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Condensed Consolidated Statements of Cash Flows (unaudited) - USD ($)
$ in Thousands
6 Months Ended
Jun. 30, 2016
Jun. 30, 2015
Cash flows from operating activities:    
Net loss $ (72,253) $ (419,696)
Adjustments to reconcile net loss to net cash used in operating activities:    
Stock-based compensation expense 117,414 120,645
Depreciation and amortization expense 31,378 30,428
Deferred income taxes 22,858 6,346
Other non-cash items, net 3,436 6,045
Changes in operating assets and liabilities:    
Accounts receivable, net (12,954) (21,197)
Inventories (7,779) (9,426)
Prepaid expenses and other assets (7,971) (15,397)
Accounts payable (23,821) (3,033)
Accrued expenses and other liabilities (14,562) 8,098
Accrued restructuring expense (2,892) (26,012)
Deferred revenues (7,131) (9,303)
Net cash provided by (used in) operating activities 25,723 (332,502)
Cash flows from investing activities:    
Purchases of marketable securities (470,077) (125,655)
Maturities of marketable securities 332,316 741,725
Payment for acquisition of variable interest entity 0 80,000
Expenditures for property and equipment (27,892) (23,978)
Increase in restricted cash and cash equivalents 0 (21,975)
Investment in CRISPR Series B preferred stock (3,075) 0
Decrease in restricted cash and cash equivalents (VIE) 8,397 2,277
(Increase) decrease in other assets (159) 87
Net cash (used in) provided by investing activities (160,490) 492,481
Cash flows from financing activities:    
Issuances of common stock under benefit plans 33,702 87,850
Payments on capital lease obligations (7,538) (14,441)
Proceeds from capital lease financing 0 13,386
Payments on construction financing lease obligation (209) (184)
Net cash provided by financing activities 25,955 86,611
Effect of changes in exchange rates on cash (90) (1,306)
Net (decrease) increase in cash and cash equivalents (108,902) 245,284
Cash and cash equivalents—beginning of period 714,768 625,259
Cash and cash equivalents—end of period 605,866 870,543
Supplemental disclosure of cash flow information:    
Cash paid for interest 41,325 42,885
Cash paid for income taxes 1,237 1,022
Issuances of common stock exercises from employee benefit plans receivable $ 161 $ 166