More than 500 Yale men served the Confederacy in some capacity (Yale's Confederates - Nathaniel Hughes). Graduate Judah Benjamin was the Confederacy's Secretary of State and Secretary of War. Samuel Morse was a prominent public opponent of Lincoln and Emancipation. Senator John Calhoun was a prominent advocate for the Fugitive Slave Law and opponent of abolition. Eli Whitney invented the cotton gin which set the stage for industrial scale cotton production and slavery in America. It is remarkable to read Whitney's letters concerning the invention and his schemes for plantations in the South and encounter the utter disregard for slave labor he was enabling and personally exploiting.
Princeton University had a very strong to connection with the South. According to the Princeton Alumni Weekly over 200 Princeton alumni enlisted in the Confederate service, including at least seven brigadier generals. John C. Breckinridge, US Vice President and Confederate general, attended Princeton (1838-39) for graduate study. "U.S. Supreme Court justice James Wayne 1808 concurred in the Dred Scott decision that claimed black Americans had 'no rights which the white man was bound to respect.'” Twenty-two ante-bellum US Senators were educated at Princeton, including Alfred Iverson who "gave ferocious speeches threatening secession." Rev. George Armstrong 1832 wrote The Christian Doctrine of Slavery in 1857, arguing that slaves enjoyed better protections against capitalist exploitation by the rich than did poor whites in the North. http://paw.princeton.edu/issues/2011/03/23/pages/4092/index.xml
Richard Sears McCulloh, scion of an old Scots Protestant Maryland family, graduate of Princeton and Columbia University professor of chemistry was possibly the New York City draft riots principal arsonist. He turned up in Richmond after the riots, offering to make weapons of mass destruction for the Confederacy. He eventually weaponized poison gas, but not in time for it to be used in the war.
Columbia University's most famous Confederate was John Slidell, a New Yorker who transplanted to Louisiana and became a US Senator. Slidell became involved with the Trent Affair after being appointed Confederate emissary to France when he was captured by the Union while transiting the Atlantic aboard British steamer RMS Trent. August Belmont, leader of the North's "loyal" Democrats and American agent for the Rothschilds, became Slidell's protégé after he married Slidell's niece.
The notorious Bradish Johnson also should be numbered among Columbia's Confederates. Johnson was the business partner of Moses Lazarus, father of poet Emma Lazarus. Johnson & Lazarus owned sugar refining and distilling operations in New York City and dairies that used the distillery byproducts to feed the cows. The Johnson & Lazarus "swill" milk that allegedly killed thousands of New York children became the subject of Frank Leslie's famous muckraking expose. The sugar for the distilleries came from plantations Johnson owned in Louisiana. During the Civil War Johnson had the audacity to petition Lincoln to readmit Louisiana as a slave state, and sued the Union army for "plundering" his plantations.
Like Columbia, Brown is less forthcoming about its Confederate army sons, but Brown has done a remarkable job exposing its and Rhode Island's deep and profitable involvement with the slave trade.
http://www.brown.edu/Research/Slavery_Justice/report/
Arguably, The University of Pennsylvania's most prominent Confederate was James Murray Mason (1818), Confederate envoy to Britain, who was caught up in The Trent affair with Slidell. However, alumnus General John C. Pemberton, CSA, surrendered his army to Grant at Vicksburg, Miss., July 4, 1863. Teddy Roosevelt's uncle Irvine Bulloch left Penn to serve on the Confederate raider Alabama, which his brother James, the Confederacy's agent in England, had procured to wage war on the high seas against the Union.
https://ia600307.us.archive.org/21/items/universityofpenn01jord/universityofpenn01jord.pdf
Arguably, The University of Pennsylvania's most prominent Confederate was James Murray Mason (1818), Confederate envoy to Britain, who was caught up in The Trent affair with Slidell. However, alumnus General John C. Pemberton, CSA, surrendered his army to Grant at Vicksburg, Miss., July 4, 1863. Teddy Roosevelt's uncle Irvine Bulloch left Penn to serve on the Confederate raider Alabama, which his brother James, the Confederacy's agent in England, had procured to wage war on the high seas against the Union.
https://ia600307.us.archive.org/21/items/universityofpenn01jord/universityofpenn01jord.pdf