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Proteomics and proteogenomics analysis of sweet potato (Ipomoea batatas) leaf and root

ABSTRACT: Two complementary protein extraction methodologies coupled with an automated proteomic platform were employed to analyze tissue-specific proteomes and characterize biological and metabolic processes in sweet potato. A total of 74,255 peptides corresponding to 4,321 nonredundant proteins were successfully identified. Data were compared to predicted protein accessions for Ipomea species and mapped on the sweet potato transcriptome and haplotype-resolved genome. A proteogenomics analysis successfully mapped 12,902 peptides against the transcriptome or genome, representing 90.4% of the total 14,275 uniquely identified peptides, predicted 741 new protein-coding genes, and specified 2726 loci where annotations can be further improved. Overall, 39,916 peptides mapped to 3,143 unique proteins in leaves, and 34,339 peptides mapped to 2,928 unique proteins in roots; 32% and 27% unique identified proteins were leaves- and roots-specific, respectively.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Ipomoea Batatas

TISSUE(S): Plant Cell, Root, Leaf

SUBMITTER: George Popescu

LAB HEAD: George V Popescu

PROVIDER: PXD012999 | Pride | 2019-05-30

REPOSITORIES: Pride

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Project description:The purpose of this experiment was to do investigatge the transcriptional effect of anti-TNF treatment in patients suffering from rheumatoid arthritis. Two series of hybridizations were performed. Each hybridization was done with a technical replicate (the same amount of RNA taken from the same amplified RNA aliquot labeled in two separate reactions and hybridized onto two separate arrays). In the first series of hybridizations RNA exptracted from biopsies taken before treatment was hybridized in a common reference design to enable comparisons between patients. In the second series RNA from biopsies taken after and before treatment were hybridized on the same chip in a direct design to enable investigation of the effect of treatment. 10 patients (8 females and 2 males, median age 54, range 25-69) meeting the American College of Rheumatology (ACR) criteria for RA were recruited for this study. All patients received infliximab (an antibody directed against TNF-alpha) infusions 3mg/kg at week 0 and than after 2 weeks and 6 weeks. Five of these patients were receiving prednisolon and all ten patients were treated with methotrexate to a maximum of 20 mg per week. Synovial biopsies were obtained during arthroscopy from all patients before and after a median of 9 weeks of treatment (with one exception, patient 7 where the second biopsy was obtained during open surgery). Biopsies were taken at the site of inflammation close to cartilage (cc) or not close to cartilage (ncc), defined as less or more than 1.5 cm away from cartilage, respectively. One biopsy was taken before and after treatment from patient 5, 7, 9 and 10. Multiple biopsies were retrieved before and/or after treatment from patient 1, 2, 3, 4, 6 and 7. Due to small amounts of RNA available for patient 9 it was only used in the second series of hybridizations. The average biopsy weight was 22 mg. The ethical committee at the Karolinska Hospital approved all experiments on human cells and tissues. Informed consent was obtained from all study subjects.

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Proteomics and proteogenomics analysis of sweet potato (Ipomoea batatas) leaf and root

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