Transcriptome data of control and infected larval guts.

is an obligate fungal pathogen of honeybee larvae that leads to chalkbrood, which causes heavy losses for the apiculture in China and many other countries. In this article, guts of 4-, 5-, 6-day-old larvae challenged by (AmT1, AmT2, AmT3) and normal 4-day-old larval guts (AmCK) were sequenced using next-generation sequencing technology. On average, 29,196,197, 28,690,943, 29,779,715 and 30,496,725 raw reads were yielded from these four groups; an average of 29,540,895 clean reads were obtained after quality control. In addition, the mapping ratio of clean reads in treatment and control groups to the genome were over 97.16%. For more insight please see "Uncovering the immune responses of larval gut to infection utilizing transcriptome sequencing" [1]. The raw data were submitted to the National Centre for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database under accession numbers: SRR4084091, SRR4084092, SRR4084095, SRR4084096, SRR4084097, SRR4084098, SRR4084099, SRR4084100, SRR4084101, SRR4084102, SRR4084093, SRR4084094.