USDA via Stop Animal Exploitation Now A goat with a tumor on its neck, photographed by a USDA inspector at Santa Cruz Biotechnology.

One of the world's largest suppliers of antibodies for scientific research on Friday agreed to pay a record $3.5 million fine and stop selling its products to settle government allegations it abused goats and rabbits.

Santa Cruz Biotechnology, based in Dallas, resolved U.S. Department of Agriculture allegations dating to 2012 that its mistreatment of animals at a California facility violated the Animal Welfare Act. Government inspectors said they found sick and injured goats not receiving medical care, a goat that was shot in the head without euthanasia, and a barn full of hidden animals.

Santa Cruz neither admitted nor denied the USDA allegations. Still, the company agreed to surrender its license as a dealer of antibodies, and to end its registration as an animal research facility. The $3.5 million fine, due by May 31, is the largest ever under the Animal Welfare Act, according to the Humane Society of the United States.

Santa Cruz did not immediately respond to requests for comment.

"This is the most significant victory in the area of animal research for the animal rights movement, ever," said Michael A. Budkie of the nonprofit Stop Animal Exploitation Now. "I’m speechless."

The antibodies Santa Cruz extracted from the blood of its goats and rabbits were widely used in biomedical research labs across the globe. A 2012 survey by The Scientist found that more than half of labs using antibodies were working with specimens from Santa Cruz.

The company first came under fire in 2005, when it paid a $4,600 fines to the USDA to settle citations that included improper euthanasia and keeping more animals than it was authorized. Since 2012, the company has been hit with three additional complaints, most recently in 2015, when USDA charged it had "willfully violated" the Animal Welfare Act. Inspectors found “repeated failures to provide minimally adequate and expeditious veterinary care and treatment to animals,” according to the complaint.

USDA via Stop Animal Exploitation Now A goat with a wound on its hind leg, as photographed by a USDA inspector at Santa Cruz Biotechnology's California facility.

Goats referenced in the complaint had an array of ailments, including leg injuries, respiratory issues, dermatitis, anemia, weight loss and a rattlesnake bite. Some of the ailing goats went days before a veterinarian saw them, and some died during the wait. Rather than give dying goats euthanasia, the USDA said one goat was shot in the head and another was allowed to suffer for two weeks.

USDA officials discovered a secret barn during a 2012 inspection near the company’s facility in San Luis Obispo, where it was keeping more than 800 goats -- at least 12 of them sick -- out of view of regulators. USDA said "the existence of the site was denied even when directly asked."

The company's problems worsened in February -- two months before a scheduled hearing on the USDA allegations -- when Nature reported that government inspectors found that thousands of animals at the California facility had disappeared. It remains unclear what happened to them.

The disappearance of the animals sparked a boycott of Santa Cruz by scientists.

The massive USDA penalty "should serve as a loud and clear message to all research facilities, animal dealers, exhibitors and airlines regulated under this law," Cathy Liss, president of the Animal Welfare Institute, said in a statement.

People for the Ethical Treatment of Animals said in a statement it was "relieved" the USDA was putting Santa Cruz "out of the animal abuse business."