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| Sunday, August 21st , 2016 |
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| 1B Aaron Williams was designated for assignment. |
| 2B Mike Barksdale was designated for assignment. |
| Tuesday, July 5th , 2016 |
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| Activated CL Keith Penny from the injured list. |
| Saturday, June 25th , 2016 |
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| Placed CL Keith Penny on the 10-day injured list, retroactive to 06/24/2016. |
| Sunday, June 12th , 2016 |
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| RF Nate Humby was designated for assignment. |
| CF Eric Day was designated for assignment. |
| 3B Jeff Stenger was designated for assignment. |
| RP Danny Pocock was designated for assignment. |
| 1B Alberto Almejo was designated for assignment. |
| RP Jonas Hoerman was designated for assignment. |
| C Jake Fisher was designated for assignment. |
| RP Alex Perea was designated for assignment. |
| RP Steve Jones was designated for assignment. |
| LF David Pacheco was designated for assignment. |
| RP Ch'ang-chieh Jung was designated for assignment. |
| RP Arthur Kinnersley was designated for assignment. |
| CF Erik Windham was designated for assignment. |
| RP Mike Castillo was designated for assignment. |
| RF Gil Soto was designated for assignment. |
| SP Brian Tisdale was designated for assignment. |
| CF Jose Saenz was designated for assignment. |
| Promoted RP Nash Lonie to Triple A Oakland. |
| Demoted RP Brent Pickford to Advanced Prospect League Golden State. |
| Promoted SP Justin Craig to Triple A Oakland. |
| Promoted LF Alex Ventura to Triple A Oakland. |
| Promoted 3B Mike Stanford to Triple A Oakland. |
| Received CL Gene Shepard from Triple A Oakland. |
| Received RP Tony Sanchez from Triple A Oakland. |
| Received 1B Chusuke Doi from Triple A Oakland. |
| SS Aaron Dow was designated for assignment. |
| RP David Gray was designated for assignment. |
| Promoted CF Doug Harmon to Triple A Oakland. |
| Received RF Paul McKemie from Prospect League Huntsville. |
| Received 2B Alex Salinas from Triple A Oakland. |
| Received LF Chad Winfrey from Prospect League Huntsville. |
| 3B Alex Perez was designated for assignment. |
| Promoted CL Bernd van Dongen to Triple A Oakland. |
| Received RP Keith Penny from Triple A Oakland. |
| Received 3B Fuminobu Hayase from Advanced Prospect League Golden State. |
| Wednesday, June 1st , 2016 |
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| Received RF Nate Humby from Prospect League Huntsville. |
| Saturday, May 14th , 2016 |
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| Received CF Eric Day from Prospect League Huntsville. |
| Received CF Doug Harmon from Advanced Prospect League Golden State. |
| Friday, May 13th , 2016 |
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| Received 1B Alberto Almejo from Advanced Prospect League Golden State. |
| Received C Matt Cobb from Advanced Prospect League Golden State. |
| Received C Jake Fisher from Advanced Prospect League Golden State. |
| Received C Roy Glenn from Advanced Prospect League Golden State. |
| Received RP David Gonzalez from Advanced Prospect League Golden State. |
| Received LF Jayden Henderson from Advanced Prospect League Golden State. |
| Received RP Jonas Hoerman from Prospect League Huntsville. |
| Received RP Steve Jones from Advanced Prospect League Golden State. |
| Received RP Ch'ang-chieh Jung from Advanced Prospect League Golden State. |
| Received RP Arthur Kinnersley from Advanced Prospect League Golden State. |
| Received LF David Pacheco from Advanced Prospect League Golden State. |
| Received RP Alex Perea from Advanced Prospect League Golden State. |
| Received 3B Alex Perez from Advanced Prospect League Golden State. |
| Received RP Danny Pocock from Prospect League Huntsville. |
| Received 3B Jeff Stenger from Advanced Prospect League Golden State. |
| Received CF Erik Windham from Advanced Prospect League Golden State. |
| Sunday, May 1st , 2016 |
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| Promoted RF Kyle Wilt to Major League San Francisco. |
| Promoted SP Brandon Hooks to Major League San Francisco. |
| Promoted 3B David Osterloh to Major League San Francisco. |
| Thursday, January 7th , 2016 |
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| Promoted C Conor O'Hagan to Triple A Oakland. |
| Received RP Gene Shepard from Advanced Prospect League Golden State. |
