The present disclosure provides methods and systems for amplifying nucleic acid samples. In some aspects, the methods and systems described provided can be useful in conducting multiple nucleic acid amplification reactions in parallel. In some embodiments, methods and systems provided herein can be useful in conducting reverse transcription and DNA amplification in parallel. Moreover, in some aspects, the methods and systems described herein can be useful in analysis of nucleic acid samples. In some embodiments, methods and systems provided herein can be useful for conducting multiple series of primer extension reactions, which can aid in analysis of a nucleic acid sample.