Vaccine-induced time- and age-dependent mucosal immunity to gastrointestinal parasite infection
Wei Liu1,†, Tom N. McNeilly2,†,*, Mairi Mitchell2, Stew T.G. Burgess2, Alasdair J. Nisbet2, Jacqueline B. Matthews2,3, and Simon A. Babayan1,*
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK,
- The Moredun Research Institute, Pentlands Science Park, EH26 0PZ, Scotland, UK,
- Roslin Technologies Limited, Roslin Innovation Centre, University of Edinburgh, Easter Bush, EH25 9RG, Scotland, UK
†These authors contributed equally to this work
*To whom correspondence should be addressed; E-mail: simon.babayan@glasgow.ac.uk, tom.mcneilly@moredun.ac.uk
Table of contents
Supplementary data
multiqc_report_biopsy.html
The quality control MultiQC report of biopsy RNAseq samples based on the FASTQC data.
ipa_3V_6V.ods
Ingenuity Pathway analysis (IPA) results for all the WGCNA clusters shown in Figure 2.
gene_cluster_masigpro.ods
Differentially expressed gene list between the ageing groups. The expression levels are shown in Supplementary Figure 5C.
Raw transcriptomes
Transcriptomes are available at the Sequence Read Archive (SRA) BioProject ID: PRJNA827252; SRA Study ID: SRP370649 and BioSample IDs: SAMN27607111–SAMN27607290.
Sequencing parameters
- RNAseq using nextSeq 500
- Organism and tissue type: Ovis aries abomasum
- Extraction method used: Qiagen RNeasy mini kit
- Suspension buffer used: RNAse free water
- read depth: 20M reads, paired-ends (named R1 and R2 in sequence files)
Code
- RNAseq and parasitology: preparation of RNAseq data for analysis
- WGCNA: clustering of transcript counts using Weighted Gene Network Analysis
- ElasticNet: supervised machine learning of WGCNA correlates of worm burdens
- WGCNA_python_elasticnet_pathway: analysis of immune pathways extracted from WGCNA correlates of parasite burdens
Data used for the analysis
Each filename follows the scheme:
[sheepID][group][sampling week]_[sample run].fastq.gz
File & sample list:
| Sample ID | Age, Vaccine, Timepoint |
|---|---|
| 6565g1w1 | 3mo Vaccinated Week1 |
| 6615g1w1 | 3mo Vaccinated Week1 |
| 6622g1w1 | 3mo Vaccinated Week1 |
| 6642g1w1 | 3mo Vaccinated Week1 |
| 6917g1w1 | 3mo Vaccinated Week1 |
| 6925g1w1 | 3mo Vaccinated Week1 |
| 6937g1w1 | 3mo Vaccinated Week1 |
| 6588g2w1 | 3mo Control Week1 |
| 6625g2w1 | 3mo Control Week1 |
| 6626g2w1 | 3mo Control Week1 |
| 6634g2w1 | 3mo Control Week1 |
| 6915g2w1 | 3mo Control Week1 |
| 6931g2w1 | 3mo Control Week1 |
| 6935g2w1 | 3mo Control Week1 |
| 6940g2w1 | 3mo Control Week1 |
| 6565g1w2 | 3mo Vaccinated Week2 |
| 6615g1w2 | 3mo Vaccinated Week2 |
| 6622g1w2 | 3mo Vaccinated Week2 |
| 6642g1w2 | 3mo Vaccinated Week2 |
| 6917g1w2 | 3mo Vaccinated Week2 |
| 6925g1w2 | 3mo Vaccinated Week2 |
| 6937g1w2 | 3mo Vaccinated Week2 |
| 6588g2w2 | 3mo Control Week2 |
| 6625g2w2 | 3mo Control Week2 |
| 6626g2w2 | 3mo Control Week2 |
| 6634g2w2 | 3mo Control Week2 |
| 6915g2w2 | 3mo Control Week2 |
| 6931g2w2 | 3mo Control Week2 |
| 6935g2w2 | 3mo Control Week2 |
| 6940g2w2 | 3mo Control Week2 |
| 6565g1w3 | 3mo Vaccinated Week3 |
| 6615g1w3 | 3mo Vaccinated Week3 |
| 6622g1w3 | 3mo Vaccinated Week3 |
| 6642g1w3 | 3mo Vaccinated Week3 |
| 6917g1w3 | 3mo Vaccinated Week3 |
| 6925g1w3 | 3mo Vaccinated Week3 |
| 6937g1w3 | 3mo Vaccinated Week3 |
| 6588g2w3 | 3mo Control Week3 |
| 6625g2w3 | 3mo Control Week3 |
| 6626g2w3 | 3mo Control Week3 |
| 6634g2w3 | 3mo Control Week3 |
| 6915g2w3 | 3mo Control Week3 |
| 6931g2w3 | 3mo Control Week3 |
| 6935g2w3 | 3mo Control Week3 |
| 6940g2w3 | 3mo Control Week3 |
| 6565g1w4 | 3mo Vaccinated Week4 |
| 6615g1w4 | 3mo Vaccinated Week4 |
| 6622g1w4 | 3mo Vaccinated Week4 |
| 6642g1w4 | 3mo Vaccinated Week4 |
| 6917g1w4 | 3mo Vaccinated Week4 |
| 6925g1w4 | 3mo Vaccinated Week4 |
| 6937g1w4 | 3mo Vaccinated Week4 |
| 6588g2w4 | 3mo Control Week4 |
| 6625g2w4 | 3mo Control Week4 |
| 6626g2w4 | 3mo Control Week4 |
| 6634g2w4 | 3mo Control Week4 |
| 6915g2w4 | 3mo Control Week4 |
| 6931g2w4 | 3mo Control Week4 |
| 6935g2w4 | 3mo Control Week4 |
| 6940g2w4 | 3mo Control Week4 |
| 6565g1w5 | 3mo Vaccinated Week5 |
| 6615g1w5 | 3mo Vaccinated Week5 |
| 6622g1w5 | 3mo Vaccinated Week5 |
| 6642g1w5 | 3mo Vaccinated Week5 |
| 6917g1w5 | 3mo Vaccinated Week5 |
| 6925g1w5 | 3mo Vaccinated Week5 |
| 6937g1w5 | 3mo Vaccinated Week5 |
| 6588g2w5 | 3mo Control Week5 |
| 6625g2w5 | 3mo Control Week5 |
| 6626g2w5 | 3mo Control Week5 |
| 6634g2w5 | 3mo Control Week5 |
| 6915g2w5 | 3mo Control Week5 |
| 6931g2w5 | 3mo Control Week5 |
| 6935g2w5 | 3mo Control Week5 |
| 6940g2w5 | 3mo Control Week5 |
| 6565g1w7 | 3mo Vaccinated Week7 |
| 6615g1w7 | 3mo Vaccinated Week7 |
| 6622g1w7 | 3mo Vaccinated Week7 |
| 6642g1w7 | 3mo Vaccinated Week7 |
| 6917g1w7 | 3mo Vaccinated Week7 |
| 6925g1w7 | 3mo Vaccinated Week7 |
| 6937g1w7 | 3mo Vaccinated Week7 |
| 6588g2w7 | 3mo Control Week7 |
| 6625g2w7 | 3mo Control Week7 |
| 6626g2w7 | 3mo Control Week7 |
| 6634g2w7 | 3mo Control Week7 |
| 6915g2w7 | 3mo Control Week7 |
| 6931g2w7 | 3mo Control Week7 |
| 6935g2w7 | 3mo Control Week7 |
| 6940g2w7 | 3mo Control Week7 |
| 6576g3w1 | 6mo Vaccinated Week1 |
| 6647g3w1 | 6mo Vaccinated Week1 |
| 6652g3w1 | 6mo Vaccinated Week1 |
| 6905g3w1 | 6mo Vaccinated Week1 |
| 6910g3w1 | 6mo Vaccinated Week1 |
| 6911g3w1 | 6mo Vaccinated Week1 |
| 6928g3w1 | 6mo Vaccinated Week1 |
| 6595g4w1 | 6mo Control Week1 |
| 6635g4w1 | 6mo Control Week1 |
| 6639g4w1 | 6mo Control Week1 |
| 6653g4w1 | 6mo Control Week1 |
| 6902g4w1 | 6mo Control Week1 |
| 6923g4w1 | 6mo Control Week1 |
| 6934g4w1 | 6mo Control Week1 |
| 6939g4w1 | 6mo Control Week1 |
| 6576g3w2 | 6mo Vaccinated Week2 |
| 6647g3w2 | 6mo Vaccinated Week2 |
| 6652g3w2 | 6mo Vaccinated Week2 |
| 6905g3w2 | 6mo Vaccinated Week2 |
| 6910g3w2 | 6mo Vaccinated Week2 |
| 6911g3w2 | 6mo Vaccinated Week2 |
| 6928g3w2 | 6mo Vaccinated Week2 |
| 6595g4w2 | 6mo Control Week2 |
| 6635g4w2 | 6mo Control Week2 |
| 6639g4w2 | 6mo Control Week2 |
| 6653g4w2 | 6mo Control Week2 |
| 6902g4w2 | 6mo Control Week2 |
| 6923g4w2 | 6mo Control Week2 |
| 6934g4w2 | 6mo Control Week2 |
| 6939g4w2 | 6mo Control Week2 |
| 6576g3w3 | 6mo Vaccinated Week3 |
| 6647g3w3 | 6mo Vaccinated Week3 |
| 6652g3w3 | 6mo Vaccinated Week3 |
| 6905g3w3 | 6mo Vaccinated Week3 |
| 6910g3w3 | 6mo Vaccinated Week3 |
| 6911g3w3 | 6mo Vaccinated Week3 |
| 6928g3w3 | 6mo Vaccinated Week3 |
| 6595g4w3 | 6mo Control Week3 |
| 6635g4w3 | 6mo Control Week3 |
| 6639g4w3 | 6mo Control Week3 |
| 6653g4w3 | 6mo Control Week3 |
| 6902g4w3 | 6mo Control Week3 |
| 6923g4w3 | 6mo Control Week3 |
| 6934g4w3 | 6mo Control Week3 |
| 6939g4w3 | 6mo Control Week3 |
| 6576g3w4 | 6mo Vaccinated Week4 |
| 6647g3w4 | 6mo Vaccinated Week4 |
| 6652g3w4 | 6mo Vaccinated Week4 |
| 6905g3w4 | 6mo Vaccinated Week4 |
| 6910g3w4 | 6mo Vaccinated Week4 |
| 6911g3w4 | 6mo Vaccinated Week4 |
| 6928g3w4 | 6mo Vaccinated Week4 |
| 6595g4w4 | 6mo Control Week4 |
| 6635g4w4 | 6mo Control Week4 |
| 6639g4w4 | 6mo Control Week4 |
| 6653g4w4 | 6mo Control Week4 |
| 6902g4w4 | 6mo Control Week4 |
| 6923g4w4 | 6mo Control Week4 |
| 6934g4w4 | 6mo Control Week4 |
| 6939g4w4 | 6mo Control Week4 |
| 6576g3w5 | 6mo Vaccinated Week5 |
| 6647g3w5 | 6mo Vaccinated Week5 |
| 6652g3w5 | 6mo Vaccinated Week5 |
| 6905g3w5 | 6mo Vaccinated Week5 |
| 6910g3w5 | 6mo Vaccinated Week5 |
| 6911g3w5 | 6mo Vaccinated Week5 |
| 6928g3w5 | 6mo Vaccinated Week5 |
| 6595g4w5 | 6mo Control Week5 |
| 6635g4w5 | 6mo Control Week5 |
| 6639g4w5 | 6mo Control Week5 |
| 6653g4w5 | 6mo Control Week5 |
| 6902g4w5 | 6mo Control Week5 |
| 6923g4w5 | 6mo Control Week5 |
| 6934g4w5 | 6mo Control Week5 |
| 6939g4w5 | 6mo Control Week5 |
| 6576g3w7 | 6mo Vaccinated Week7 |
| 6647g3w7 | 6mo Vaccinated Week7 |
| 6652g3w7 | 6mo Vaccinated Week7 |
| 6905g3w7 | 6mo Vaccinated Week7 |
| 6910g3w7 | 6mo Vaccinated Week7 |
| 6911g3w7 | 6mo Vaccinated Week7 |
| 6928g3w7 | 6mo Vaccinated Week7 |
| 6595g4w7 | 6mo Control Week7 |
| 6635g4w7 | 6mo Control Week7 |
| 6639g4w7 | 6mo Control Week7 |
| 6653g4w7 | 6mo Control Week7 |
| 6902g4w7 | 6mo Control Week7 |
| 6923g4w7 | 6mo Control Week7 |
| 6934g4w7 | 6mo Control Week7 |
| 6939g4w7 | 6mo Control Week7 |