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Table 1 RNA-seq sample descriptions and metrics

From: Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms

Sample Replicates Host/location Description Main developmental process Specific developmental processes No. of genes expressed (% totala) Comparison No. of up-regulatedb (% of expressed genes) GOIc
Larvae 3 × apx. 550 pooled S2–S3 Larvae Beetle (Tribolium spp.)/haemocoel 5-day old, mid-metamorphosis Larvae Cysticercoid morphogenesis Specification of primary body axes (AP/DV/LR) involving differentiation of juvenile worm and cyst-/tail-forming poles. Nascent nerve-muscle development in cyst and juvenile poles (e.g. rostellar apparatus, suckers) 10,257 (83%) Larvae cf. Whole Adult 2266 (18%) 72
Whole Adult 3 × whole, gravid worms Mouse (Mus musculus)/bile duct Whole, gravid worms Strobilar and sexual development (encompassing all processes below) 10,139 (82%) Whole Adult cf. Larvae 3087 (30%) n/a
Scolex-Neck 1 × 13, 1 × 14, 1 × 43 pooled scolex + neck pieces (~ 0.5 cm each)   Scolex and ‘neck’ (including a variable number of nascent segments) Proglottisation and strobilation Formation of nascent segments and proglottids; cellular integration into existing muscle, nerve and excretory systems 9564 (77%) Scolex-Neck cf. Mid/Scolex-Neck cf. End 1052 (11%)/812 (8%) 61/49
Mid 1 × 11, 1 × 12, 1 × 15 pooled pieces (~ 2.5 cm each)   Segments with mature proglottids Sexual maturation Gametogenesis and maturation of female system; fertilisation 10,170 (82%) Mid cf. Scolex-Neck/Mid cf. End 2066 (20%)/457 (4.5%) 60/16
End 1 × 11, 1 × 12, 1 × 17 pooled pieces (~ 2.5 cm each)   Sub-terminal, gravid segments Egg and embryo maturation Embryogenesis; proglottid senescence 10,095 (82%) End cf. Scolex-Neck/End cf. Mid 1440 (14%)/924 (9%) 22/18
  1. aOf 12,371 gene models in the PRJEB124 release of the Hymenolepis microstoma genome (www: parasite.wormbase.org). Raw and normalised RNA-seq counts are listed in Additional file 1
  2. bDifferentially expressed gene models are listed in Additional file 2
  3. cGenes of interest: signalling components, transcription factors and post-transcriptional/translational regulators (highlighted in Table S2.2-S2.5, Additional file 2)