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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.

The Gray family papers document the family relationships of William and Eckley Gray, while serving in the Union Army, and Lucy Doan Gray, William's wife and Eckley's mother, as she managed the family farm in New Salem, Illinois.

The papers of William and Eckley Gray present an unusual view of side-by-side service of a father and son during the Civil War. As a junior officer and enlisted man, respectively, the Grays present strikingly different personalities, the stable and directed father paired with his unstable and seemingly rudderless son. Information on military aspects of the war is relatively scarce in the Gray papers. However, the collection provides excellent insight into the effect of the war on family relationships, hinting obliquely at some of the long term effects that the war had on some of its participants.

In a sense, the heart of the collection is the letters written by Lucy Gray. More than anything, the anguished tone of her letters stands out, as she pleads with the men to return home and assist the family and farm, or as she complains about the Eckley's profligacy, drinking and gambling. The tension between mother and son, and his occasional, half-hearted efforts to patch things between them take on a particularly tragic tone given the apparent aimlessness of his later life and his death by drug abuse.

Among the more interesting individual letters in the collection are three letters from Eckley to his mother, one describing a night-time bombardment at Vicksburg (1863 July 9), another discussing the anti-Lincoln attitudes of the soldiers of the Veterans Reserve Corps (1864 October 10), and an extraordinary letter (July 19, 1864), bemoaning Lincoln's latest call for troops and his apparent inhumanity.

The Gray Family Papers include a manuscript receipt book dating circa 1840s-1860s, which belonged to William Gray. The recipes are largely medicinal, including entries for treatment of influenza, Dr. Thomas Hopes remedy for cholera morbus, a powder of mandrake, plaster for a lame back, Beeches Black salve, saline laxative, Beeches emetic, anti-billious powder, lotion for "Falling of the hair & Impetigo," a treatment that "cured Mr Gess's boy of Epilepsy of five years Standing The boy is 9 years old," mild counter-irritating linaments, ipicac, lotion for "falling of The hair and all scaly Eruptions," paste for piles, Dr. White's Toothache Drops, diaphoretic powder, a treatment "for Secondary Syphilis," and a treatment for cholera. Opium is an ingredient in multiple recipes. Non-medical recipes include an entry for making gunpowder from sawdust and several short recipes for corn bread and tea bread.