warnings notwithstanding, there was every reason to expect the Smilow building to be protected; the building was designed to withstand surges 20 percent higher than had historically occurred.

Dr. Fishell said that his lab alone lost about 2,500 mice. Other programs at the Smilow center, including research into cancer, cardiovascular disease and epigenetics, lost a combined 7,500 more animals, both mice and rats, according to faculty estimates. The animals were an important resource, but research in all of these areas is broadly based and will continue, university officials said.

"It's an absolute tragedy any way you look at it," Dr. Fishell said.

The colonies are bred to carry some of the same genetic glitches thought to contribute to disorders in humans like high blood pressure, cancer or epilepsy. The Fishell lab has been studying the effect of specific genetic mutations on neurons that inhibit runaway electrical activity in the brain. Such neural overheating is associated with seizures, among other mental symptoms. The mouse lines included about 40 genetic variants.

Medical centers typically have veterinarians on hand, as well as other lab staff, to feed and care for research animals. "That facility is top-notch, one of the leading centers in the country, so the loss is just terrible," said Dr. Yariv Houvras, a cancer researcher at NewYork-Presbyterian/Weill Cornell Medical Center.

The loss is the second major blow to basic research in developmental disorders in just the past several months. In June, a freezer failure at the Harvard Brain Bank in Belmont, Mass., ruined 150 brain specimens, many of them from people with autism who died young.

Lines of genetically altered animals, like brain banks, are painstakingly built up over time. But the mouse colonies can be restored, researchers said; many of the rodents lost in the storm have genetic relatives living elsewhere, and those animals could be used to begin the process.

Already scientists at two research centers, the University of Pennsylvania and Cold Spring Harbor Laboratory on Long Island, have pledged to donate animals to restart some of the Smilow center's colonies. "That's the one really positive thing to come out of this," Dr. Fishell said. "Individuals in the research community, who in most businesses would be considered my competitors, have been eager to help."