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The Alexander Thompson papers consist of the papers of three generations of Thompsons: Captain Alexander Thompson (1759-1809), Colonel Alexander Ramsey Thompson (1793-1837), and Reverend Alexander Ramsey Thompson (1822-1895). These papers document the military service of Captain Thompson in United States army (1793-1809); Colonel Thompson's military service (1819-1837); attempts by Colonel Thompson's widow Mary Thompson to secure a military pension (1838-1849); and the career of Reverend Thompson, a Union Army chaplain and Presbyterian minister, along with his family letters (1850-1932).

The Alexander Thompson papers (653 items) consist of the papers of three generations of Thompsons: Captain Alexander Thompson (1759-1809), Colonel Alexander Ramsey Thompson (1793-1837), and Reverend Alexander Ramsey Thompson (1822-1895). The collection is comprised of 494 letters and documents, 1 diary, 25 photographs, 103 religious writings and hymns, and 30 items of printed material. These papers document the military service of Captain Thompson in the United States Army (1793-1809); Colonel Thompson's military service (1819-1837); attempts by Colonel Thompson's widow, Mary Thompson, to secure a military pension (1838-1849); and the career of Reverend Thompson, Union Army chaplain and Presbyterian minister, along with his family letters (1850-1932).

The Correspondence and Documents series (494 items) is made up of three subseries, one for each Alexander Thompson represented in the collection.

The Captain Alexander Thompson subseries (255 items) consists of letters and documents related to Thompson's army career, including 37 military records (pay rolls, musters, and accounts) and 14 provisional returns. The bulk of the letters are to and from the war office in Philadelphia and from fellow army officers. These provide administrative documentation for the fledgling American military, as well as specific details on Thompson's assignments at Governor's Island, West Point, Fort Niagara, and Detroit. Topics covered include his efforts to provision and pay his troops, fortify his outposts, and recruit soldiers.

• April 19, May 7 and 24, and June 20, 1795: Letters from Thompson to New York Governor George Clinton, concerning the French navy and the fort at Governor's Island
• July 9, 15, and 18, 1795: Letters between Colonel Louis de Tousard and Thompson concerning prisoners, troops, and musicians at Governor's Island
• December 5, 1795: Letter fromThompson to Alexander Hamilton concerning a lawsuit involving Thompson's professional conduct at Governor's Island
• March 29, 1796: Letter to Thompson warning of a mutiny on Governor's Island
• September 14, 1800: Letter from Thompson to John Jacob Ulrich Rivardi concerning small pox at Detroit
• February 17, 1801: Letter from Thompson to Major Moses Porter, concerning filling the United States officer corps with Americans instead of foreign commanders
• January 20, 1803: May 1 and August 24, 1807: Letters and bills to and from Thompson and Secretary of War Henry Dearborn concerning payments for travel
• October 15, 1804: Instructions from Thompson to Doctor Frances La Barons concerning trading for pelts at Michilimackinac
• September 1807: News from a friend in St. Louis describing army activities there

The Colonel Alexander R. Thompson subseries (137 items) documents his post-War of 1812 military career, and his wife's efforts to secure a pension after his death. These include letters from fellow officers and friends, a few retained copies of Thompson's letters, and 55 letters to and from Mary Thompson and various prominent government officials concerning military pensions. In many of Mary's letters she described episodes in her husband's military career, including wounds and sicknesses suffered while on duty.

• November 27, 1816: Captain Kearny at Sackets Harbor to Thompson concerning securing pay to Mrs. Niblock for washing clothes for the army
• January 12, 1817: Major W.J. Worth at Sackets Harbor to Thompson describing a celebration at the newly build Madison Barracks
• May 13, 1833: George Brooke at Fort Howard (Green Bay) to Thompson describing his journey across Lake Huron
• August 28, 1833: Benjamin F. Larneal to Thompson concerning shipping a piano to Michigan
• April 28, 1836: Thompson to his nephew Alexander Thompson, describing the encampment and fortifications at Camp Sabine, Louisiana, and the lawless state of Texas - "the country is consequently infested with robbers and pirates
• February 21, 1837: Mary Thompson to General Winfield Scott seeking a promotion for her sick husband
• March 6, 1840: Mary to her brother-in-law William Thompson, relating her difficulties securing a pension
• 1842-1845: Letters to and from Mary Thompson to New York Governor Hamilton Fish and members of the Senate and the House of Representatives, including John Jordan Crittenden and Thomas Hart Benton
• October 8, 1847: E. Backay at San Juan to Mary Thompson containing a description of the Mexican-American War
• March 13, 1853: Department of the Interior to Mary Thompson concerning her request for a land bounty

The Reverend Alexander R. Thompson subseries (102 items) contains Thompson's letters and 25 of his children's letters. Of note are the items documenting his Civil War service as chaplain of the 17th Regiment of Connecticut Volunteers and at the Roosevelt Hospital. These include many letters from solders and former parishioners serving throughout the country. Also present are letters discussing Thompson and his family's travels around New York and New England, and to the Canary Islands, Quebec, and San Francisco. The post-1872 letters largely concern Thompson's children.

• November 28, 1861: Albion Brooks to Thompson describing the soldier's Thanksgiving dinner at Burnside Camp, Annapolis, Maryland
• January 16, 1862: Leonard Woolsey Bacon to Thompson concerning chaplains' aids
• July 2, 1863: A small diagram of the Union fleet on the Mississippi River in front of Vicksburg
• June 4, 1864: Moses Smith of the 8th Connecticut Regiment to Thompson describing the battle at Cold Harbor
• September 25, 1865: E.A. Russell to Thompson describing hearing Julia Ward Howe's "Battle Hymn of the Republic" on board a steam ship: "I feel like after hearing it sung like one inspired for the work. I do think it is very near Gods work."
• September 27, 1865: Five verses of the "Battle Hymn of the Republic" copied on board the Steamship United States
• September 23, 1871: Gin Bon, secretary of the Chinese Young Men's Christian Society of San Francisco, to Thompson concerning his support of the group and enclosing four photographs of members

The Diary series (1 item, 372 pages) is the personal journal of Reverend Alexander Ramsey Thompson for 1861. The diary is deeply personal and includes Thompson's thoughts on personal, spiritual, and political matters, as well as his thoughts on the outbreak of the Civil War and his decision to join the army as a chaplain. In the back of the diary are 5 newspaper clippings concerning New York University commencements.

• April 13 and 16, 1861: Thoughts on the siege and bombardment at Fort Sumter
• July 22 and 24, 1861: Thoughts on First Bull Run
• August 31, 1861: Discussion of seeing a hippopotamus at Barnum's Museum

The Photographs series (25 items) contains undated family pictures, images of houses and landscapes, and commercial photographs of buildings in Europe.

Four additional photographs are located with the letter of September 23, 1871. These are portraits of Chinese Americans, one taken by Chinese photographer Lai Yong of San Francisco, and one of letter writer Gin Bon, secretary of the Chinese Young Men's Christian Society. Gin Bon's portrait contains watercolored highlights. The hymn book for the Roosevelt Hospital in the Printed Materials series contains family photographs, including a group picture in which many of the sitters are holding tennis rackets.

The Religious Writings series is composed of two subseries: Sermons and Ecclesiastical History Notes, and Hymns. Though largely undated and unattributed, these writings were all likely created by Reverend Thompson. The Sermons and Ecclesiastical History notes subseries (61 items) contains 58 sermon notes that Thompson wrote in the 1890s, much of which was written on Roosevelt Hospital stationery. Some of these are outlines while others are fully formed sermons. He also wrote notes on ecclesiastical history in two notebooks dated 1881 (232 pages), and on the Hebrew language in an undated notebook (58 pages). The Hymns subseries (42 items) contains 9 manuscript hymns, 16 printed hymns, and 17 volumes of manuscript hymns. They consist of transcribed and translated hymns, Bible quotations, and ballad lyrics. Two of the printed hymns, both Christmas carols, include music for four voices.

The Printed Material series (30 items) is comprised of 18 newspaper clippings and 12 miscellaneous printed items. The newspaper clippings are an essay by Reverend Thompson entitled "The Burial of Moses," and an address from Thompson delivered at the unveiling of a Gettysburg monument for the 17th Connecticut Volunteers. The Miscellaneous Printed Items subseries contains 12 items, including ephemera related to New York University commencements; an engraving of author, nurse, and charity organizer Isabella Graham; an annual report for the Brooklyn Nursery (1888); and a Roosevelt Hospital hymnal in which someone has inserted photograph clippings of Reverend Thompson, his wife, and others.

The Eaton-Shirley family papers consist of personal diaries, correspondence, military papers, legal and business documents, printed materials, and photographs. A primary figure in the collection, John Eaton, Jr., was Civil War Superintendent of the Freedmen and later Commissioner of Education under Grant. The papers also contains substantial material from other Eaton family members, including military papers and correspondence of his brother, Lucien B. Eaton, and papers of the Shirley family (the family of John Eaton, Jr.’s wife, Alice E. Shirley).

The Eaton papers consist of 1,903 items, dating from September 1790 to July 30, 1939. The bulk of the collection falls between 1850 and 1906. The papers contain 318 letters, 9 diaries/journals, 60 personal documents of John Eaton Jr., 275 legal documents and business papers, 112 military documents, 923 photographs, 84 printed items, and 122 miscellaneous items.

The majority of the correspondence is personal and relates to family matters. The 168 letters of John Eaton, Jr., contain extensive biographical information. Of particular interest are 44 Civil War-era letters including information about the freedmen, three letters pertaining to the publication of The Post, and two with content regarding the Ku Klux Klan. The collection also contains 22 letters to and from Alice (Shirley) Eaton, 31 letters to and from Lucien Eaton, and 32 miscellaneous letters from members of the Eaton family. Of the 30 letters written by Alice Eaton's parents (James and Adelaine Shirley), 10 letters regard compensation for the damage done to the Shirley House during the Civil War. Various other members of the Shirley family wrote 15 letters, and 20 letters are from other people unrelated to the Eaton and Shirley families.

John Eaton Jr.’s aunt, Ruth Dodge Eaton, wrote two diaries which consist almost entirely of Christian hymns and essays. John Eaton Jr.'s uncle, Horace Eaton, wrote one diary that contains Christian material written while he attended Dartmouth College. John Eaton, Jr., wrote two diaries, one of which he wrote as a youth, and the other as a student at Dartmouth. Other journals include two by John Eaton Jr.'s brothers, Frederick and Charles, and a household account book, kept by his sister Christina. Of particular importance is Alice Shirley’s diary, in which she described pre-civil war tensions between the north and the south, speculation on the upcoming Siege of Vicksburg, the early stages of the Siege of Vicksburg, and very personal feelings regarding her marriage to John Eaton, Jr.

The 60 personal papers of John Eaton Jr. include 17 documents regarding his appointments and titles, two documents about freedmen, and 41 miscellaneous address cards and invitations (including an invitation to the opening of the Brooklyn Bridge).

Of the 275 legal papers, 74 documents pertain to the sale of land in Mississippi; 7 concern Robert M. Jones’s claim to Choctaw Nation lands; and 25 relate to estate papers, deeds of trust and documents about the proceedings of Adelaine Shirley’s post-war relief claims; and a receipt for the sale of an African American woman. The remaining 176 legal papers are miscellaneous financial documents, such as tax documents, checks, and receipts.

Of the 112 military documents, 58 pertain to John Eaton, Jr., 7 of which are about freedmen. The military documents of Lucien B. Eaton number 54.

The 923 photographs consist of six photo albums, 31 cased daguerreotypes and ambrotypes, 144 cabinet cards, and 421 loose photographs and snapshots all depicting members of the Eaton and Shirley families, scenic locations, and the Shirley House.

Of the 84 printed items in the collection, 49 newspaper clippings pertain to the occupational and personal activities of John Eaton, Jr., and 9 miscellaneous clippings relate to the Eaton family. The remaining 26 items are published pamphlets, including addresses and reports concerning John Eaton, Jr.; a sermon written by Horace Eaton; a report of proceedings of an Ohio Brigade reunion; an Anti-Slavery Almanac from 1838; and an incomplete piece describing the history and restoration of the Shirley House.

The 122 miscellaneous papers of the John Eaton, Jr., collection consist of 53 recipes and 69 miscellaneous items including a partial autobiography of Alice Eaton.