title: Uninjured liver [CTRL1]

status: Public on Apr 07 2022

city: NEW YORK

first: Robert

middle: F

last: Schwabe

address: 1130 ST NICHOLAS AVE - ROOM 916B

description:
CTRL1
Whole liver tissue, uninjured.
Bulk RNA-seq
tpm_values_genes_kallisto_whole_liver.txt

data_processing:
Bulk RNA-seq:
20M paired-end 100bp sequencing was performed using the Illumina NovaSeq 6000.
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
A pseudoalignment to a kallisto index was created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
Differentially expressed genes were tested using DESeq2. Normalization was done internally using DESeq2's specialized algorithm and normalization to compare across samples, was performed using the TPM (transcripts per million) method.
scRNA-seq:
10x Genomics' cellranger pipeline was used to process the data (v2.1.1).
BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference mm10 (mouse).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bulk RNA-seq: Text files include TPM values for each Sample.
Supplementary_files_format_and_content: scRNA-seq: Raw counts in MatrixMarket (mtx) format, barcodes.tsv, genes.tsv.

extract_protocol:
Total RNA was column purified (Qiagen mini).
Construct libraries using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions.

value: LratCre+, TdTom+ in C57BL/6J

tag: liver damage

value: Whole liver


title: GI-ME-N_Solv_2

status: Public on Aug 04 2022

type: genomic

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

description: Solvent-treated

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol.

data_processing: Illumina files were read and processed using the R package minfi (v. 1.28.4). The arrays were normalized using the quantile algorithm. Probes with detection p.value above 0.1 were discarded.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Neuroblastoma cell line

label_protocol: 350-500 ng genomic DNA from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo Research Corporation, Orange, US) according to the manufacturer recommendations. Each sample was whole genome amplified and enzymatically fragmented following the instructions in the Illumina Infinium HD Assay Methylation Protocol Guide .

growth_protocol: Cells were grown under standard conditions in a humidified atmosphere at 37°C and 5% CO2.

extract_protocol: Genomic DNA was extracted and purified from cell samples using Qiagen QIAamp DNA Mini Kit according to standard instructions.

treatment_protocol: 24h after seeding, adherent cells were treated with solvent (DMSO) or 30 nM panobinostat for 18 h.

tag: gender

value: female

tag: cell line

value: GI-ME-N

tag: treatment

value: Solvent-treated


title: Uninjured liver [CTRL2]

type: SRA

state: NY

department: Medicine

country: USA

institute: Columbia University

description:
CTRL2
Whole liver tissue, uninjured.
Bulk RNA-seq
tpm_values_genes_kallisto_whole_liver.txt

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: liver

tag: strain

tag: tissue


title: Uninjured liver [CTRL3]

description:
CTRL3
Whole liver tissue, uninjured.
Bulk RNA-seq
tpm_values_genes_kallisto_whole_liver.txt


title: Aged satellite cell ATAC-Seq 1

status: Public on Mar 15 2022

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

country: Canada

institute: McGill University

library_source: genomic

data_processing:
Illumina BaseSpace software was used for basecalling.
Data was analyzed using ENCODE pipeline https://github.com/ENCODE-DCC/atac-seq-pipeline
Peaks were called using MACS2(v2.1.0)
Optimal peaks per condition were determined using the IDR pipeline https://github.com/nboley/idr
Project’s Website (reproducible notebooks): https://csglab.github.io/transcriptional_reprogramming_muscle_cells/
Genome_build: mm10

source_name: satellite cells

extract_protocol: 5000 satellite cells were isolated by Fluorescence-Activated Cell Sorting (FACS), selected for the GFP+/DAPI-, from 2 young and 2 aged Pax7-eGFP male mice, and sorted directly into ATAC-Seq Lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin). Following the lysis, cells were washed with wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) and spun down at 800g. Tagmentation was performed for 20 minutes at 37 °C in transposition mixture (5 μl of Tagment DNA (TD) buffer, 3.2 μl PBS, 0.89 μl Tn5, 0.1% Tween-20, 0.01% Digitonin and 0.75 μl water). After tagmentation, DNA was purified using column purification and PCR amplification with Illumina Nextera XT adapters was performed. The amplified DNA was then size selected and purified for sequencing. Each sample was processed using a modified version of the OMNI ATAC-Seq protocol (Corces, M. R. et al. Nature Methods, 2017).

tag: age

value: 25 months

value: skeletal muscle


title: Young satellite cell ATAC-Seq 1

value: 4 weeks


title: Aged satellite cell ATAC-Seq 2

value: 26 months


title: HC-36 Day 0 (P6.A10)

status: Public on Mar 09 2022

city: Bethesda

first: William

middle: W

last: Lau

state: MD

address: 4 Memorial Drive

department: Laboratory of Immune System Biology

institute: National Institute of Allergy and Infectious Diseases

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P6.A10

data_processing:
fastq generation by Illumina bcl2fastq (2.20)
reads were adapter trimmed and standardized to 100 bp across plates using trimmomatic (0.38), then mapped to hg38 genome using the STAR aligner (2.6)
PCR duplicates were removed using UMI-tools (0.5.3)
gene-level expression quantification was performed using the featureCounts function in the subread package (1.6.2)
filtering of lowly expressed genes followed by read depth and technical effect normalization by RUVSeq (1.18)
Genome_build: hg38
Supplementary_files_format_and_content: gene expression (raw and normalized) as comma-separated values (csv)

molecule: polyA RNA

source_name: Whole Blood

extract_protocol:
Blood was drawn directly into the Tempus™ Blood RNA Tube (Thermo Fisher Scientific, Waltham, MA) according to manufacturer’s protocol. Two Tempus tubes were collected at each study timepoint. The blood sample from each Tempus tube was aliquoted in to two 4.5mL cryovials (General lab supplier). These cryovials were directly stored at -80°C. RNA was isolated from tempus blood using the QIAsymphony RNA Kit (Qiagen, Gaithersburg, MD) on QIAsymphony SP instrument (Qiagen, Gaithersburg, MD). On the QIAsymphony, RNA CT 800 protocol was selected and used for RNA isolation. The instrument was set up according to the manufacturer’s protocol and the elution volume for RNA samples was set to 100µl. The final volume of the eluted RNA samples ranged from 65 – 95 µl.
RNA-seq libraries were prepared manually using Universal Plus mRNA-Seq with NuQuant, Human Globin AnyDeplete (Tecan Genomics, Redwood City, CA) according to manufacturer’s protocol. For each sample, 500ng of total RNA was used to isolate mRNA via poly(A) selection. Captured mRNA was washed, fragmented, and primed with the mix of random and oligo(dT) primers. After cDNA synthesis, ends were repaired and ligated with Unique Dual Index (UDI) adaptor pairs. Unwanted abundant transcripts from rRNA, mtRNA and globin were removed using AnyDeplete module. Remaining library was amplified by 14 cycles of PCR and purified with AMPure XP reagent (Beckman Coulter, Indianapolis, IN).

value: Whole Blood

tag: subject id

tag: age at sample drawn

tag: Sex

value: Male

tag: race

value: Multiple Race

tag: ethnicity

value: Hispanic or Latino

tag: group

value: HC

tag: vaccine type

value: Flucelvax

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects

value: AE

tag: visit

value: Day 0

tag: days since vaccination

tag: library plate

tag: library well


title: Young satellite cell ATAC-Seq 2


title: COVR-15 Day 7 (P6.A09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P6.A09

value: White

value: Non-Hispanic

value: COVR

tag: symptomatic

value: Y

tag: duration of illness

tag: long-covid symptoms

value: N

value: Day 7

tag: days since covid-19 diagnosis


title: GI-ME-N_Panob_2

description: Panobinostat-treated

tag: gender

value: female

tag: cell line

value: GI-ME-N

tag: treatment

value: Panobinostat-treated


title: COVR-7 Day 7 (P6.A07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P6.A07

tag: tissue

value: Whole Blood

tag: subject id

tag: age at sample drawn

tag: Sex

value: Female

tag: race

value: Fluzone High Dose


title: HC-39 Day 28 (P6.A05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P6.A05

value: Black

tag: ethnicity

tag: group

tag: vaccine type

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects

value: Day 28


title: HC-39 Day 0 (P6.A04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P6.A04

value: HC

value: Flucelvax

tag: visit

tag: days since vaccination

tag: library plate

tag: library well


title: HC-36 Day 1 (P6.A11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P6.A11

value: Male

value: Multiple Race

value: Hispanic or Latino

value: AE

value: Day 1


title: GI-ME-N_Solv_3

description: Solvent-treated

tag: gender

value: Solvent-treated


title: COVR-7 Day 0 (P6.A06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P6.A06

value: White

value: Non-Hispanic

value: COVR

tag: symptomatic

value: Y

tag: duration of illness

tag: long-covid symptoms

value: N

value: Day 0

tag: days since covid-19 diagnosis


title: GI-ME-N_Panob_3

description: Panobinostat-treated

value: female

tag: cell line

value: GI-ME-N

tag: treatment

value: Panobinostat-treated


title: GI-ME-N_Panob_1

description: Panobinostat-treated


title: Control-1 control (P6.A03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P6.A03

tag: tissue

value: Whole Blood

tag: subject id

value: control


title: Control-1 control (P6.A02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P6.A02


title: Control-2 control (P6.A01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P6.A01


title: COVR-15 Day 0 (P6.A08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P6.A08

tag: age at sample drawn

tag: Sex

value: Male

tag: race

tag: ethnicity

tag: group

value: Flucelvax


title: COVR-9 Day 0 (P5.H04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.H04

value: Female

value: Hispanic or Latino

tag: vaccine type

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects

tag: visit

tag: days since vaccination


title: HC-4 Day 7 (P5.H03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.H03

value: Black

value: HC

value: AE

value: Day 7

tag: library plate

tag: library well


title: COVR-9 Day 1 (P5.H02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.H02

value: White

value: COVR

tag: symptomatic

tag: duration of illness

tag: long-covid symptoms

value: Day 1

tag: days since covid-19 diagnosis


title: COVR-1 Day 7 (P5.G04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.G04

tag: tissue

tag: subject id

value: Non-Hispanic

value: Y


title: COVR-33 Day 1 (P5.H01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.H01

tag: age at sample drawn

tag: Sex


title: COVR-1 Day 1 (P5.F04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.F04

tag: race

tag: ethnicity


title: Control-2 control (P5.E04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.E04


title: COVR-33 Day 28 (P5.G01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.G01

tag: group

tag: vaccine type

value: Day 28


title: HC-40 Day 1 (P5.F02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.F02

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects


title: COVR-6 Day 7 (P5.E03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.E03

value: N

tag: visit

tag: days since vaccination


title: HC-40 Day 7 (P5.E01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.E01

value: Whole Blood

tag: library plate

tag: library well


title: COVR-1 Day -7 (P5.E02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.E02

tag: symptomatic

tag: duration of illness

value: Day -7


title: HC-4 Day -7 (P5.F03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.F03


title: COVR-33 Day 0 (P5.F01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.F01

tag: long-covid symptoms

value: Day 0

tag: days since covid-19 diagnosis


title: COVR-6 Day -7 (P5.C05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.C05

tag: tissue

tag: subject id

value: Male

value: Flucelvax


title: HC-4 Day 1 (P5.D01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.D01

tag: age at sample drawn

tag: Sex

value: Female


title: COVR-6 Day 1 (P5.C03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.C03

tag: race

tag: ethnicity


title: COVR-9 Day -7 (P5.D03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.D03

value: Hispanic or Latino

tag: group

tag: vaccine type


title: HC-40 Day -7 (P5.C02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.C02

value: HC

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects


title: COVR-1 Day 28 (P5.B05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.B05

value: AE

tag: visit

tag: days since vaccination


title: HC-4 Day 28 (P5.B04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.B04

value: Black

tag: library plate

tag: library well


title: HC-40 Day 28 (P5.B03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.B03

value: White


title: Control-1 control (P5.B01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.B01

value: control


title: COVR-9 Day 7 (P5.A05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.A05

value: COVR

tag: symptomatic

tag: duration of illness

value: Day 7


title: COVR-1 Day 0 (P5.C04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.C04

value: Non-Hispanic

value: Y

tag: long-covid symptoms

tag: days since covid-19 diagnosis


title: HC-4 Day 0 (P5.C01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.C01

tag: tissue

tag: subject id


title: COVR-33 Day -7 (P5.B02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.B02

tag: age at sample drawn

tag: Sex


title: HC-40 Day 0 (P5.A02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.A02

tag: race

tag: ethnicity


title: COVR-32 Day 0 (P4.H12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.H12

tag: group

tag: vaccine type

value: Fluzone High Dose


title: COVR-33 Day 7 (P5.A01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.A01

value: Whole Blood

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects


title: COVR-6 Day 28 (P5.A03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.A03

value: N

tag: visit

value: Day 28

tag: days since vaccination


title: COVR-9 Day 28 (P5.A04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.A04

tag: library plate

tag: library well


title: COVR-28 Day 28 (P4.H09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.H09

value: Male

tag: symptomatic

tag: duration of illness


title: COVR-28 Day 1 (P4.H11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.H11

tag: long-covid symptoms

value: Flucelvax

value: Day 1

tag: days since covid-19 diagnosis


title: HC-39 Day 0 (P4.H08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.H08

tag: tissue

tag: subject id

value: Female

value: Day 0


title: COVR-6 Day 0 (P5.D04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P5.D04

tag: age at sample drawn

tag: Sex

value: AE


title: HC-39 Day -7 (P4.H07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.H07

tag: race

value: Black

tag: ethnicity

value: HC

value: Day -7


title: COVR-30 Day 7 (P4.H05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.H05

value: White

tag: group

value: COVR

tag: vaccine type


title: HC-37 Day 28 (P4.H06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.H06

value: Non-Hispanic

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects


title: COVR-29 Day 0 (P4.H10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.H10

value: Y

tag: visit

tag: days since vaccination


title: HC-34 Day 7 (P4.H04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.H04

value: Day 7

tag: library plate

tag: library well


title: HC-38 Day -7 (P4.H03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.H03

value: Whole Blood


title: COVR-26 Day 1 (P4.H02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.H02

value: Asian

tag: symptomatic

tag: duration of illness

value: N


title: HC-32 Day 1 (P4.H01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.H01

value: Male

value: Fluzone High Dose


title: Control-2 control (P4.G12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.G12

value: control


title: HC-38 Day 1 (P4.G11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.G11

value: Flucelvax

value: Day 1


title: COVR-25 Day 7 (P4.G07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.G07

tag: long-covid symptoms

value: AE

tag: days since covid-19 diagnosis


title: HC-32 Day 7 (P4.G08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.G08

tag: tissue

tag: subject id


title: HC-33 Day 28 (P4.G10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.G10

tag: age at sample drawn

tag: Sex

value: Female

value: Multiple Race

value: Day 28


title: HC-38 Day 7 (P4.G09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.G09

tag: race

value: White

tag: ethnicity

value: HC


title: HC-37 Day 1 (P4.G05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.G05

value: Non-Hispanic

tag: group

tag: vaccine type


title: pBAD_yffP1000_mutCS, 1000 bp insert, mut SceI site

status: Public on Apr 17 2022

city: Moscow

first: Anastasiia

last: Okhtienko

address: Akademika Kurchatova square 2

country: Russia

institute: Institute of Molecular Genetics, Russian Academy of Sciences

data_processing:
All libraries were quality checked before further processing using FastQC (v0.11.9).
Trimmomatik (v0.36) was used to remove adapters, eliminate reads shorter than 14 bp and to cut reads longer than 24 bp.
Reads were aligned onto the reference genome E.coli (MG1655 Refseq: NC_000913.3 or BW25113 Refseq: CP009273.1) and plasmid (pBAD_CbAgo_lacI_full, pBAD_CbAgo_lacI_dec or pBAD_CS_yffP) via bowtie (v1.3.1) allowing zero mismatches and unique alignment
Alligned .sam files were converted to binary .bam, sorted using samtools (v. 1.15)
The E. coli  genome was divided into intervals of length 1 kb using custom Python script. bedtools (v2.30.0) was used to intersect the resulted bed file with the bam file. smDNA counts were expressed in terms of RPKM. Reads from “+” and “-” strands were selected with samtools view –F/ -f 16. For them, the coverage was calculated separately according to the method described above.
Assembly: NC_000913.3 / CP009273.1 with manually added CbAgo gene (802798-810180)
Supplementary files format and content: tsv files include count values for 1kb genome intervals (both strands and + / - separately)
Library strategy: DNA-seq (smDNA)

organism: Escherichia coli

growth_protocol: Cells from plate were grown in LB media supplemented with antibiotics and the  inducing agent (0.1% L-arabinose or/and anhydrotetracycline, 200 ng/ml)  at 18˚C until OD 600 = 1.0

extract_protocol:
Cells were collected by centrifugation (6000 g, 6 min at 4 °C) and pellets were frozen at -20 °C. Pellets were defrosted at room temperature and diluted with 30 ml lysis buffer (40 mM tris HCl pH 7.9, 150 mM NaCl) in the presence of ½ tb of protease inhibitor cocktail EDTA-free (Roche). After filtration using 170 mkm nylon filters samples were lysed using high-pressure homogenizer cell disruptor PEC at 30 kpsi twice and then centrifugated (17000 rpm R21A rotor Hitachi, 15 min at 4 °C twice). Clarified lysate was incubated with 0.3 ml prewashed Co2+beads (Clontech) for 140 min at +4 °C with rotation in top-bottom direction. Suspension was centrifugated 3 min 500 g at +4 °C, supernatant (flowthrough) was removed. Beads were washed twice with 25 ml ice-cold lysis buffer for 5 min, 4 times with 1 ml  lysis buffer 10 mM imidazole and CbAgo was eluted with lysis buffer contained 200 mM imidazole 0.33 ml 3 times. Fractions were analyzed using protein PAGE, 0.3 ml of each elution fraction was Proteinase K treated (100 μg, 1 h 37 °C) and elution fractions with CbAgo were combined. Deproteinazed samples were treated with 0.5 ml phenol-chloroform-isoamyl alcohol (25:24:1) pH 7.5-8, vortex for 10 seconds, centrifugated 2 min at 21000 g. Supernatant was washed twice with 0.5 ml chloroform. Nucleic acids from final aqueous phase were ethanol precipitated in the presence of PINK coprecipitant and 30 mM sodium acetate pH 5.0 for 1h in liquid nitrogen or overnight at -70 °C. Samples were centrifugated for 30 min, 21000 g at +4 °C and pellets were washed with 70% ice-cold EtOH. Air-dried pellets were diluted in nuclease-free water (40 mkl per sample). 10% of each sample was dephosphorylate using rSAP (NEB) in 1x PNK buffer for 30 min at 37 °C, rSAP was inactivated for 10 min at 75 °C. Dephosphorylated samples were subsequently radiolabelled with γ-P32-ATP using T4 polynucleotide kinase (NEB), oligos ladder (12-70 nt) was also radiolabelled at this point. Radiolabelled samples were mixed with correspondent 20 μl of nontreated samples and resolved on 19% PAGE gel with 8M urea in 1x TBE and visualized on a Typhoon FLA 9500 imager (GE Healthcare) with position labels. Gel slices corresponding to 14–22 nt were cut from gel and crushed in 0.4 M NaCl overnight at 20 °C with constant shaking 1000 rpm on bench tube shaker. Gel slices were removed and solution with nucleic acids was ethanol precipitated as described, DNA was resuspended in 20 μl nuclease-free water.
Small DNAs were ligated with Illumina-compatible adaptors. Samples (20 μl) were mixed with 8 μl of 5x Rapid Ligation buffer (ThermoFisher), 2 μl of 100 μM 5′-adaptor, 2 μl of 100 μM of 3′-linker, 2 μl of 100 μM bridge 1, 2 μl of 100 μM bridge 2 and 800 units of T4-ligase (NEB) and incubated 16 h at room temperature. Ligated DNA fragments were sliced from 19% urea PAGE and eluted from gel slices as described. The libraries were PCR amplified with RP1 and indexing primers (TrueSeq) and NEBNext Ultra II Q5 Master Mix with adjusting number of cycles using product visualization on 6% native PAGE gel with SYBR Gold staining. Amplified libraries were also cut from native 6% PAGE in blue light, and PCR products were extracted in 0.4 M NaCl and precipitated as described. smDNA libraries were sequenced using the HiSeq2500 platform (Illumina) in the rapid run mode (50-nucleotide single-end reads)

tag: strain

tag: genotype

value: BW27784 araB::PBAD-I-SceI lacIq lacZc- lacZ+

tag: plasmid


title: COVR-31 Day 7 (P4.G06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.G06

value: COVR

value: Y

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects

tag: visit

value: Day 7

tag: days since vaccination

tag: library plate


title: COVR-32 Day 28 (P4.G04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.G04

value: Whole Blood

tag: symptomatic

tag: duration of illness

tag: long-covid symptoms

tag: days since covid-19 diagnosis

tag: library well


title: HC-34 Day -7 (P4.G01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.G01

tag: tissue

tag: subject id

tag: age at sample drawn

tag: Sex

tag: race

value: Day -7


title: COVR-31 Day 0 (P4.F12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.F12

tag: ethnicity

tag: group

value: N

tag: vaccine type

value: Day 0


title: HC-39 Day 1 (P4.G02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.G02

value: Black

value: Flucelvax

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects


title: COVR-24 Day 1 (P4.F11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.F11

value: AE

tag: visit

value: Day 1

tag: days since vaccination


title: HC-31 Day -7 (P4.F10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.F10

value: Male

tag: library plate


title: COVR-30 Day -7 (P4.F09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.F09

tag: symptomatic

tag: duration of illness


title: COVR-24 Day 0 (P4.F08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.F08

value: Female

tag: long-covid symptoms

tag: days since covid-19 diagnosis


title: Control-1 control (P4.F05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.F05

tag: tissue

value: control

tag: library well


title: COVR-27 Day 1 (P4.F07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.F07

tag: subject id

tag: age at sample drawn

value: White


title: COVR-27 Day 7 (P4.F02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.F02

tag: Sex

tag: race

value: Non-Hispanic


title: HC-33 Day 1 (P4.F01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.F01

value: Multiple Race

tag: ethnicity

tag: group

value: HC


title: Control-1 control (P4.F03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.F03


title: HC-33 Day 0 (P4.F04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.F04

tag: vaccine type

tag: influenza vaccination count (previous 10 years)


title: HC-31 Day 28 (P4.F06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.F06

tag: vaccine side effects

tag: visit

value: Day 28


title: HC-31 Day 0 (P4.E09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.E09

tag: days since vaccination

tag: library plate


title: COVR-29 Day 1 (P4.E12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.E12

value: COVR

tag: symptomatic

value: Y

tag: duration of illness


title: COVR-26 Day 0 (P4.E07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.E07

value: Whole Blood

value: Asian

tag: long-covid symptoms

tag: days since covid-19 diagnosis


title: Control-2 control (P4.E10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.E10

tag: tissue

tag: library well


title: HC-35 Day 0 (P4.E08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.E08

tag: subject id

tag: age at sample drawn

value: Day 0


title: COVR-26 Day -7 (P4.E11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.E11

tag: Sex

tag: race

value: N

value: Day -7


title: HC-39 Day 7 (P4.E06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.E06

value: Black

tag: ethnicity

tag: group

value: Flucelvax

value: AE

value: Day 7


title: COVR-32 Day -7 (P4.G03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.G03

value: Male

tag: vaccine type

value: Fluzone High Dose

tag: influenza vaccination count (previous 10 years)


title: HC-35 Day -7 (P4.E04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.E04

value: Female

value: White

value: Non-Hispanic

tag: vaccine side effects

tag: visit


title: HC-32 Day 28 (P4.E02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.E02

value: HC

value: Day 28

tag: days since vaccination

tag: library plate


title: COVR-25 Day 28 (P4.D11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.D11

value: COVR

tag: symptomatic

value: Y

tag: duration of illness


title: HC-34 Day 1 (P4.D12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.D12

value: Whole Blood

value: Day 1


title: HC-36 Day 7 (P4.E01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.E01

value: Multiple Race

value: Hispanic or Latino


title: COVR-27 Day 0 (P4.D09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.D09

tag: long-covid symptoms

value: N

value: Day 0

tag: days since covid-19 diagnosis


title: HC-37 Day -7 (P4.D08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.D08

tag: tissue

value: Flucelvax

value: AE

value: Day -7

tag: library well


title: COVR-30 Day 28 (P4.D06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.D06

tag: subject id

tag: age at sample drawn

value: Male


title: COVR-31 Day -7 (P4.D07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.D07

tag: Sex

value: Female

tag: race


title: COVR-29 Day 7 (P4.D01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.D01

value: White

tag: ethnicity

tag: group

value: Day 7


title: HC-35 Day 28 (P4.D03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.D03

value: Non-Hispanic

value: HC

tag: vaccine type

tag: influenza vaccination count (previous 10 years)


title: COVR-31 Day 1 (P4.D02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.D02

value: COVR

tag: vaccine side effects

tag: visit


title: COVR-27 Day 28 (P4.C12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.C12

value: Y

value: Day 28

tag: days since vaccination

tag: library plate


title: HC-38 Day 0 (P4.C10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.C10

value: Whole Blood


title: HC-37 Day 7 (P4.C11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.C11


title: COVR-24 Day 7 (P4.D04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.D04

tag: symptomatic

tag: duration of illness


title: COVR-32 Day 7 (P4.C09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.C09

tag: long-covid symptoms

value: Fluzone High Dose

tag: days since covid-19 diagnosis


title: HC-35 Day 7 (P4.C07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.C07

tag: tissue

tag: library well


title: Control-1 control (P4.C06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.C06

tag: subject id

value: control


title: COVR-32 Day 1 (P4.C05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.C05

tag: age at sample drawn

tag: Sex

value: Day 1


title: COVR-25 Day -7 (P4.E05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.E05

tag: race

tag: ethnicity

value: N


title: COVR-31 Day 28 (P4.C03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.C03

tag: group

tag: vaccine type

value: Flucelvax


title: Control-1 control (P4.C04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.C04


title: COVR-30 Day 0 (P4.B11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.B11

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects

value: AE

value: Day 0


title: COVR-30 Day 1 (P4.C01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.C01

value: Male

tag: visit

tag: days since vaccination


title: HC-37 Day 0 (P4.B09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.B09

tag: library plate


title: COVR-24 Day -7 (P4.B12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.B12

value: Female

tag: symptomatic

tag: duration of illness

value: Day -7


title: HC-33 Day 7 (P4.B08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.B08

value: Multiple Race

value: Day 7


title: COVR-26 Day 7 (P4.D10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.D10

value: Asian

value: Non-Hispanic

tag: long-covid symptoms

tag: days since covid-19 diagnosis


title: HC-38 Day 28 (P4.C02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.C02

tag: tissue

value: White

value: HC

tag: library well


title: HC-36 Day 0 (P4.B06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.B06

value: Whole Blood

tag: subject id

tag: age at sample drawn

value: Hispanic or Latino


title: HC-35 Day 1 (P4.B05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.B05

tag: Sex

tag: race


title: COVR-29 Day 28 (P4.B04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.B04

tag: ethnicity

tag: group

value: COVR

value: Y

value: Day 28


title: HC-34 Day 0 (P4.B03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.B03

tag: vaccine type

value: Flucelvax

tag: influenza vaccination count (previous 10 years)


title: HC-36 Day -7 (P4.C08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.C08

tag: vaccine side effects

value: AE

tag: visit


title: HC-34 Day 28 (P4.B10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.B10

tag: days since vaccination

tag: library plate


title: COVR-29 Day -7 (P4.A09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.A09

tag: symptomatic

tag: duration of illness


title: HC-31 Day 1 (P4.A12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.A12

value: Day 1


title: COVR-28 Day -7 (P4.A08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.A08

value: Male

tag: long-covid symptoms

value: N

tag: days since covid-19 diagnosis


title: COVR-28 Day 0 (P4.A06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.A06

tag: tissue

value: Day 0

tag: library well


title: HC-33 Day -7 (P4.B02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.B02

tag: subject id

tag: age at sample drawn

value: Female

value: Multiple Race

value: Day -7


title: COVR-28 Day 7 (P4.B07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.B07

tag: Sex

tag: race

value: Non-Hispanic

value: Day 7


title: COVR-27 Day -7 (P4.A05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.A05

value: White

tag: ethnicity

tag: group


title: HC-31 Day 7 (P4.A04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.A04

value: Whole Blood

value: HC

tag: vaccine type

tag: influenza vaccination count (previous 10 years)


title: Control-2 control (P4.A11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.A11

tag: visit

value: control


title: COVR-26 Day 28 (P4.A03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.A03

value: Asian

value: COVR

value: Y

tag: vaccine side effects

tag: days since vaccination


title: HC-32 Day -7 (P4.A10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.A10

value: Fluzone High Dose

value: AE

tag: library plate


title: COVR-24 Day 28 (P4.A01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.A01

tag: symptomatic

tag: duration of illness

value: Flucelvax

value: Day 28


title: COVR-25 Day 0 (P4.A02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.A02

value: Male

tag: long-covid symptoms

value: N

value: Day 0

tag: days since covid-19 diagnosis


title: HC-30 Day 1 (P3.H11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.H11

tag: tissue

value: Multiple Race

value: Day 1

tag: library well


title: HC-22 Day 28 (P3.H10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.H10

tag: subject id

tag: age at sample drawn

value: Female

value: Non-Hispanic


title: COVR-21 Day 7 (P3.H09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.H09

value: Whole Blood

tag: Sex

tag: race

value: White

value: Day 7


title: HC-29 Day 1 (P3.H08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.H08

tag: ethnicity

tag: group

value: HC


title: COVR-17 Day 7 (P3.H05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.H05

value: COVR

tag: vaccine type

tag: influenza vaccination count (previous 10 years)


title: COVR-19 Day 0 (P3.H06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.H06

tag: vaccine side effects

tag: visit


title: COVR-22 Day 7 (P3.H07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.H07

value: Hispanic or Latino

value: Y

tag: days since vaccination

tag: library plate


title: COVR-25 Day 1 (P4.B01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.B01

tag: symptomatic

tag: duration of illness

value: AE


title: HC-25 Day 7 (P3.H04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.H04

value: Fluzone High Dose


title: Control-1 control (P3.G09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.G09

value: control


title: HC-25 Day 0 (P3.G12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.G12


title: HC-32 Day 0 (P4.A07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P4.A07

value: Male


title: HC-30 Day 28 (P3.G07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.G07

value: Flucelvax

value: Day 28


title: COVR-23 Day 0 (P3.H01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.H01

tag: long-covid symptoms

value: Day 0

tag: days since covid-19 diagnosis


title: HC-24 Day 1 (P3.H02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.H02

tag: tissue

value: Black

value: Day 1

tag: library well


title: HC-28 Day -7 (P3.G06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.G06

tag: subject id

tag: age at sample drawn

value: Female

value: Non-Hispanic

value: Day -7


title: COVR-21 Day 0 (P3.G08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.G08

value: Whole Blood

tag: Sex

tag: race

value: White

value: N


title: HC-24 Day -7 (P3.G11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.G11

tag: ethnicity

tag: group

value: HC


title: HC-28 Day 7 (P3.G02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.G02

tag: vaccine type

tag: influenza vaccination count (previous 10 years)

value: Day 7


title: HC-30 Day 7 (P3.G01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.G01

value: Multiple Race

tag: vaccine side effects

tag: visit


title: HC-29 Day 0 (P3.G05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.G05

value: Fluzone High Dose

tag: days since vaccination

tag: library plate


title: HC-21 Day -7 (P3.F11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.F11

value: Asian

value: AE


title: COVR-19 Day 7 (P3.G10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.G10

value: Male

value: COVR

tag: symptomatic

value: Flucelvax


title: HC-24 Day 28 (P3.F09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.F09

value: Black

value: Day 28


title: Control-1 control (P3.F12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.F12

value: control


title: HC-26 Day 28 (P3.F10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.F10

value: Hispanic or Latino


title: HC-27 Day 1 (P3.F06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.F06

value: Non-Hispanic

value: Day 1


title: HC-29 Day 7 (P3.F07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.F07

value: Whole Blood

value: Female

value: White


title: COVR-18 Day 7 (P3.F05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.F05

value: Y

tag: duration of illness

tag: long-covid symptoms

value: Day 7


title: COVR-22 Day -7 (P3.F08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.F08

tag: tissue

value: Multiple Race

value: N

value: Day -7

tag: days since covid-19 diagnosis


title: HC-24 Day 0 (P3.F04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.F04

tag: subject id

value: HC

value: Fluzone High Dose

value: AE

value: Day 0

tag: library well


title: COVR-16 Day 7 (P3.E12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.E12

tag: age at sample drawn

tag: Sex

value: COVR

value: Flucelvax


title: COVR-18 Day -7 (P3.F02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.F02

value: Male

tag: race

tag: ethnicity


title: COVR-23 Day 1 (P3.F03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.F03

value: Non-Hispanic

tag: group

tag: vaccine type


title: COVR-20 Day 1 (P3.H12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.H12

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects

value: Day 1


title: COVR-20 Day -7 (P3.F01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.F01

value: Whole Blood

tag: visit

tag: days since vaccination


title: HC-27 Day 7 (P3.H03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.H03

tag: library plate


title: HC-23 Day 28 (P3.G03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.G03

value: Female

value: Day 28


title: HC-30 Day -7 (P3.G04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.G04


title: HC-25 Day -7 (P3.E08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.E08

value: White


title: COVR-18 Day 0 (P3.E09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.E09

tag: symptomatic

value: Y

tag: duration of illness


title: Control-2 control (P3.E10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.E10

tag: tissue

value: control


title: COVR-21 Day 28 (P3.E04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.E04

tag: long-covid symptoms

value: N

tag: days since covid-19 diagnosis


title: COVR-19 Day 28 (P3.E02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.E02

tag: subject id

tag: library well


title: HC-25 Day 1 (P3.E06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.E06

tag: age at sample drawn

tag: Sex


title: COVR-21 Day 1 (P3.E05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.E05

tag: race

tag: ethnicity


title: COVR-22 Day 28 (P3.D11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.D11

value: Multiple Race

value: Hispanic or Latino

tag: group

tag: vaccine type


title: HC-26 Day 0 (P3.E01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.E01

value: HC

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects


title: HC-23 Day 0 (P3.E03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.E03

tag: visit

tag: days since vaccination


title: HC-23 Day -7 (P3.D10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.D10

value: Day -7

tag: library plate


title: HC-28 Day 0 (P3.D09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.D09

value: AE

value: Day 0


title: COVR-23 Day 28 (P3.E11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.E11

value: COVR

tag: symptomatic

tag: duration of illness

value: Flucelvax


title: HC-23 Day 1 (P3.D06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.D06

tag: tissue

value: Non-Hispanic


title: HC-30 Day 0 (P3.D12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.D12

value: Male


title: COVR-23 Day -7 (P3.D07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.D07

value: Whole Blood

tag: long-covid symptoms

tag: days since covid-19 diagnosis


title: HC-21 Day 1 (P3.D02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.D02

tag: subject id

value: Asian

value: Day 1

tag: library well


title: COVR-18 Day 28 (P3.D01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.D01

tag: age at sample drawn

tag: Sex

value: White

value: Day 28


title: COVR-20 Day 0 (P3.C11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.C11

value: Female

tag: race

tag: ethnicity

value: Y


title: COVR-22 Day 0 (P3.D04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.D04

value: Multiple Race

tag: group

value: N

tag: vaccine type

value: Healthy


title: Control-1 control (P3.D05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.D05

value: control


title: HC-22 Day 0 (P3.C09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.C09

value: HC

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects

value: AE


title: HC-29 Day -7 (P3.C10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.C10

value: Fluzone High Dose

tag: visit

value: Day -7

tag: days since vaccination


title: COVR-22 Day 1 (P3.D03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.D03

value: Hispanic or Latino

value: COVR

tag: symptomatic

value: Flucelvax

tag: library plate


title: COVR-17 Day 28 (P3.C07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.C07

tag: tissue

value: Whole Blood

value: Non-Hispanic

tag: duration of illness


title: HC-29 Day 28 (P3.C06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.C06

value: White


title: COVR-20 Day 7 (P3.C08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.C08

tag: long-covid symptoms

value: Day 7

tag: days since covid-19 diagnosis


title: HC-27 Day -7 (P3.E07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.E07

tag: subject id

value: Male

tag: library well


title: HC-26 Day 7 (P3.C04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.C04

tag: age at sample drawn

tag: Sex


title: HC-28 Day 1 (P3.C05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.C05

value: Female

tag: race

tag: ethnicity

value: Day 1


title: HC-28 Day 28 (P3.B12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.B12

tag: group

tag: vaccine type

value: Day 28


title: COVR-20 Day 28 (P3.B11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.B11

value: Y

value: N

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects


title: COVR-23 Day 7 (P3.D08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.D08

tag: visit

tag: days since vaccination


title: COVR-19 Day 1 (P3.C01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.C01

tag: symptomatic

tag: library plate


title: COVR-17 Day -7 (P3.C02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.C02

tag: tissue

tag: duration of illness


title: COVR-21 Day -7 (P3.C03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.C03

tag: long-covid symptoms

tag: days since covid-19 diagnosis


title: COVR-16 Day -7 (P3.B05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.B05

tag: subject id

tag: library well


title: COVR-16 Day 28 (P3.B06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.B06

tag: age at sample drawn

tag: Sex


title: HC-27 Day 0 (P3.C12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.C12

tag: race

tag: ethnicity

value: HC

value: Day 0


title: Control-1 control (P3.B07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.B07

value: control


title: HC-26 Day 1 (P3.B09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.B09

value: Multiple Race

tag: group

tag: vaccine type

value: AE


title: Control-1 control (P3.B02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.B02


title: HC-21 Day 28 (P3.B10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.B10

value: Asian

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects


title: HC-24 Day 7 (P3.A08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.A08

value: Black

value: Fluzone High Dose

tag: visit

tag: days since vaccination


title: COVR-16 Day 0 (P3.B08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.B08

value: Whole Blood

value: Non-Hispanic

value: COVR

tag: symptomatic

value: Flucelvax

tag: library plate


title: HC-27 Day 28 (P3.B04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.B04

tag: tissue

value: Male

value: White


title: COVR-17 Day 0 (P3.A09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.A09

value: Female

tag: duration of illness

tag: long-covid symptoms


title: HC-25 Day 28 (P3.A10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.A10

tag: subject id

value: Day 28


title: COVR-17 Day 1 (P3.B01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.B01

value: Y

value: N

value: Day 1

tag: days since covid-19 diagnosis

tag: library well


title: COVR-19 Day -7 (P3.A12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.A12

tag: age at sample drawn

tag: Sex

value: Day -7


title: HC-26 Day -7 (P3.B03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.B03

tag: race

value: Multiple Race

tag: ethnicity

value: Hispanic or Latino

value: HC


title: HC-21 Day 0 (P3.A06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.A06

value: Asian

tag: group

tag: vaccine type

value: AE

value: Day 0


title: HC-22 Day -7 (P3.A04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.A04

value: Whole Blood

value: Non-Hispanic

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects


title: HC-23 Day 7 (P3.A05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.A05

value: Flucelvax

tag: visit

value: Day 7

tag: days since vaccination


title: COVR-16 Day 1 (P3.A03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.A03

value: White

value: COVR

tag: symptomatic

tag: library plate


title: HC-22 Day 7 (P3.A02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.A02

tag: tissue

value: Female


title: HC-22 Day 1 (P3.A07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.A07


title: HC-21 Day 7 (P3.A01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.A01

value: Male


title: HC-15 Day 28 (P2.H10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.H10

value: Day 28


title: COVR-13 Day -7 (P2.H07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.H07

value: Y

tag: duration of illness

tag: long-covid symptoms

value: N


title: HC-16 Day -7 (P2.H11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.H11

tag: subject id

value: Day -7


title: HC-18 Day 0 (P2.H09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.H09

tag: library well


title: HC-15 Day 1 (P2.H04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.H04

tag: age at sample drawn

value: Healthy

value: Day 1


title: HC-18 Day 1 (P2.H05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.H05

tag: Sex

value: Asian

value: HC


title: COVR-9 Day 1 (P2.H08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.H08

tag: race

value: Hispanic or Latino

value: AE

tag: days since covid-19 diagnosis


title: COVR-7 Day 0 (P2.H03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.H03

value: Whole Blood

tag: ethnicity

value: Non-Hispanic

tag: group

value: Fluzone High Dose

value: Day 0


title: COVR-18 Day 1 (P3.A11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P3.A11

value: White

value: COVR

tag: vaccine type

value: Flucelvax

tag: influenza vaccination count (previous 10 years)


title: Control-1 control (P2.H02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.H02

tag: visit

value: control


title: Control-1 control (P2.H01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.H01


title: HC-16 Day 1 (P2.G12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.G12

value: Female

tag: vaccine side effects

tag: days since vaccination


title: COVR-12 Day 7 (P2.G09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.G09

tag: symptomatic

value: Y

value: Day 7

tag: library plate


title: COVR-11 Day 0 (P2.G11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.G11

tag: tissue

value: N


title: COVR-15 Day 1 (P2.G06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.G06

value: Male

tag: duration of illness

tag: long-covid symptoms

value: Day 1


title: COVR-12 Day 0 (P2.G10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.G10

tag: subject id

tag: library well


title: COVR-8 Day -7 (P2.G01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.G01

tag: age at sample drawn

tag: Sex

value: Day -7


title: COVR-14 Day -7 (P2.F11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.F11

tag: race

value: Multiple Race

value: Hispanic or Latino

tag: days since covid-19 diagnosis


title: COVR-14 Day 1 (P2.F10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.F10

value: Whole Blood

tag: ethnicity

tag: group


title: COVR-15 Day 0 (P2.G05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.G05

value: Non-Hispanic

tag: vaccine type

tag: influenza vaccination count (previous 10 years)


title: HC-13 Day 0 (P2.G08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.G08

value: HC

value: Fluzone High Dose

tag: vaccine side effects

value: AE

tag: visit


title: HC-14 Day 28 (P2.F07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.F07

value: White

value: Day 28

tag: days since vaccination


title: HC-19 Day 28 (P2.F08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.F08

value: Asian

value: Flucelvax

tag: library plate


title: COVR-10 Day 1 (P2.H12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.H12

tag: tissue

value: Female

value: COVR

tag: symptomatic

value: Y


title: COVR-7 Day -7 (P2.F09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.F09

tag: duration of illness

tag: long-covid symptoms

value: N


title: COVR-11 Day -7 (P2.F06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.F06

tag: subject id

tag: library well


title: HC-15 Day 0 (P2.H06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.H06

tag: age at sample drawn

tag: Sex

value: Day 0


title: COVR-11 Day 1 (P2.F05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.F05

tag: race

value: Day 1


title: COVR-12 Day 1 (P2.F03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.F03

tag: ethnicity

tag: days since covid-19 diagnosis


title: COVR-12 Day -7 (P2.F02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.F02

tag: group

tag: vaccine type

value: Day -7


title: COVR-15 Day 28 (P2.F04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.F04

value: Male

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects


title: Control-2 control (P2.E12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.E12

value: Whole Blood

tag: visit

value: control


title: COVR-13 Day 1 (P2.E09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.E09

value: Non-Hispanic

tag: days since vaccination

tag: library plate


title: HC-12 Day 7 (P2.E08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.E08

tag: tissue

value: HC

value: Day 7


title: COVR-14 Day 28 (P2.G07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.G07

value: Multiple Race

value: Hispanic or Latino

tag: symptomatic

tag: duration of illness


title: Control-1 control (P2.E07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.E07

tag: subject id


title: HC-18 Day 28 (P2.E11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.E11

value: Asian

value: AE

value: Day 28

tag: library well


title: HC-13 Day -7 (P2.E04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.E04

tag: age at sample drawn

value: Female

value: White

value: Fluzone High Dose


title: HC-17 Day -7 (P2.E05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.E05

tag: Sex

value: Flucelvax


title: HC-17 Day 7 (P2.F12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.F12

tag: race


title: COVR-10 Day 7 (P2.G02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.G02

tag: ethnicity

value: COVR

value: Y

tag: long-covid symptoms


title: COVR-15 Day -7 (P2.D12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.D12

value: Male

tag: group

value: N

value: Day -7

tag: days since covid-19 diagnosis


title: HC-20 Day 28 (P2.E01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.E01

value: Whole Blood

value: Non-Hispanic

tag: vaccine type

tag: influenza vaccination count (previous 10 years)


title: COVR-14 Day 0 (P2.D11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.D11

tag: vaccine side effects

tag: visit

value: Day 0


title: HC-20 Day 7 (P2.D10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.D10

value: HC

value: Day 7

tag: days since vaccination

tag: library plate


title: HC-20 Day 0 (P2.D09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.D09

tag: tissue


title: HC-20 Day 1 (P2.D07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.D07

value: Day 1


title: COVR-9 Day 7 (P2.D06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.D06

value: Hispanic or Latino

tag: symptomatic

tag: duration of illness

value: AE


title: HC-19 Day -7 (P2.D05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.D05

tag: subject id

value: Female

value: Asian

tag: library well


title: HC-17 Day 1 (P2.D02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.D02

tag: age at sample drawn

tag: Sex

value: White


title: COVR-13 Day 7 (P2.D04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.D04

tag: race

tag: ethnicity

value: Flucelvax


title: COVR-8 Day 0 (P2.D03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.D03

tag: group

value: COVR

tag: long-covid symptoms


title: HC-19 Day 1 (P2.F01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.F01

tag: vaccine type


title: HC-18 Day 7 (P2.C12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.C12

tag: influenza vaccination count (previous 10 years)


title: HC-13 Day 28 (P2.E06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.E06

value: Fluzone High Dose

tag: vaccine side effects

value: Day 28


title: HC-19 Day 0 (P2.C11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.C11

tag: visit


title: HC-18 Day -7 (P2.C07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.C07

tag: days since vaccination


title: HC-16 Day 28 (P2.C06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.C06

tag: library plate


title: COVR-14 Day 7 (P2.C08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.C08

tag: tissue

value: Male

value: Multiple Race

value: Y

value: N

tag: days since covid-19 diagnosis


title: HC-17 Day 0 (P2.C05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.C05

value: Whole Blood

value: Non-Hispanic

value: Day 0


title: HC-12 Day 1 (P2.C10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.C10

value: HC

value: Day 1


title: COVR-11 Day 7 (P2.C04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.C04

tag: symptomatic

value: Day 7


title: HC-15 Day -7 (P2.C03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.C03

tag: subject id

value: Female

value: Day -7


title: HC-12 Day 28 (P2.E02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.E02

value: White

value: AE

tag: library well


title: COVR-13 Day 28 (P2.B12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.B12

tag: age at sample drawn

value: COVR

tag: duration of illness

value: Flucelvax


title: COVR-13 Day 0 (P2.B11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.B11

tag: Sex

tag: race


title: HC-16 Day 7 (P2.C01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.C01

tag: ethnicity

tag: group


title: COVR-9 Day 28 (P2.B10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.B10

value: Hispanic or Latino

tag: long-covid symptoms

tag: vaccine type

value: Day 28


title: HC-20 Day -7 (P2.D08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.D08

value: Male

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects


title: HC-14 Day -7 (P2.B08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.B08

tag: visit

tag: days since vaccination


title: HC-12 Day 0 (P2.B06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.B06

tag: tissue

tag: library plate


title: COVR-8 Day 7 (P2.B09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.B09

tag: symptomatic

value: Y

tag: days since covid-19 diagnosis


title: COVR-12 Day 28 (P2.B05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.B05

tag: subject id

tag: library well


title: HC-16 Day 0 (P2.B07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.B07

tag: age at sample drawn


title: HC-14 Day 0 (P2.B04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.B04

tag: Sex


title: COVR-10 Day 28 (P2.B03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.B03

tag: race

tag: duration of illness


title: COVR-11 Day 28 (P2.B02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.B02

tag: ethnicity

tag: group

value: N


title: COVR-10 Day 0 (P2.D01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.D01

value: Whole Blood

tag: long-covid symptoms

tag: vaccine type


title: COVR-8 Day 1 (P2.A11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.A11

value: Non-Hispanic

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects


title: HC-14 Day 1 (P2.B01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.B01

tag: visit

tag: days since vaccination


title: HC-19 Day 7 (P2.C09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.C09

tag: tissue

value: Asian

tag: library plate


title: HC-15 Day 7 (P2.A12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.A12

value: HC


title: COVR-9 Day 0 (P2.A09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.A09

tag: symptomatic

value: Day 0

tag: days since covid-19 diagnosis


title: COVR-8 Day 28 (P2.A08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.A08

tag: subject id

tag: library well


title: HC-17 Day 28 (P2.E03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.E03

tag: age at sample drawn

tag: Sex


title: Control-2 control (P2.A05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.A05

value: control


title: HC-14 Day 7 (P2.A06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.A06

tag: race

value: Day 7


title: HC-13 Day 1 (P2.A07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.A07

value: Female

tag: ethnicity

value: Fluzone High Dose

value: Day 1


title: Control-1 control (P2.A02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.A02


title: HC-13 Day 7 (P2.A04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.A04

value: White

tag: group

value: AE


title: COVR-7 Day 28 (P2.A01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.A01

value: COVR

tag: duration of illness

tag: long-covid symptoms


title: COVR-6 Day 0 (P1.H11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.H11

tag: vaccine type

value: Flucelvax

tag: influenza vaccination count (previous 10 years)


title: COVR-6 Day 1 (P1.H10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.H10

value: Male

tag: vaccine side effects

tag: visit


title: HC-3 Day 7 (P1.H09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.H09

tag: tissue

tag: days since vaccination


title: COVR-4 Day 0 (P1.H08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.H08

tag: symptomatic

value: Y

tag: library plate


title: COVR-3 Day 7 (P1.H05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.H05

tag: subject id

value: N

tag: days since covid-19 diagnosis


title: HC-1 Day 7 (P1.H03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.H03

value: Whole Blood

tag: age at sample drawn

tag: library well


title: HC-4 Day 1 (P1.H02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.H02

tag: Sex

tag: race

value: Black

value: Non-Hispanic


title: COVR-5 Day 0 (P1.H01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.H01

tag: ethnicity

tag: group


title: COVR-1 Day 1 (P1.G11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.G11

tag: duration of illness

tag: long-covid symptoms


title: HC-9 Day 0 (P1.G09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.G09

value: Asian

value: HC

tag: vaccine type

tag: influenza vaccination count (previous 10 years)


title: HC-2 Day -7 (P1.G12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.G12

tag: vaccine side effects

tag: visit

value: Day -7


title: COVR-10 Day -7 (P2.A10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.A10

tag: tissue

tag: days since vaccination


title: HC-10 Day -7 (P1.H04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.H04

tag: library plate


title: HC-3 Day 7 (P1.G06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.G06

tag: subject id

value: Day 7


title: HC-8 Day 7 (P1.G04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.G04


title: COVR-3 Day 1 (P1.G02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.G02

tag: symptomatic

tag: days since covid-19 diagnosis


title: COVR-2 Day 1 (P1.F12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.F12

tag: age at sample drawn

value: Female

tag: library well


title: HC-7 Day 28 (P1.G03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.G03

tag: Sex

tag: race

value: Day 28


title: HC-5 Day 28 (P1.F10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.F10

tag: ethnicity

value: Hispanic or Latino

tag: group


title: HC-12 Day -7 (P2.A03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P2.A03

value: White


title: HC-9 Day 7 (P1.F08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.F08

value: AE


title: COVR-3 Day 28 (P1.F09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.F09

value: COVR

tag: duration of illness

tag: long-covid symptoms

value: Fluzone High Dose


title: HC-11 Day 0 (P1.G05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.G05

value: Male

tag: vaccine type

tag: influenza vaccination count (previous 10 years)

value: Day 0


title: HC-9 Day -7 (P1.F04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.F04

value: Flucelvax

tag: vaccine side effects

tag: visit


title: HC-8 Day 1 (P1.F03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.F03

tag: tissue

value: Whole Blood

value: Day 1

tag: days since vaccination


title: COVR-6 Day 28 (P1.H06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.H06

tag: subject id

value: Non-Hispanic

value: Y

value: N

tag: library plate


title: HC-5 Day 0 (P1.F05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.F05

value: Black

value: HC


title: HC-2 Day 1 (P1.F01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.F01


title: HC-3 Day 1 (P1.E12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.E12


title: COVR-2 Day 7 (P1.F02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.F02

value: Female

tag: symptomatic

value: Day 7

tag: days since covid-19 diagnosis


title: HC-10 Day 1 (P1.E11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.E11

tag: age at sample drawn

tag: library well


title: HC-5 Day 1 (P1.E09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.E09

tag: Sex

tag: race

value: Hispanic or Latino


title: COVR-2 Day -7 (P1.E10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.E10

tag: ethnicity

tag: group

value: Day -7


title: HC-4 Day -7 (P1.E08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.E08

value: AE


title: HC-2 Day 28 (P1.E06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.E06

value: White

value: Day 28


title: HC-11 Day 7 (P1.F11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.F11

value: Male

value: Fluzone High Dose


title: HC-11 Day 28 (P1.E03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.E03


title: HC-6 Day 0 (P1.E04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.E04

value: Flucelvax

value: Day 0


title: HC-3 Day 0 (P1.E02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.E02

value: Whole Blood


title: HC-9 Day 28 (P1.D12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.D12

value: Asian

value: Non-Hispanic


title: Control-2 control (P1.E01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.E01

value: control


title: COVR-6 Day -7 (P1.E05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.E05

value: COVR

value: Y

tag: duration of illness

tag: long-covid symptoms

value: N


title: HC-11 Day 1 (P1.D10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.D10

value: HC

tag: vaccine type

tag: influenza vaccination count (previous 10 years)

value: Day 1


title: COVR-5 Day 7 (P1.D06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.D06

value: Female

tag: vaccine side effects

tag: visit

value: Day 7


title: COVR-4 Day 28 (P1.D07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.D07

tag: tissue

value: White

tag: days since vaccination


title: HC-1 Day -7 (P1.G10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.G10

tag: subject id

value: AE

value: Day -7

tag: library plate


title: COVR-5 Day 28 (P1.D11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.D11

tag: symptomatic

value: Day 28

tag: days since covid-19 diagnosis


title: HC-2 Day 0 (P1.D05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.D05

tag: age at sample drawn

value: Male

value: Fluzone High Dose

tag: library well


title: HC-4 Day 28 (P1.F06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.F06

value: Whole Blood

tag: Sex

tag: race

value: Black

value: Flucelvax


title: COVR-5 Day 1 (P1.D03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.D03

tag: ethnicity

value: Non-Hispanic

tag: group


title: COVR-5 Day -7 (P1.D08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.D08

value: COVR

tag: duration of illness

tag: long-covid symptoms


title: HC-11 Day -7 (P1.D04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.D04

tag: vaccine type

tag: influenza vaccination count (previous 10 years)


title: HC-7 Day 7 (P1.C12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.C12

tag: vaccine side effects

tag: visit


title: COVR-4 Day 1 (P1.D01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.D01

tag: tissue

value: Y

tag: days since vaccination


title: HC-3 Day 28 (P1.C11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.C11

tag: subject id

tag: library plate


title: HC-8 Day 28 (P1.D09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.D09


title: HC-10 Day 0 (P1.D02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.D02

value: Day 0


title: HC-10 Day 28 (P1.C09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.C09

value: HC


title: HC-7 Day 0 (P1.C08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.C08


title: COVR-2 Day 0 (P1.C04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.C04

tag: symptomatic

value: N

tag: days since covid-19 diagnosis


title: COVR-1 Day 7 (P1.C06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.C06

tag: age at sample drawn

value: Female

tag: library well


title: HC-10 Day 7 (P1.C10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.C10

tag: Sex

tag: race

value: Day 7


title: HC-6 Day 7 (P1.G01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.G01

value: White

tag: ethnicity

tag: group


title: HC-3 Day 1 (P1.C03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.C03

value: Day 1


title: COVR-1 Day 28 (P1.C02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.C02

tag: duration of illness

tag: long-covid symptoms

value: AE


title: COVR-4 Day 7 (P1.B12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.B12

tag: vaccine type

tag: influenza vaccination count (previous 10 years)


title: HC-8 Day -7 (P1.B08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.B08

tag: vaccine side effects

tag: visit

value: Day -7


title: HC-7 Day 1 (P1.B09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.B09

tag: tissue

value: Male

tag: days since vaccination


title: HC-9 Day 1 (P1.B10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.B10

tag: subject id

value: Asian

tag: library plate


title: COVR-4 Day -7 (P1.B11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.B11

value: Whole Blood

tag: symptomatic

tag: days since covid-19 diagnosis


title: COVR-3 Day -7 (P1.B07)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.B07

tag: age at sample drawn

value: Fluzone High Dose

tag: library well


title: HC-8 Day 0 (P1.B06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.B06

tag: Sex

tag: race


title: HC-3 Day -7 (P1.B05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.B05

tag: ethnicity

tag: group


title: HC-6 Day 28 (P1.B03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.B03

value: Flucelvax

value: Day 28


title: HC-1 Day 28 (P1.B04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.B04

value: Non-Hispanic


title: HC-5 Day 7 (P1.B01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.B01

value: Black

value: Hispanic or Latino


title: COVR-3 Day 0 (P1.A10)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.A10

value: COVR

value: Y

tag: duration of illness

tag: long-covid symptoms

value: Day 0


title: HC-6 Day -7 (P1.A11)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.A11

value: Female

value: HC

tag: vaccine type

tag: influenza vaccination count (previous 10 years)


title: HC-7 Day -7 (P1.B02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.B02

value: White

tag: vaccine side effects

tag: visit


title: HC-4 Day 0 (P1.A05)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.A05

tag: tissue

value: AE

tag: days since vaccination


title: HC-6 Day 1 (P1.A12)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.A12

tag: subject id

value: Day 1

tag: library plate


title: COVR-2 Day 28 (P1.A09)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.A09

tag: symptomatic

value: N

tag: days since covid-19 diagnosis


title: HC-2 Day 7 (P1.A02)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.A02

tag: age at sample drawn

value: Male

value: Day 7

tag: library well


title: HC-3 Day 0 (P1.A06)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.A06

value: Whole Blood

tag: Sex

tag: race

value: Fluzone High Dose


title: HC-1 Day 1 (P1.A08)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.A08

tag: ethnicity

tag: group

value: Flucelvax


title: HC-1 Day 0 (P1.A01)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.A01

value: Non-Hispanic


title: HC-3 Day -7 (P1.A04)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.A04

value: Day -7


title: COVR-1 Day 0 (P1.A03)

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.A03

tag: duration of illness

tag: long-covid symptoms


title: baf180-s81-prol1

status: Public on Mar 04 2022

city: Farmington

first: Sabriya

last: Syed

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

data_processing:
Basecalling performed by BGI
Sequenced reads were processed using the SOAPnuke software.  Reads were trimmed for the adaptor sequence and filtered for low quality reads and stored in FASTQ format.
HISAT2 was used for genome mapping to mm10 after which a complete reference transcriptome was generated using StringTie, Cufflinks and CPC.
The SOAPnuke output was then mapped to the reference transcriptome using Bowtie2 and RSEM was used to calculate gene expression levels.
Differential gene expression was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: C2C12_Baf180 shRNAs

growth_protocol: Mouse C2C12 cells (obtained from ATCC) were maintained at sub-confluent densities in proliferation media containing Dulbecco’s Modified Eagle’s Medium (DMEM, #11965118, Gibco) supplemented with 10% calf serum (#26140079, Gibco) and 1% pen/strep (#15140163, Gibco).

extract_protocol:
TRIzol was used to harvest total RNA from proliferating C2C12 myoblasts transduced with lentivirus for scr, Brd9, Baf180 and Baf250A shRNA.
RNA libraries were prepared by the Beijing Genomics Institute (BGI) for sequencing on a BGISEQ-500

treatment_protocol: Proliferating C2C12 myoblasts were transduced with lentivirus for a control sequence shRNA (scr) and shRNA against Brd9, Baf180, Baf250A in the presence of 8 µg/ml polybrene and selected with 2 µg/ml puromycin (Invitrogen). Transduced myoblasts were maintained with 1 µg/ml puromycin.

tag: cell line

tag: cell type

value: mouse myoblast cell line

tag: genotype/variation

value: Baf180 shRNAs


title: baf250-s06-prol1

source_name: C2C12_Baf250A shRNAs

value: Baf250A shRNAs


title: brd9-s39-prol2

source_name: C2C12_Brd9 shRNAs

value: Brd9 shRNAs


title: brd9-s39-prol1


title: scr-prol1

source_name: C2C12_scramble shRNAs

value: scramble shRNAs


title: scr-prol2


title: GM12878_HiCAR_rep2

status: Public on Feb 28 2022

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

data_processing:
reads were aligned to hg38 reference genome using bwa mem with flags -SP.
Alignments were parsed and paired end tags (PET) were generated using the pairtools
PET with low mapping quality (MAPQ < 10) were filtered out. PET with the same coordinate on the genome or mapped to the same digestion fragment were removed.
Uniquely mapped PET were then flipped as side1 with the lower genomic coordinate and aggregated into contact matrices in the cooler  format using the cooler tools
MPAS is used to call the significant chromatin interaction.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: Chromatin interactions  called by MAPS, provided in BEDPE formate. Raw_count for RNA-seq libraries generated by feature counts.

growth_protocol: WA01 were cultured in Matrigel (corning, 354230) coated plates with Stabilized feeder-free maintenance medium mTeSRTM Plus (STEMCELL, #05825). mTeSRTM Plus was changed every other day.  GM12878 cells were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks, cells were maintained between 200,000-800,000 cells/ml. mESCs  were cultured in KnockOut™ Serum Replacement with Leukemia Inhibitory Factor (LIF)

extract_protocol:
For crosslinking, cells were washed once by PBS, then treated by accutase (biolegend, #423201) for 10mins at 37°C. After removing the accutase, cells were resuspended by DMEM. Formaldehyde was added to the final concentration of 1%, incubated at room temperature for 10mins. Glycine was added to the final concentration of 0.2M, incubated at room temperature for 10 mins to quench formaldehyde.
HiCAR libraries were constructed following the method in the HiCAR manuascript. RNA libaraies were constructed following the SMART-seq2 protocol.
HiCAR


title: GM12878_HiCAR_rep4

data_processing:
Reads were aligned to hg38 reference genome using bwa mem with flags -SP.
Alignments were parsed and paired end tags (PET) were generated using the pairtools
PET with low mapping quality (MAPQ < 10) were filtered out.
Uniquely mapped PET were then flipped as side1 with the lower genomic coordinate and aggregated into contact matrices in the cooler  format using the cooler tools
MAPS is used to call the significant chromatin interaction fro HiCAR library.
Genome_build: hg38
Supplementary_files_format_and_content: Chromatin interactions  identified by MAPS, provided in BEDPE formate.

growth_protocol: WA01 were cultured in Matrigel (corning, 354230) coated plates with Stabilized feeder-free maintenance medium mTeSRTM Plus (STEMCELL, #05825). mTeSRTM Plus was changed every other day.  GM12878 cells were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks, cells were maintained between 200,000-800,000 cells/ml.

extract_protocol:
For crosslinking, cells were washed once by PBS, then treated by accutase (biolegend, #423201) for 10mins at 37°C. After removing the accutase, cells were resuspended by DMEM. Formaldehyde was added to the final concentration of 1%, incubated at room temperature for 10mins. Glycine was added to the final concentration of 0.2M, incubated at room temperature for 10 mins to quench formaldehyde.
HiCAR libraries were constructed following the method in the HiCAR manuascript.

treatment_protocol: For NPC induction, the transgenic WA01 were seeded onto Matrigel coated 24-well plates at 200k-400k cells per well. And cultured in STEMdiff™ SMADi Neural Induction media (Stemcell Catalog # 08581). Media was changed every day. Cells were harvested at the end of day 3.  For ME induction, the transgenic WA01 were seeded onto Matrigel coated at a density of around 1x104 cells/cm2 and cultured in differentiation media (E8 with 5ng/ml BMP4 and 25ng/ml Activin A). Media was changed every day. Cells were harvested at the end of day2.


title: GM12878_HiCAR_rep3


title: GM12878_HiCAR_rep1