The Middlesex was built at Sunderland in 1839. 
Convicts transported to New South Wales on the Middlesex were convicted in counties throughout Ireland - Queen's Co., Dublin, Cork, Armagh, Antrim, Monaghan, Waterford, Westmeath, Tyrone, Longford, Waterford, Londonderry, Galway, Roscommon, King's Co., Co. Down, Donegal, Cavan, Louth, Kerry, Kildare, Wicklow, Fermanagh, Mayo, Sligo and Wexford. One man was convicted of desertion in Mauritius.
Many had been convicted of various forms of stealing and robbery; others of more serious crimes of manslaughter, forgery, rape, malicious assault, aggravated assault, murder, arson and perjury (John Fleming from Bathurst NSW). Several had been convicted of white-boy crimes including
Four were court-martialled in Ireland for desertion:
Michael Burns from Wicklow. Court-martialled in Dublin for desertion
David Clarke from Edinburgh. Court-martialled in Cork for desertion
James Smith from York. Court-martialled in Dublin for desertion
Michael Thomas from Co. Kerry court-martialled in Cork 5 April 1839.
According to the Commercial Journal another was court-martialled in Mauritius for desertion . His name is not included in the printed convict indents.
The Military Guard was commanded by Lieutenant Murray of the 50th regiment, Ensign Scott of 51st regiment; 1 serjeant and 27 rank and file of the 51st regiment with their wives (6) and 9 children. 
Cabin passengers included Mr. J.G. Symonds and Mr. R. Uniacke, clerk to the Commissariat Department
The Middlesex departed Dublin 6 July 1839.
SURGEON JOHN BAIRD
John Baird kept a Medical Journal from 1st June 1839 to 1st February 1840. Two hundred prisoners + 1 man from Mauritius came under his care. Several convicts fell victim to dysentery. The only instance of scurvy was in that of a man who was suffering from mental illness and refused to eat fresh provisions when they were available, imagining that any change from the general diet of the convicts was from some design against his life. 
Those treated by the surgeon during the voyage included:
John Geraghty, age 22, convict;
George Beedell, age 22, private guard;
John Kelly, age 17, convict;
John Murphy, age 40, convict;
Michael Dowling, age 20, convict;
Jeremiah Crowley, age 20, convict;
William Johnstone, age 15, convict;
Patrick Tully, age 19, convict;
James Smith, age 20, convict;
Patrick Crelly, age 18, convict;
Charles Kearnes, age 39, convict;
Joseph K O'Brien, age 23, convict;
William Cornwall, age 21, convict;
Michael Delaney, age 17, convict, died 9 August 1839 at 8 am.
Laurence Flanagan, age 28, convict; died 28 October 1839 at 8.30 pm.
Thomas McCabe, age 21, convict; died 30 October 1839 at 0.30 am
John Kearney, age 32, convict; died 16 December 1839 at 5 pm.
Patrick Loughran, age 28, convict; died 20 December 1839 at 9 pm.
Timothy Costillo, age 37, convict; died 16 January 1840 at 8.30 pm.
Henry Mullen, age 26, convict; taken ill at sea; died 4 January 1840 at 8 pm.
Patrick Buckley, age 21, convict; taken ill at sea; died 3 January 1840 at 5 am. 
In the early part of the voyage the Middlesex encountered heavy gales during which she lost her fore and main topmasts and one man (an apprentice) was lost overboard. They were obliged to put into Port Louis, Mauritius for provision and water on 25th November and departed there on 14th December 1839. They were so long delayed that there were rumours that the ship had been lost at sea.
The Sydney Herald reported the arrival.....The Middlesex arrived from Dublin on Saturday 25th January 1840, with one hundred and ninety-four convicts, under the superintendent of Dr. Baird. R.N. This vessel made the longest passage that has been made by any vessel lately, having sailed so long ago as the 6th July, six months and a half since. 
NOTES AND LINKS
1). Hunter Valley convicts and passengers arriving on the Middlesex in 1840
2). Convict ships bringing detachments of the 51st regiment included the Neptune, Waterloo, William Jardine, Bengal Merchant, Lord Lyndoch, Westmoreland, Clyde, Earl Grey, Portsea, Elphinstone, John Barry, Blenheim, Waverley and the Middlesex.
3). County Cork Asizes - Charge of Murder
Andrew, Edward and Timothy Barrett, Timothy (John) Crowley, and Timothy (Jerry) Crowley, and Thomas and John Flynn, were given in charge for having on the 22nd July last at Clounbogue near Kilbritain, wilfully and feloniously struck Cornelius Collins on the head ith stones and hurlies, thereby causing two mortal wounds of which he died on the 30th of the same month. All the prisoners with the exception of Andrew Barret, were at half past two oclock found guilty of manslaughter. Sentence deferred. - Freemans Jounral 22 March 1839. p. 1
4). The case of John Fleming is an interesting one as the indent states that he was a native of Bathurst, New South Wales and 19 years of age. In the article below he was stated to be a deserter from the 97th regt., He was convicted of perjury in Queen's County, Ireland in March 1839 ......
Queen's County Assizes - Murder of Lord Norbury - Charge of Perjury - Maryborough -
An Englishman, named John Fleming, who had been a deserter from the 97th Regiment, was placed at the bar, and arraigned for wilful and corrupt perjury.
The clerk of the crown read the indictment, which set forth that whereas the late Lord Norbury had been murdered at a certain time and place, by some persons unknown, the prisoner had afterwards gone before a Magistate of the county named Matthew Cassan, and swore to a variety of circumstances said to be connected with that murder, and that amongst other things he charged a person named Abraham Walton with the commissio of that crime. The indictment also set forth that all the material allegations in his informations were false, and that he swore to the truth of them, knowning them to be false, at the time of his so swearing. He was asked was he guilty, and he replied that he was.
Chief Justice Doherty - Are you aware of the nature of the charge against you?
Prisoner - I am
Chief Justice, - It is not alone that you are charged with swearing falsely, but you are charged with having done so knowingly, maliciously and corruptly and that with the intent of taking away the life of a fellow creature, or perhaps the lives of many - do you say you are guilty of that chare
Prisoner - I do
Mr. Arabin counsel for the crown - We were in a prosition to prove the case now against him by the clearest and most incontrovertible testimony; it is perhaps the worst case of perjury that ever came before a court of justice.
Chief Justice to the prisoner - Your pleas springs from good motives, and that you now feel some contrition for the awful crime which you have committed. Up to the moment of your being arraigned here I was not aware of the nature of the charge against you. I am almost lost in astonshment at the depravity that could induce you to falsely charge a fellow creatrue with that abominable murder - instigated no doubt, by the hope of reward; and I must say that the punishment which the law metes out for the crime of perjury is quite inadequate to your offence. If you had committed the murder with which you falsely charged another, and came forward and acknowledged your guilty, you would be far less culpable than you are by attempting to take away the life of an innocent fellow being for the hope of reward; and I am afraid that your retreat now, when arraigned at the bar, does not spring from a compunction of conscience, but from a knowledge that the charge against yo uwas so well founded that you could make no defence. The sentence of the court is, that you be imprisoned for one calendar mmonth, and then transported for seven years. - . - Kerry Evening Post 23 March 1839
. Sydney Herald 27 January 1840
. Asiatic Journal and Monthly Miscellany
. Convict Indents. State Archives NSW; Series: NRS 12189; Item: [X642A]; Microfiche: 741
 Commercial Journal 29 January 1840
 Bateson, Charles & Library of Australian History (1983). The convict ships, 1787-1868 (Australian ed). Library of Australian History, Sydney. pp354 - 355
 Journal of John Baird. Ancestry.com. UK, Royal Navy Medical Journals, 1817-1857 Original data: The National Archives. Kew, Richmond, Surrey.
 National Archives Reference: ADM 101/54/1 Description: Medical journal of the Middlesex, convict ship, for 1 June 1839 to 1 February 1840 by John Baird, Surgeon and Superintendent, during which time the said ship was employed on a voyage to Sydney, New South Wales