Multi-omics identify LRRC15 as a COVID-19 severity predictor and persistent pro-thrombotic signals in convalescence

RNA sequencing, SomaLogic proteomics and flow cytometry data were generated for two cohorts of end-stage kidney disease patients with COVID-19. The Wave 1 cohort consists of samples collected from patients during the first wave of COVID-19 in early 2020, while samples were collected for the Wave 2 cohort in the following year.

This data deposition includes the RNA-seq counts, SomaScan proteomics, flow cytometry and clinical metadata associated with the study. For further information about the study and data, see the associated GitHub repository (https://github.com/jackgisby/covid-longitudinal-multi-omics) or our pre-print (https://doi.org/10.1101/2022.04.29.22274267). The repository also contains code to replicate our analysis of the data.

The raw RNA-seq reads were processed using the nf-core RNA-seq v3.2 pipeline before htseq-count was used to generate a raw counts matrix, which is included in this deposition (htseq_counts.csv). Three files make up the proteomics data: sample_technical_meta.csv, feature_meta.csv and soma_abundance.csv. The first two files contain metadata columns for the samples and protein features, respectively. The final file includes the unprocessed protein abundance data. The files general_panel.csv and t_cell_panel.csv contain the flow cytometry data, split into the general and T-cell panels, respectively. Finally, clinical metadata is available for the two cohorts described in this study (w1_metadata.csv, w2_metadata.csv).

The features in the clinical metadata include:

Column Name
Data Type
Description

sample_id
Character
Unique identifier for samples

individual_id
Character
Unique identifier for individuals

ethnicity
Character
The individual's ethnicity (asian, white, black or other)

sex
Character
The individual's sex (M or F)

calc_age
Integer
Age in years

ihd
Character
Information on coronary heart disease

previous_vte
Character
Whether individuals have had venous thromboembolism

copd
Character
Whether individuals have chronic obstructive pulmonary disease

diabetes
Character
Whether individuals have diabetes, and, if so, the type of diabetes

smoking
Character
Smoking status

cause_eskd
Character
Cause of ESKD

WHO_severity
Character
The peak (WHO) severity for the patient over the disease course

WHO_temp_severity
Character
The (WHO) severity at time of sampling

fatal_disease
Logical
Whether the disease was fatal

case_control
Character
Whether the individual was COVID-19 POSITIVE or NEGATIVE at time of sampling. Convalescent patients are denoted by the label RECOVERY

radiology_evidence_covid
Character
Evidence of COVID-19 from radiology

time_from_first_symptoms
Integer
The number of days since the individual first experienced COVID symptoms at time of sampling

time_from_first_positive_swab
Integer
The number of days since the individual's first positive swab was taken at time of sampling