Plasma cell‐free transcriptome profiling in blood plasma from chronic liver disease patients

Supplementary data associated with the data descriptor with title: "Plasma cell‐free transcriptome profiling in blood plasma from chronic liver disease patients" File description: Analyses_results_summary.xlsx: Overview of results showed in the technical validation section. A summary of the contents can be found in the “summary” tab in the file annotation_cohort1.csv: laboratory and clinical annotation of samples/patients belonging to cohort 1. annotation_cohort2.csv: laboratory and clinical annotation of samples/patients belonging to cohort 2. CodeBook_ann_cohort1.xlsx: extended description of variables included in the cohort 1 annotation. CodeBook_ann_cohort2.xlsx: extended description of variables included in the cohort 2 annotation. circRNA_diffexpr.csv: differential abundance analysis of circRNA results, includes detected circRNA with p adjusted < 0.05 and abs(logFC) > 2. hepatocyte_signature_deconvolution.csv: results of the vector regression to deconvolve cell types of origin within the plasma cell-free transcriptome. SuplFig1.pdf: Supplementary figure 1. Gene set enrichment and cellular signatures in NAFLD vs. no NAFLD (cohort 1).(a) Gene set enrichment analysis (GSEA) using GO and Hallmark databases (|NES| > 1, FDR < 0.25). (b) Hepatocyte-specific gene expression (CPM counts, left) and singscore-derived hepatocyte signature (right). (c) Volcano plot of differentially expressed circRNAs (|log2FC| > 2, p < 0.05), identifying 97 dysregulated circRNAs. Significance levels: *p < 0.05, **p < 0.01, ***p < 0.001. SuplFig2.pdf: Supplementary figure 2. Gene set enrichment and cellular signature analysis in cirrhosis vs absence of cirrhosis (cohort 1). (a) Gene set enrichment analysis (GSEA) using GO and Hallmark databases (|NES| > 1, FDR < 0.25). (b) Hepatocyte-specific gene expression (CPM counts, left) and singscore-derived hepatocyte signature (right). (c) Volcano plot showing the differential expression of circRNAs. Statistical significance is indicated as *p < 0.05, **p < 0.01, and ***p < 0.001. SuplFig3.pdf: Supplementary figure 3. Gene set enrichment and cellular signatures in high vs. low fibrosis (cohort 2). (a) Gene set enrichment analysis (GSEA) using GO and Hallmark databases(|NES| > 1, FDR < 0.25). (b) Hepatocyte-specific gene expression (CPM counts, left) and singscore-derived hepatocyte signature (right). (c) Deconvolution analysis showing proportions of neutrophils, NK cells, B cells, and platelets. Significance levels: *p < 0.05, **p < 0.01, ***p < 0.001. SuplFig4.pdf: Supplementary figure 4. Gene set enrichment and cellular signatures in NASH patients at risk of HCC progression (cohort 2). (a) Gene set enrichment analysis (GSEA) using GO and Hallmark databases. (|NES| > 1, FDR < 0.25). (b) Hepatocyte-specific gene expression (CPM counts, left) and singscore-derived hepatocyte signature (right). (c) Deconvolution analysis showing proportions of neutrophils, goblet cells, B cells, and platelets. Significance levels: *p < 0.05, **p < 0.01, ***p < 0.001. Total_RNA_description.pdf: text describing the findings of the Gene set enrichment, hepatocyte signature, circRNA analyses. data_user_agreement.pdf: data user agreement to be signed in order to request access to the dataset deposited in the EGA repository (includes data access and data transfer agreements) DTA_non_EU.pdf: additionall data transfer agreement for non-EU countries to be signed together with the DUA in order to request access to the dataset deposited in the EGA repository How to request access to dataset EGAD50000000775 Dataset: Raw RNA-seq data from blood plasma of patients with liver diseaseEGA Study: EGAS50000000545Data Access Committee (DAC): Ghent University — Prof. Jo Vandesompele Who can apply Access is open to qualified researchers whose proposed use complies with the Data Usage Agreement (DUA), applicable ethics approvals, and participant consent restrictions. Research Purposes include research seeking to advance the understanding of genetics, genomics, disease mechanisms, treatment of disorders, and development of associated analytical or statistical methods, consistent with participant consent and the DUA. Step-by-step process Step 1 — Create or log in to your EGA account Go to https://ega-archive.org and register for an account if you do not already have one. Your EGA account email will be used for access notifications and data download. Step 2 — Submit a Data Access Request through EGA Navigate to the dataset page:https://identifiers.org/ega.dataset/EGAD50000000775 Click “Request Access” and follow the on-screen instructions. EGA will forward the request to the Data Access Committee at Ghent University for review. Step 3 — Complete the Data Usage Agreement (DUA) Download the DUA from this Zenodo repository and complete all required fields, including: User Institution name and address Project abstract (Appendix II) Registered users table (Appendix II) EGA account holders table (Appendix II) The DUA must be signed by: an authorised representative of the User Institution (e.g. research office or department head), and the Principal Investigator of the project. Step 4 — Additional requirements for certain international transfers For certain transfers outside the EU/EEA, UGent may require additional GDPR-related transfer documentation (e.g. Standard Contractual Clauses) before access can be granted. Your institution is located in… Document to complete EU / EEA only data_user_agreement.pdf Outside EU / EEA data_user_agreement.pdf and DTA_non_EU.pdf Fill in all highlighted fields: institution details, PI contact information, research purpose, and the DTA ID number (leave blank — UGent will assign this). Sign where indicated. Step 5 — Send the signed documents to UGent Email the signed documents (scanned or digitally signed PDF) to: UGent Technology Transfer [e-mail] Sint-Pietersnieuwstraat 259000 GhentBelgium Please copy: Prof. Jo [e-mail] Step 6 — Await approval and counter-signature The DAC will review the request. Once approved, UGent will counter-sign the agreement and notify EGA. EGA will then grant access permissions for downloading the dataset. For instructions to reproduce the results in the publication check the github repository: https://github.com/OncoRNALab/GCP_exRNA_liver.git