Self employed

The short answer is yes, depreciation allowed or allowable would be subtracted from the basis allocated to the business portion of the home.  It may/may not be subject to recapture under section 1250.

I'm including two links here, one for Pub 544, Sales & Other Dispositions of Assets

https://www.irs.gov/publications/p544

and the other for Pub 587, Business Use of Your Home

https://www.irs.gov/publications/p587

This is from Pub 587

"

If the part of your property used for business is within your home, such as a room used as a home office for a business or rooms used to provide daycare, you do not need to allocate gain on the sale of the property between the business part of the property and the part used as a home. In addition, you do not need to report the sale of the business part on Form 4797, Sales of Business Property. This is true whether or not you were entitled to claim any depreciation. However, you cannot exclude the part of any gain equal to any depreciation allowed or allowable after May 6, 1997. See Depreciation, later."

I would start with Pub 587.  Things get a little complicated and the answer may depend on exactly what years you used the property for business and if depreciation was allowed or allowable. (as can been seen in the above paragraph)