Vaccine-induced time- and age-dependent mucosal immunity to gastrointestinal parasite infection

Wei Liu^1,†, Tom N. McNeilly^2,†,*, Mairi Mitchell², Stew T.G. Burgess², Alasdair J. Nisbet², Jacqueline B. Matthews^2,3, and Simon A. Babayan^1,*

1. Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK,
2. The Moredun Research Institute, Pentlands Science Park, EH26 0PZ, Scotland, UK,
3. 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
  • ipa_3V_6V.ods
  • gene_cluster_masigpro.ods
• Raw transcriptomes
  • Sequencing parameters
• Code
• Data used for the analysis

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

1. RNAseq and parasitology: preparation of RNAseq data for analysis
2. WGCNA: clustering of transcript counts using Weighted Gene Network Analysis
3. ElasticNet: supervised machine learning of WGCNA correlates of worm burdens
4. 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