title: HeLa_Val_B

city: Epalinges

first: Manuele

last: Rebsamen

address: Chemin des Boveresses 155 - CP 51

department: Department of Biochemistry

institute: University of Lausanne

description: RNA-Seq (3' end)

data_processing:
Basecalling: Illumina2bam, version 1.17
Adapter and quality trimming: cutadapt, version 1.16
Mapping: STAR, version 2.5.2b
Quantification: ESAT
Assembly: hg38
Supplementary files format and content: count_tbl.tsv: Tab-separated text file includes counts.

growth_protocol: HeLa were provided by M. Hentze and checked for mycoplasma infection by PCR or ELISA. Cell lines were authenticated by STR profiling. Cells were kept in DMEM (Gibco or Sigma) supplemented with 10% (v/v) FBS (Gibco) and antibiotics (100 U/ml penicillin and 100 mg/ml streptomycin, Gibco or Sigma) and shifted to specific nutrient restricted media for the different assay.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini kit including a DNase I digest step.
RNA-sequencing (RNA-seq) libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) according to the manufacturer’s protocol.

treatment_protocol: HeLa cells were seeded in full media (DMEM Gibco, 10% FBS, antibiotics). After 24h, media was removed, and after a wash with PBS, substituted with DMEM media lacking the indicated amino acid supplemented with 10% dialyzed FBS (Gibco cat. 26400-044). Starvation media lacking a specific amino acid were prepared by complementing amino acid free DMEM media (i.e., devoid of all 15 amino acids normally present, custom made by PAN biotech) with the other 14 amino acids (from individual powders, SIGMA). DMEM media reconstituted with all 15 amino acids and 10% dialyzed FBS as well as full media served as controls. After 16h, media was removed and cells were harvested in cold PBS.

value: HeLa

tag: cell type compact id

tag: condition (depleted compound)

value: Val


title: HeLa_Tyr_B

status: Public on Mar 26 2022

type: SRA

country: Switzerland

description: RNA-Seq (3' end)

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

source_name: cell line

tag: cell line

value: Tyr


title: 15L_SW620_PBS

city: Saugus

first: Michael

last: Raabe

state: MA

address: 3214 Founders Way

country: USA

institute: Massachusetts General Hospital

data_processing:
reads trimmed and quality checked using skewer
aligned to hg38 and repeat elements using STAR
reads assigned to genes and repeats (Gencode and repeat masker) using featureCounts
unassigned reads remapped to Repbase consensus sequence
Assembly: GRCH38; REP
Supplementary files format and content: rawcounts in .tsv format

molecule: total RNA

source_name: xenograft

growth_protocol: For 3D culture (tumorspheres), serum-free media (RPMI, DMEM, or DMEM/F12) was supplemented with 20 μl/ml B27+ 20 ng/ml EGF + 20 ng/ml bFGF (ThermoFisher). Cells were plated in ultra-low attachment plates (Corning). For xenografts, SW620 or HCT116 cell lines stably transduced with Luciferase (1 x 106) were injected in the flank of six-week old female nude mice (Charles River Laboratories) at a 1:1 ratio with Matrigel (Sigma Aldrich).

extract_protocol:
RNA was isolated using Trizol reagent (ThermoFisher) or the AllPrep DNA/RNA/protein mini kit (Qiagen #80004) according to manufacturer recommendations. For ChIP-seq, HCT116, HCT8, DLD1, and SW620 cells were cross-linked with formaldehyde (1% final) for 10 min at room temperature. Cross-linked cells were quenched with glycine (125 mM final) for 5 min, followed by two washes in cold PBS. Nuclei were then isolated from 20 million cells as previously described (67), and chromatin was sheared to 250-bp average size using a Covaris S220. Immunoprecipitations were performed using 1000 μg of sheared chromatin lysate and 5 μg of p53 antibody (p53 D07; Santa Cruz, sc-47698) preconjugated to protein G beads (Invitrogen). ChIP reactions were incubated for 16 hours at 4°C with rotation and then washed four times in wash buffer [50 mM Hepes-HCl (pH 8), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, and 0.5% N-laurylsarcosine], followed by one wash in ChIP final wash buffer (1× tris-EDTA (TE) Buffer and 50 mM NaCl). Immunoprecipitated DNA was eluted from washed beads, reverse cross-linked overnight, purified, and used to construct libraries.
Clontech/Takara SMARTer Stranded Total RNA-seq PICO v2 kit (Clontech/Takara 634414) for RNA-seq. For ChIP-seq, libraries were prepared using NEBNext Ultra reagents (New England Biolabs).

treatment_protocol: For cell lines in 3D culture, cell lines were treated with DMSO or 1-10 micromolar 3TC for 1 or 7 days before extraction. For Xenografts, mice were randomized and divided into treatment arms: Control (PBS), and Lamivudine (3TC).  3TC was solubilized in PBS and administered intraperitoneally at a dosage of 50 mg/kg 3 times a week. In the control group, PBS was administered intraperitoneally. Mice were treated for 20 days, and tumor volume was measured every 5 days through IVIS imaging. At 20 days mice were euthanized according to IACUC guidelines.

tag: sequencing pool

tag: treatment

value: PBS


title: HeLa_Thr_B

description: RNA-Seq (3' end)

value: Thr


title: HeLa_Gln_B

description: RNA-Seq (3' end)

value: Gln


title: HeLa_Trp_B

description: RNA-Seq (3' end)

value: Trp


title: HeLa_Lys_B

description: RNA-Seq (3' end)

value: Lys


title: 14N_SW620_PBS


title: HeLa_Phe_B

description: RNA-Seq (3' end)

value: Phe


title: 12L_HCT116_3TC


title: 15R_SW620_3TCAZA


title: 12N_HCT116_AZA

value: AZA


title: HeLa_Met_B

description: RNA-Seq (3' end)

value: Met


title: Naive_male_rep1

city: St. Louis

first: Lite

last: Yang

state: MO

address: 4922 Parkview Place

institute: Washington University in St. Louis

data_processing:
Raw fastq files are prepared by demultiplexing Illumina Nextseq runs using v3 indrops python scripts (github/indrops). Barcoded nuclei in a biological sample are divided into 2-3 tubes and their libararies are prepared and sequenced separately, which are then added together for each sample informatically after mapping.
All  subsequent processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops), using the default version 3 parameters.
inDrops.py first filters reads based on information present in read files 2,3, and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).  For read 3, the library indices provided to the indrop.py custom pipeline are given in the yaml files. Libraries called "not_included_in_study_*" were not included in the study, but their indexes should be specified when using the indrop.py pipeline for demultiplexing.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes (revealed by Read 2 and 4) against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81 or GRCh38.85) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene. Resulting raw count files are provided and called  *.counts.tsv.gz.
10X Genomics gene expression assay data were demultiplexed and mapped using cellranger
10X Genomics ATAC assay data were demultiplexed and mapped using cellranger-atac
Assembly: mm10
Supplementary files format and content: Raw counts tables from each sample were then combined by their respective experiment into the raw counts files available in GEO

organism: Mus musculus

source_name: Trigeminal ganglia

extract_protocol:
For snRNA-seq data, mouse trigeminal ganglia were dissociated into a single nuclei suspension as described in Renthal et al. 2020 and Yang et al. 2021. Briefly, tissue was dissociated by dounce homogenization and clarified by ultracentrifugation through a Optiprep gradient based on a protocol (Mo et al. Neuron 2015) and modified in Renthal et al. 2020. For snATAC-seq samples, TG were collected using a non-gradient protocol described previously (Slyper et al., 2020), and GFP+ nuclei were sorted and collected using FACS.
inDrops libraries were constructued as described in Zilionis et al., Nat. Protoc. 2017. 10X Genomics gene expression assay and ATAC assay were prepared according to the user manuals.
single-nucleus RNA-seq

tag: tissue

value: Trigeminal ganglia

tag: strain

tag: Sex

value: Male

tag: assay

value: inDrops

tag: headache model

value: Naive

tag: hours after treatment


title: 12R_HCT116_AZA


title: HeLa_Ile_B

description: RNA-Seq (3' end)

value: Ile


title: 11L_HCT116_3TC


title: HeLa_Gly_B

description: RNA-Seq (3' end)

value: Gly


title: HeLa_His_B

description: RNA-Seq (3' end)

value: HeLa

value: His


title: 10R_HCT116_3TCAZA

value: 3TC + AZA


title: HeLa_Cys_B

description: RNA-Seq (3' end)

value: Cys


title: 12B_HCT116_3TCAZA


title: 13N_SW620_3TC


title: 14R_SW620_AZA


title: 11B_HCT116_3TCAZA


title: 10N_HCT116_AZA


title: HeLa_Recon_B

description: RNA-Seq (3' end)

value: Recon


title: HeLa_noAA_B

description: RNA-Seq (3' end)

value: noAA


title: HeLa_Ser_B

description: RNA-Seq (3' end)

value: Ser


title: HeLa_Val_A

description: RNA-Seq (3' end)

value: Val


title: HeLa_Tyr_A

description: RNA-Seq (3' end)

value: Tyr


title: 11N_HCT116_3TC


title: HeLa_Gln_A

description: RNA-Seq (3' end)

value: Gln


title: 10B_HCT116_AZA

value: AZA


title: NS132-SW620-DMSO-D7-A

tag: tumorsphere

value: Established

tag: time point

value: DMSO


title: 14L_SW620_AZA


title: HeLa_Trp_A

description: RNA-Seq (3' end)

value: Trp


title: HeLa_Arg_B

description: RNA-Seq (3' end)

value: Arg


title: HeLa_Leu_B

description: RNA-Seq (3' end)

value: Leu


title: NS132-SW620-DMSO-D7-C


title: NS132-SW620-3TC-D7-C


title: NS132-SW620-3TC-D7-B


title: 11R_HCT116_3TCAZA


title: HeLa_Ser_A

description: RNA-Seq (3' end)


title: HeLa_Phe_A

description: RNA-Seq (3' end)

value: Phe


title: HeLa_Leu_A

description: RNA-Seq (3' end)

value: HeLa


title: NS132-SW620-3TC-D7-A


title: NS132-HCT8-3TC-D7-C


title: HeLa_Met_A

description: RNA-Seq (3' end)

value: Met


title: NS132-HCT8-DMSO-D7-A


title: HeLa_Lys_A

description: RNA-Seq (3' end)

value: Lys


title: NS132-HCT8-DMSO-D7-C


title: NS132-HCT8-DMSO-D7-B


title: NS132-HCT8-3TC-D7-B


title: NS132-HCT8-3TC-D7-A


title: HeLa_Cys_A

description: RNA-Seq (3' end)

value: Cys


title: HeLa_Ile_A

description: RNA-Seq (3' end)

value: Ile


title: NS132-HCT116-DMSO-D7-C


title: HeLa_Gly_A

description: RNA-Seq (3' end)

value: Gly


title: 10L_HCT116_3TCAZA

value: 3TC + AZA


title: NS132-HCT116-DMSO-D7-A


title: NS132-HCT116-3TC-D7-C


title: HeLa_His_A

description: RNA-Seq (3' end)

value: His


title: NS132-HCT116-DMSO-D7-B


title: HeLa_Arg_A

description: RNA-Seq (3' end)


title: NS132-HCT116-3TC-D7-B


title: HeLa_Recon_A

description: RNA-Seq (3' end)

value: Recon


title: HeLa_noAA_A

description: RNA-Seq (3' end)

value: noAA


title: HeLa_Thr_A

description: RNA-Seq (3' end)

value: Thr


title: NS132-DLD1-DMSO-D7-C

value: Established


title: MPAF_DMSO_0.001%_24h_2

city: Bonn

first: Kai

last: Funke

state: NRW

address: Venusberg-Campus 1

department: Pathology, Developmental Pathology

country: Germany

institute: University Hospital Bonn

description:
Control sample to "MPAF_THZ531_100nM_24h" and "MPAF_YKL5124_10nM_24h"
DE66NGSUKBR115676

data_processing:
QC of raw sequencing reads and trimming were performed in Trim Galore! 0.4.5 (Brabraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore), using a phred score cutoff of 30 and minimum sequence length of 30 after trimming.
Mapping was done using HISAT2 2.1
Transcript quantification and annotation was done using StringTie 1.3.3. Gene annotation information was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org) for the human genome (GRCh38.p13). We used the python script (preDE.py) included in the StringTie package to prepare gene-level count matrices for analysis of differential gene expression.
Differential expression was tested with DESeq2 1.16.1. Pseudogenes were removed from the count matrices based on “biotype” annotation information extracted from Biomart (R-package biomaRt). Low counts were removed by the independent filtering process implemented in DESeq2.
Assembly: All samples were mapped to the human genome (GRCh38.p13).
Supplementary files format and content: comma-separated text files include raw counts, tab-delimited supplementary text files include DEseq2 normalized counts and DESeq2 differential expression analysis outputs for each comparison

growth_protocol: 2102EP cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin (pen/strep) and 200 mM L-glutamine (L-glu), MPAF cells were cultured in DMEM + 10% FBS + 1% pen/strep + 200 mM L-glu + 1% non-essential amino acids, TCam2 cells were cultured in RPMI + 10 % FBS + 1% pen/strep and 200 mM L-glu. All cells were kept at 37 °C and 7.5 % CO2.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany)
The RNA quality control, library preparation (QuantSeq 3'-mRNA Library Prep (Lexogen, USA)) and RNA sequencing were performed by the Core Facility Next Generation Sequencing (University of Bonn, Germany).
An Illumina HiSeq 2500 V4 device (producing >10 million, 50bp 3'-end reads per sample) was used.

treatment_protocol: Cells were treated for 1 h or 24 h with NVP2 (10 nM), SY0351 (10 nM), YKL5124 (100 nM), THZ531 (100 nM), or corresponsding DMSO control (0,0001 % or 0,001 %).

tag: cell type

value: Human Adult Fibroblasts


title: MPAF_DMSO_0.001%_24h_3

description:
Control sample to "MPAF_THZ531_100nM_24h" and "MPAF_YKL5124_10nM_24h"
DE39NGSUKBR115677


title: NS132-HCT116-3TC-D7-A


title: NS132-DLD1-3TC-D7-C


title: MPAF_DMSO_0.001%_24h_1

description:
Control sample to "MPAF_THZ531_100nM_24h" and "MPAF_YKL5124_10nM_24h"
DE93NGSUKBR115675


title: NS131-SW620-DMSO-D7-C

value: DMSO


title: NS132-DLD1-DMSO-D7-A


title: NS132-DLD1-3TC-D7-B


title: MPAF_YKL5124_100nM_24h_2

description:
N/A
DE34NGSUKBR115670


title: MPAF_YKL5124_100nM_1h_2

description:
N/A
DE37NGSUKBR115616


title: NS132-DLD1-DMSO-D7-B


title: MPAF_YKL5124_100nM_24h_1

description:
N/A
DE61NGSUKBR115669


title: MPAF_YKL5124_100nM_24h_3

description:
N/A
DE07NGSUKBR115671


title: MPAF_YKL5124_100nM_1h_1

description:
N/A
DE64NGSUKBR115615


title: NS131-SW620-DMSO-D7-B


title: NS131-SW620-DMSO-D7-A


title: NS131-SW620-3TC-D7-C


title: NS131-SW620-3TC-D7-B


title: MPAF_DMSO_0.001%_1h_1

description:
Control sample to "MPAF_THZ531_100nM_1h" and "MPAF_YKL5124_10nM_1h"
DE53NGSUKBR115619


title: MPAF_DMSO_0.001%_1h_3

description:
Control sample to "MPAF_THZ531_100nM_1h" and "MPAF_YKL5124_10nM_1h"
DE40NGSUKBR115659


title: MPAF_DMSO_0.001%_1h_2

description:
Control sample to "MPAF_THZ531_100nM_1h" and "MPAF_YKL5124_10nM_1h"
DE26NGSUKBR115620


title: NS132-DLD1-3TC-D7-A


title: MPAF_YKL5124_100nM_1h_

description:
N/A
DE94NGSUKBR115657


title: NS131-HCT8-DMSO-D7-B


title: MPAF_THZ531_100nM_24h_3

description:
N/A
DE23NGSUKBR115674


title: NS131-HCT8-DMSO-D7-A


title: MPAF_THZ531_100nM_1h_2

description:
N/A
DE80NGSUKBR115618


title: NS131-SW620-3TC-D7-A


title: MPAF_THZ531_100nM_24h_1

description:
N/A
DE77NGSUKBR115672


title: MPAF_DMSO_0.0001%_24h_1

description:
Control sample to "MPAF_NVP2_10nM_24h" and "MPAF_SY0351_10nM_24h"
DE44NGSUKBR115684


title: MPAF_THZ531_100nM_1h_

description:
N/A
DE67NGSUKBR115658


title: MPAF_THZ531_100nM_1h_1

description:
N/A
DE10NGSUKBR115617


title: MPAF_DMSO_0.0001%_1h_3

description:
Control sample to "MPAF_NVP2_10nM_1h" and "MPAF_SY0351_10nM_1h"
DE88NGSUKBR115668


title: NS131-HCT8-DMSO-D7-C


title: NS131-HCT8-3TC-D7-B


title: NS131-HCT8-3TC-D7-A


title: MPAF_DMSO_0.0001%_24h_3

description:
Control sample to "MPAF_NVP2_10nM_24h" and "MPAF_SY0351_10nM_24h"
DE87NGSUKBR115686


title: NS131-HCT116-DMSO-D7-B


title: NS131-HCT116-3TC-D7-C


title: NS131-HCT116-DMSO-D7-A


title: NS131-HCT116-DMSO-D7-C


title: MPAF_THZ531_100nM_24h_2

description:
N/A
DE50NGSUKBR115673


title: MPAF_DMSO_0.0001%_1h_2

description:
Control sample to "MPAF_NVP2_10nM_1h" and "MPAF_SY0351_10nM_1h"
DE18NGSUKBR115667


title: MPAF_DMSO_0.0001%_24h_2

description:
Control sample to "MPAF_NVP2_10nM_24h" and "MPAF_SY0351_10nM_24h"
DE17NGSUKBR115685


title: MPAF_SY0351_10nM_24h_2

description:
N/A
DE98NGSUKBR115682


title: MPAF_SY0351_10nM_24h_3

description:
N/A
DE71NGSUKBR115683


title: NS131-HCT8-3TC-D7-C


title: NS131-DLD1-DMSO-D7-C


title: NS131-HCT116-3TC-D7-B


title: NS131-DLD1-DMSO-D7-A


title: NS131-DLD1-DMSO-D7-B


title: MPAF_SY0351_10nM_1h_3

description:
N/A
DE72NGSUKBR115665


title: MPAF_SY0351_10nM_24h_1

description:
N/A
DE28NGSUKBR115681


title: NS131-DLD1-3TC-D7-C


title: MPAF_NVP2_10nM_24h_3

description:
N/A
DE55NGSUKBR115680


title: NS131-DLD1-3TC-D7-A


title: NS131-HCT116-3TC-D7-A


title: MPAF_NVP2_10nM_1h_2

description:
N/A
DE83NGSUKBR115661


title: TCam2_DMSO_0.001%_24h_3

description:
Control sample to "TCam2_THZ531_100nM_24h" and "TCam2_YKL5124_10nM_24h"
DE73NGSUKBR115647

value: Seminoma


title: MPAF_NVP2_10nM_1h_1

description:
N/A
DE13NGSUKBR115660


title: NS121-SW620-DMSO-D7-C

value: Novel


title: NS131-DLD1-3TC-D7-B


title: MPAF_NVP2_10nM_24h_1

description:
N/A
DE12NGSUKBR115678


title: MPAF_NVP2_10nM_1h_3

description:
N/A
DE56NGSUKBR115662


title: NS121-HCT8-DMSO-D7-C


title: MPAF_DMSO_0.0001%_1h_1

description:
Control sample to "MPAF_NVP2_10nM_1h" and "MPAF_SY0351_10nM_1h"
DE45NGSUKBR115666


title: NS121-SW620-3TC-D7-A


title: NS121-HCT8-DMSO-D7-B


title: NS121-SW620-DMSO-D7-A


title: MPAF_NVP2_10nM_24h_2

description:
N/A
DE82NGSUKBR115679


title: TCam2_DMSO_0.001%_24h_1

description:
Control sample to "TCam2_THZ531_100nM_24h" and "TCam2_YKL5124_10nM_24h"
DE30NGSUKBR115645


title: MPAF_SY0351_10nM_1h_2

description:
N/A
DE02NGSUKBR115664


title: NS121-SW620-3TC-D7-B


title: NS121-SW620-DMSO-D7-B


title: TCam2_DMSO_0.001%_1h_3

description:
Control sample to "TCam2_THZ531_100nM_1h" and "TCam2_YKL5124_10nM_1h"
DE91NGSUKBR115614


title: TCam2_DMSO_0.001%_24h_2

description:
Control sample to "TCam2_THZ531_100nM_24h" and "TCam2_YKL5124_10nM_24h"
DE03NGSUKBR115646


title: MPAF_SY0351_10nM_1h_1

description:
N/A
DE29NGSUKBR115663


title: NS121-HCT8-3TC-D7-C


title: TCam2_DMSO_0.001%_1h_1

description:
Control sample to "TCam2_THZ531_100nM_1h" and "TCam2_YKL5124_10nM_1h"
DE48NGSUKBR115612


title: TCam2_DMSO_0.001%_1h_2

description:
Control sample to "TCam2_THZ531_100nM_1h" and "TCam2_YKL5124_10nM_1h"
DE21NGSUKBR115613


title: NS121-HCT8-DMSO-D7-A


title: TCam2_YKL5124_100nM_24h_3

description:
N/A
DE41NGSUKBR115641


title: NS121-SW620-3TC-D7-C


title: TCam2_YKL5124_100nM_24h_2

description:
N/A
DE68NGSUKBR115640


title: NS121-HCT8-3TC-D7-A


title: TCam2_YKL5124_100nM_24h_1

description:
N/A
DE95NGSUKBR115639


title: NS121-HCT116-DMSO-D7-A


title: NS121-HCT116-DMSO-D7-B


title: NS121-HCT116-3TC-D7-B


title: NS121-DLD1-DMSO-D7-C


title: NS121-DLD1-3TC-D7-C


title: NS121-HCT116-3TC-D7-C


title: NS121-HCT116-3TC-D7-A


title: TCam2_THZ531_100nM_1h_1

description:
N/A
DE32NGSUKBR115609


title: TCam2_THZ531_100nM_24h_1

description:
N/A
DE14NGSUKBR115642


title: NS121-DLD1-3TC-D7-B


title: TCam2_THZ531_100nM_24h_2

description:
N/A
DE84NGSUKBR115643


title: TCam2_YKL5124_100nM_1h_2

description:
N/A
DE86NGSUKBR115607


title: NS120-SW620-DMSO-D1-C


title: TCam2_THZ531_100nM_1h_2

description:
N/A
DE05NGSUKBR115610


title: NS121-HCT8-3TC-D7-B


title: TCam2_DMSO_0.0001%_24h_1

description:
Control sample to "TCam2_NVP2_10nM_24h" and "TCam2_SY0351_10nM_24h"
DE78NGSUKBR115654


title: TCam2_DMSO_0.0001%_24h_2

description:
Control sample to "TCam2_NVP2_10nM_24h" and "TCam2_SY0351_10nM_24h"
DE51NGSUKBR115655


title: NS121-DLD1-DMSO-D7-B


title: TCam2_YKL5124_100nM_1h_1

description:
N/A
DE16NGSUKBR115606


title: TCam2_THZ531_100nM_1h_3

description:
N/A
DE75NGSUKBR115611


title: TCam2_THZ531_100nM_24h_3

description:
N/A
DE57NGSUKBR115644


title: NS121-HCT116-DMSO-D7-C


title: TCam2_DMSO_0.0001%_1h_2

description:
Control sample to "TCam2_NVP2_10nM_1h" and "TCam2_SY0351_10nM_1h"
DE52NGSUKBR115637


title: NS121-DLD1-3TC-D7-A


title: NS120-SW620-DMSO-D1-A


title: TCam2_YKL5124_100nM_1h_3

description:
N/A
DE59NGSUKBR115608


title: TCam2_DMSO_0.0001%_24h_3

description:
Control sample to "TCam2_NVP2_10nM_24h" and "TCam2_SY0351_10nM_24h"
DE24NGSUKBR115656


title: NS120-SW620-DMSO-D1-B


title: Tibialis Anterior wild-type 4

city: Angers

first: Olivier

middle: R.

last: Baris

address: 4 rue Larrey

department: CHU Angers, IBS

country: France

institute: UMR 6015 CNRS / 1083 INSERM

data_processing:
Illumina Casava software used for basecalling
Reads were mapped to Maus genome assembly of  using Tophat2, version 2.0.10, and reassembled with Cufflinks, version 2.1.1.
Sequenced reads mapped to Maus genome
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks
Assembly: Ensembl 85 (mm10)
Supplementary files format and content: tab-delimited file include FPKM values for each Sample

source_name: Tibialis anterior

growth_protocol: Total RNA was isolated from 20-30mg of the lower part of TA with Trizol.

extract_protocol:
Tibialis anterior were removed, snap frozen in liquid nitrogen and stored at -80° Celcius until needed. Total RNA were extracted using Trizol reagent.
Illumina RNASeq library Protocol
Libraries were prepared using the  Stranded  Library Prep Kit

tag: gender

value: Female

value: Tibialis anterior muscle

tag: age

value: 24 months

tag: genotype

value: wild-type


title: NS120-SW620-3TC-D1-C


title: NS120-HCT8-DMSO-D1-B


title: TCam2_DMSO_0.0001%_1h_1

description:
Control sample to "TCam2_NVP2_10nM_1h" and "TCam2_SY0351_10nM_1h"
DE79NGSUKBR115636


title: NS120-SW620-3TC-D1-A


title: TCam2_SY0351_10nM_24h_3

description:
N/A
DE08NGSUKBR115653


title: Tibialis Anterior K320E-skm 1

value: Male


title: Tibialis Anterior wild-type 2


title: Tibialis Anterior K320E-skm 2


title: Tibialis Anterior wild-type 3


title: Tibialis Anterior K320E-skm 4


title: NS120-HCT8-DMSO-D1-A


title: NS121-DLD1-DMSO-D7-A


title: TCam2_SY0351_10nM_1h_1

description:
N/A
DE09NGSUKBR115635


title: TCam2_DMSO_0.0001%_1h_3

description:
Control sample to "TCam2_NVP2_10nM_1h" and "TCam2_SY0351_10nM_1h"
DE25NGSUKBR115638


title: TCam2_SY0351_10nM_24h_1

description:
N/A
DE62NGSUKBR115651


title: TCam2_SY0351_10nM_1h_2

description:
N/A
DE36NGSUKBR115634


title: NS120-HCT8-DMSO-D1-C


title: Tibialis Anterior K320E-skm 3


title: ventral_EC_28hpf_M12D9_2

city: Shenzhen

first: Zhao

last: Shizheng

address: Shenzhen

department: LIFS

country: China

institute: Undefined

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using TrimGalore with parameters trim_galore -q 20 --phred33 --stringency 5 --length 20 -e 0.1 --paired
Trimed reads were mapped to GRCz11.94 (danRer11) genome using STAR
Mapped reads (Bam) were quantified using Rsubred package
Genome_build: GRCz11.94 (danRer11)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: Trunk DA endothelium

extract_protocol:
Single Red Eos+ cell was manually picked with micromanipulator system (NT-88-V3; Nikon) under fluorescence microscope, then washed with 2% BSA/PBS, and finally transferred into 4.4ul lysis buffer. The smart-seq2 protocol was used for whole transcriptome amplification.
Smart-seq2 oligodT captured
cDNA libraries were prepared for sequencing using standard Illumina protocols
150bp paired end RNA-seq

tag: developmental stage

value: 28 hpf

value: dorsal aorta (DA)

tag: tissue region

value: DA floor

value: endothelial cells (ECs)


title: ventral_EC_28hpf_M12D24_1


title: NS120-HCT8-3TC-D1-C

tag: cell line


title: Tibialis Anterior wild-type 1


title: TCam2_NVP2_10nM_24h_3

description:
N/A
DE89NGSUKBR115650


title: ventral_EC_28hpf_M10D6_1


title: TCam2_NVP2_10nM_24h_2

description:
N/A
DE19NGSUKBR115649


title: dorsal_EC_28hpf_3-8

value: DA roof


title: TCam2_SY0351_10nM_1h_3

description:
N/A
DE63NGSUKBR115633


title: dorsal_EC_28hpf_3-6


title: ventral_EC_28hpf_M12D22_5


title: NS120-SW620-3TC-D1-B

tag: sequencing pool


title: TCam2_SY0351_10nM_24h_2

description:
N/A
DE35NGSUKBR115652

tag: treatment


title: ventral_EC_28hpf_D12D23_1

tag: tissue


title: NS120-HCT8-3TC-D1-B


title: NS120-HCT116-DMSO-D1-C


title: ventral_EC_28hpf_M12D2_2

tag: strain


title: NS120-HCT8-3TC-D1-A


title: ventral_EC_28hpf_M8D26_7


title: ventral_EC_28hpf_M8D19_6


title: ventral_EC_28hpf_M9D9_4


title: ventral_EC_28hpf_M11D13_2


title: dorsal_EC_28hpf_3-4


title: dorsal_EC_28hpf_3-5


title: ventral_EC_28hpf_M9D15_5


title: NS120-HCT116-DMSO-D1-A


title: TCam2_NVP2_10nM_1h_2

description:
N/A
DE20NGSUKBR115631


title: NS120-HCT116-DMSO-D1-B


title: NS120-HCT116-3TC-D1-C


title: TCam2_NVP2_10nM_24h_1

description:
N/A
DE46NGSUKBR115648


title: TCam2_NVP2_10nM_1h_3

description:
N/A
DE47NGSUKBR115630


title: TCam2_NVP2_10nM_1h_1

description:
N/A
DE90NGSUKBR115632


title: 2102EP_DMSO_0.001%_24h_3

description:
Control sample to "2102EP_THZ531_100nM_24h" and "2102EP_YKL5124_10nM_24h"
DE65NGSUKBR115597

value: Embryonal Carcinoma


title: dorsal_EC_28hpf_2-8


title: dorsal_EC_28hpf_2-7


title: NS120-HCT116-3TC-D1-A


title: dorsal_EC_28hpf_2-1


title: dorsal_EC_28hpf_1-6


title: dorsal_EC_28hpf_3-3


title: 2102EP_DMSO_0.001%_24h_2

description:
Control sample to "2102EP_THZ531_100nM_24h" and "2102EP_YKL5124_10nM_24h"
DE11NGSUKBR115599


title: ventral_EC_21hpf_18

value: 21 hpf


title: NS120-DLD1-DMSO-D1-A


title: NS120-HCT116-3TC-D1-B


title: dorsal_EC_28hpf_2-5


title: ventral_EC_21hpf_16


title: NS120-DLD1-DMSO-D1-B


title: NS120-DLD1-DMSO-D1-C


title: ventral_EC_21hpf_17


title: 2102EP_DMSO_0.001%_1h_2

description:
Control sample to "2102EP_THZ531_100nM_1h" and "2102EP_YKL5124_10nM_1h"
DE87NGSUKBR115589


title: 2102EP_DMSO_0.001%_1h_1

description:
Control sample to "2102EP_THZ531_100nM_1h" and "2102EP_YKL5124_10nM_1h"
DE17NGSUKBR115588


title: NS120-DLD1-3TC-D1-C


title: NS120-DLD1-3TC-D1-B


title: ventral_EC_21hpf_9


title: 2102EP_DMSO_0.001%_24h_1

description:
Control sample to "2102EP_THZ531_100nM_24h" and "2102EP_YKL5124_10nM_24h"
DE38NGSUKBR115598


title: ventral_EC_28hpf_M12D22_7


title: D70 TMG, replicate 2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against hg19 version of the human genome and RSEM v1.2.12 software was used to estimate raw read counts and RPKM values using Ensemble transcriptome.
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq_counts.txt (Processed data file contains raw counts for each gene)

source_name: H9 cell lines from WiCell Institute

extract_protocol:
Cells at 4 different stages of neural differentiation were collected, total RNA was isolated using MasterPure RNA purification kit (Epicenter) and libraries were prepared using NEBNext rRNA Depletion Kit and purified using AMPure XP beads fromBeckman Coulter
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Both undifferentiated H9 cells and cells during differentiation were consistently treated with O-GlcNAcase inhibitor, Thiamet-G (TMG) (TOCRIS bioscience, Cat. #4390-10MG) dissolved in DMSO according to manufacturer's instructions at 40 mM concentration. The working concentration of TMG was kept at 40uM throughout the study

value: ES cell line H9

tag: time

value: TMG

tag: replicate


title: ventral_EC_21hpf_13


title: ventral_EC_21hpf_15


title: ventral_EC_21hpf_12


title: ventral_EC_21hpf_6


title: ventral_EC_21hpf_5


title: ventral_EC_21hpf_14


title: ventral_EC_21hpf_11


title: ventral_EC_21hpf_4


title: ventral_EC_21hpf_10


title: 2102EP_YKL5124_100nM_24h_3

description:
N/A
DE70NGSUKBR115604


title: 2102EP_DMSO_0.001%_1h_3

description:
Control sample to "2102EP_THZ531_100nM_1h" and "2102EP_YKL5124_10nM_1h"
DE60NGSUKBR115590


title: ventral_EC_21hpf_2


title: dorsal_EC_21hpf_18


title: ventral_EC_21hpf_7


title: 2102EP_YKL5124_100nM_24h_1

description:
N/A
DE43NGSUKBR115605


title: ventral_EC_21hpf_8


title: 2102EP_YKL5124_100nM_1h_1

description:
N/A
DE22NGSUKBR115595


title: NS120-DLD1-3TC-D1-A


title: D70 control, replicate 2


title: 2102EP_YKL5124_100nM_1h_2

description:
N/A
DE92NGSUKBR115596


title: dorsal_EC_21hpf_15


title: 2102EP_YKL5124_100nM_1h_3

description:
N/A
DE49NGSUKBR115594


title: dorsal_EC_21hpf_16


title: 2102EP_THZ531_100nM_24h_2

description:
N/A
DE81NGSUKBR115600


title: D30 TMG, replicate 1

value: control


title: 2102EP_THZ531_100nM_24h_1

description:
N/A
DE54NGSUKBR115601


title: dorsal_EC_21hpf_14


title: dorsal_EC_21hpf_13


title: D70 TMG, replicate 1


title: dorsal_EC_21hpf_12


title: ventral_EC_21hpf_1


title: ventral_EC_21hpf_3


title: 2102EP_THZ531_100nM_1h_3

description:
N/A
DE76NGSUKBR115593


title: D30 control, replicate 2


title: dorsal_EC_21hpf_10


title: 2102EP_THZ531_100nM_24h_3

description:
N/A
DE27NGSUKBR115602


title: 2102EP_YKL5124_100nM_24h_2

description:
N/A
DE97NGSUKBR115603


title: D30 control, replicate 1


title: D12 TMG, replicate 1


title: dorsal_EC_21hpf_17


title: dorsal_EC_21hpf_11


title: dorsal_EC_21hpf_9


title: 2102EP_THZ531_100nM_1h_2

description:
N/A
DE06NGSUKBR115592


title: D30 TMG, replicate 2


title: D12 TMG, replicate 2


title: D12 control, replicate 2


title: dorsal_EC_21hpf_5


title: dorsal_EC_21hpf_7


title: D70 control, replicate 1


title: APOB-specific Tet+ cells in individuals with and without sCVD, TCR

city: La Jolla

first: Vasantika

last: Suryawanshi

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

description:
Samples from 8 DRB1*07:01+ women:
Sample A3 (HIV-sCVD- 1)
Sample A4 (HIV-sCVD- 2)
Sample B1 (HIV-sCVD+ 1)
Sample B2 (HIV-sCVD+ 2)
Sample C3 (HIV+sCVD- 1)
Sample C4 (HIV+sCVD- 2)
Sample D1 (HIV+sCVD+ 1)
Sample D3 (HIV+sCVD+ 2)

data_processing:
Library strategy: TCR-seq
After demultiplexing using Cell Ranger (www.10xgenomics.com), we retrieved 1368 to 3097 cells (median 1948 cells) per a sample, and totally 21,411 cells with transcriptomes.
After doublet (DoubletFinder v3,51) and low viability (mitochondrial gene content >10%) removal and batch effect correction, 16,644 cells remained.
Doublets, low quality and proliferating cells were removed and batch effects were controlled by Harmony. The data is log2 normalized, and we used Seurat for differentially expressed genes and Dotplots, and Seaborn in Python for plotting the heatmaps.
Supplementary files format and content: Log_norm_transc.csv (Gene expression matrix)
clonotypes.csv (TCR clonotype sequences and frequency file)
Metadata.csv (Metadata file listing all biological characteristics of cells)

source_name: sorted PBMC

extract_protocol:
Frozen PBMC samples were thawed and stained with APOB-p18 DRB1*07:01 tetramer after Fc blocking and dasatinib. After live dead aqua (1:1000, Thermo Fisher Scientific) staining (in PBS, 4℃ for 20min), cells were stained with surface marker antibodies on ice in the dark for 30min. Cells were washed twice with 2 mL flow buffer (PBS with 2%FBS, Gemini Bio). The cells were sorted by the FACS sorter (FACSAria, BD) into 4 Eppendorf tubes (DNA low bind), each of which contained 100μl flow buffer. Some surplus of the sorted Th1 and Tmem were discarded. Each single cell suspension in a 1.5mL sterile Eppendorf tube containing no more than 1 million cells in 50 μL of staining buffer (2% FBS in 1X PBS) was incubated with 2.0 μL of unique hashtag oligonucleotide antibody.
Library was prepared per 10x Genomics protocol.

tag: Sex

value: female

tag: individual

value: PBMCs (Tet+, Th1, Tmem, Treg)

tag: disease state

value: with and without sCVD


title: 2102EP_THZ531_100nM_1h_1

description:
N/A
DE33NGSUKBR115591


title: D0 TMG, replicate 2


title: dorsal_EC_21hpf_2


title: 2102EP_DMSO_0.0001%_24h_3

description:
Control sample to "2102EP_NVP2_10nM_24h" and "2102EP_SY0351_10nM_24h"
DE38NGSUKBR115695


title: dorsal_EC_21hpf_6


title: dorsal_EC_21hpf_1


title: dorsal_EC_21hpf_4


title: 2102EP_DMSO_0.0001%_24h_1

description:
Control sample to "2102EP_NVP2_10nM_24h" and "2102EP_SY0351_10nM_24h"
DE76NGSUKBR115690


title: 2102EP_DMSO_0.0001%_1h_1

description:
Control sample to "2102EP_NVP2_10nM_1h" and "2102EP_SY0351_10nM_1h"
DE42NGSUKBR115623


title: D0 control, replicate 1


title: dorsal_EC_21hpf_8


title: 2102EP_DMSO_0.0001%_24h_2

description:
Control sample to "2102EP_NVP2_10nM_24h" and "2102EP_SY0351_10nM_24h"
DE65NGSUKBR115694


title: 2102EP_DMSO_0.0001%_1h_3

description:
Control sample to "2102EP_NVP2_10nM_1h" and "2102EP_SY0351_10nM_1h"
DE74NGSUKBR115629


title: 2102EP_SY0351_10nM_24h_3

description:
N/A
DE92NGSUKBR115693


title: D0 TMG, replicate 1


title: 2102EP_DMSO_0.0001%_1h_2

description:
Control sample to "2102EP_NVP2_10nM_1h" and "2102EP_SY0351_10nM_1h"
DE58NGSUKBR115626


title: dorsal_EC_21hpf_3


title: 2102EP_SY0351_10nM_24h_2

description:
N/A
DE06NGSUKBR115689


title: APOB-specific Tet+ cells in individuals with and without sCVD, GEX

data_processing:
After demultiplexing using Cell Ranger (www.10xgenomics.com), we retrieved 1368 to 3097 cells (median 1948 cells) per a sample, and totally 21,411 cells with transcriptomes.
After doublet (DoubletFinder v3,51) and low viability (mitochondrial gene content >10%) removal and batch effect correction, 16,644 cells remained.
Doublets, low quality and proliferating cells were removed and batch effects were controlled by Harmony. The data is log2 normalized, and we used Seurat for differentially expressed genes and Dotplots, and Seaborn in Python for plotting the heatmaps.
Supplementary files format and content: Log_norm_transc.csv (Gene expression matrix)
clonotypes.csv (TCR clonotype sequences and frequency file)
Metadata.csv (Metadata file listing all biological characteristics of cells)


title: C482-2_19s000452_shHLF

city: Heidelberg

first: Caroline

last: Pabst

address: Im Neuenheimer Feld 400

department: Department of Medicine V, Hematology, Oncology and Rheumatology

institute: University Hospital Heidelberg

description: low input RNA

data_processing:
RNA-seq data in fastq format were aligned using STAR v.2.5.1b to GRCh38 assembly from GENCODE release v24 and raw read abundances were estimated internally in STAR using the algorithm of HT-Seq.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts per gene for each Sample.

source_name: primary bone marrow AML cells

extract_protocol:
RNA samples were extracted using the Qiagen Rneasy mini kit per manufacturer instructions
Libraries were prepared from total RNA using the TruSeq Stranded Total RNA Library Prep Kit per manufacturer instructions

tag: assay

value: RNA-Seq

tag: biological replicate

tag: shRNA

value: shHLF

tag: technical replicate


title: C482-1_19s000451_shHLF

description: low input RNA


title: D12 control, replicate 1


title: 2102EP_SY0351_10nM_24h_1

description:
N/A
DE22NGSUKBR115692

tag: cell type


title: C482-3_19s000453_shHLF

description: low input RNA


title: C103-3_19s000450_shLUC

description: low input RNA

value: shLUC


title: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented with glucose Replicate 2

city: Golden

first: Gregg

middle: T.

last: Beckham

address: 15013 Denver West Parkway

institute: National Renewable Energy Laboratory

description:
GB062_glu_2
Total RNA with depleted ribosomal RNA

data_processing:
Raw RNA-Seq reads were mapped to the original reference genome using Bowtie and transcript abundance was analyzed using summarizeOverlaps (Lawrence et al., 2013). Calculation of transcripts per million (TPM) and prediction of differentially expressed genes were conducted using DESeq2 (Love et al., 2014).
Assembly: AE015451.2
Supplementary files format and content: log_tpm_2020_Bentley.csv: Comma-separated text file includes log tpm.

organism: Pseudomonas putida KT2440

growth_protocol: Shake flask experiments were performed by inoculating seed cultures from glycerol stocks into 5 mL of LB medium, incubating overnight at 30°C and 225 rpm. Overnight cultures were then used to inoculate a second seed culture in LB medium starting at an optical density of 0.2 measured at 600 nm (OD600) using a Beckman DU640 spectrophotometer (Beckman Coulter). The second seed cultures were incubated at 30°C at 225 rpm for 2–3 h until an OD600 of approximately 2 was reached. These seed cultures were centrifuged at 4500 rpm for 5 min, the pellets were resuspended in 1X M9 salts, and were used to inoculate the shake flasks containing modified M9 minimal media comprising 6.78 g/L Na2HPO4, 3 g/L KH2PO4, 0.5 g/L NaCl, 1 g/L NH4Cl, 2 mM MgSO4, 100 μM CaCl2, 18 μM FeSO4, and 25 mM or 30 mM glucose, as specified in text, to a starting OD600 of 0.1.

extract_protocol:
Cells pelleted from 15 mL of M9 minimal medium were flash frozen and stored at −80°C. Cells were resuspended in TRIzol (ThermoFisher-Invitrogen) and processed according to the manufacturer's protocol. The samples were then purified on an RNeasy column (Qiagen) with on-column DNase digestion. RNA was eluted off the column in 35 μL RNase free H2O (Qiagen). The RNA concentration was quantified using a Nanodrop 1000 (ThermoScientific) and RNA quality was verified by obtaining RNA Integrity Numbers (RIN) using an RNA 6000 Nanochip on an Agilent 2100 Bioanalyzer (Agilent).
Ribosomal RNA was depleted using a RiboZero rRNA Removal Kit for bacteria (Illumina). The depleted sample was purified on an RNA Clean & Concentrator-5 (Zymo Research), and then the depleted material was quantified using a Nanodrop 1000 and visualized on an Agilent 2100 Bioanalyzer instrument with an RNA 6000 Nanochip (Agilent). RNA depleted of ribosomal RNA was used as input material to synthesize cDNA libraries using a ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina) and TruSeq compatible barcodes. Pooled barcoded libraries were sequenced in one direction for 75 bases (SE75) on an Illumina NextSeq500 (Illumina) and de-multiplexed as a sequencing service provided by Vanderbilt 2.9 (VUMC VANTAGE Vanderbilt University Medical Center Technologies for Advanced Genomics).

tag: genotype

tag: carbon source

value: glucose

tag: supplement


title: N1014M-4 [miRNA-seq]

city: Shanghai

first: Xiang

last: Liping

address: 180 Fenglin Road, Xuhui, Shanghai

institute: Fudan university

data_processing:
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Library quality was assessed on the Agilent Bioanalyzer 2100 system. The sequencing libraries were sequenced on an Illumina Hiseq2500/X platform. Index of the reference genome was built using Bowtie v2.2.3.
Assembly: mm9
Supplementary files format and content: Raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Total RNAs were extracted using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: NASH


title: Pseudomonas putida KT2440 grown in a minimal medium supplemented with glucose Replicate 3

description:
KT2440_glu_3
Total RNA with depleted ribosomal RNA

value: KT2440 wildtype


title: C103-2_19s000449_shLUC

description: low input RNA


title: Pseudomonas putida KT2440 grown in a minimal medium supplemented with glucose Replicate 1

description:
KT2440_glu_1
Total RNA with depleted ribosomal RNA


title: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented with glucose Replicate 3

description:
GB062_glu_3
Total RNA with depleted ribosomal RNA


title: 2102EP_SY0351_10nM_1h_2

description:
N/A
DE69NGSUKBR115622


title: D0 control, replicate 2

tag: cell line


title: 2102EP_NVP2_10nM_24h_2

description:
N/A
DE33NGSUKBR115688

tag: treatment


title: N1014M-3 [miRNA-seq]

tag: tissue


title: Pseudomonas putida KT2440 GB062 grown in a minimal medium supplemented with glucose Replicate 1

description:
GB062_glu_1
Total RNA with depleted ribosomal RNA


title: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented with glucose Replicate 2

description:
CJ522_glu_2
Total RNA with depleted ribosomal RNA


title: 2102EP_NVP2_10nM_24h_3

description:
N/A
DE49NGSUKBR115691


title: 2102EP_SY0351_10nM_1h_1

description:
N/A
DE96NGSUKBR115621


title: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented with glucose Replicate 3

description:
CJ522_glu_3
Total RNA with depleted ribosomal RNA


title: Pseudomonas putida KT2440 CJ522 grown in a minimal medium supplemented with glucose Replicate 1

description:
CJ522_glu_1
Total RNA with depleted ribosomal RNA


title: Pseudomonas putida KT2440 grown in a minimal medium supplemented with glucose Replicate 2

description:
KT2440_glu_2
Total RNA with depleted ribosomal RNA


title: N1014C-3 [miRNA-seq]

tag: strain

value: Normal


title: N1014C-4 [miRNA-seq]


title: 2102EP_NVP2_10nM_1h_3

description:
N/A
DE31NGSUKBR115627


title: 2102EP_NVP2_10nM_24h_1

description:
N/A
DE60NGSUKBR115687


title: 2102EP_SY0351_10nM_1h_3

description:
N/A
DE04NGSUKBR115628


title: Piezo1fl/fl; FAD; biological repetition 03.

city: Xiamen

first: Hongrui

last: Zhu

state: Fujian

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District, Xiamen, Fujian Province, China

institute: Xiamen University

description:
control microglia of 5xFAD mouse
WT_FAD3

data_processing:
All sequence reads were trimmed using Cutadapt (version 1.11) and aligned with HISAT2 to Mus musculus GRCm38.After Quality control metrics were finished, expression was performed with RSEM (version 1.2.30). Differentially expressed genes were analyzed by the DESeq2 package in R (Version 3.6.1). The resulting P-values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted p-value <0.05 found by DESeq2 were assigned as differentially expressed.
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample;Matrix table with raw gene counts for every gene and every sample.

source_name: Brain

extract_protocol:
RNA from freshly isolated primary microglia in various groups was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
mRNA was purified using poly-T oligo-attached magnetic beads (Vazyme Biotech Co., Ltd). And RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). The library fragments (370 ~ 420 bp in length) were processed with the AMPure XP system (Beckman Coulter, Beverly, USA). After the PCR products were assessed using library quality on the Agilent Bioanalyzer 2100 system, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia). Then, the library preparations were sequenced on an Illumina Novaseq platform, and 150 bp paired-end reads were generated.

value: microglia

value: Piezo1fl/fl; FAD


title: 2102EP_NVP2_10nM_1h_2

description:
N/A
DE85NGSUKBR115625

value: Embryonal Carcinoma


title: N1014C-1 [miRNA-seq]


title: C103-1_19s000448_shLUC

description: low input RNA


title: N610M-4 [miRNA-seq]

value: NAFL


title: Piezo1fl/fl; FAD; biological repetition 01.

description:
control microglia of 5xFAD mouse
WT_FAD1


title: 2102EP_NVP2_10nM_1h_1

description:
N/A
DE15NGSUKBR115624


title: N1014M-2 [miRNA-seq]


title: N610M-3 [miRNA-seq]


title: Piezo1MGKO; FAD, biological repetition 03.

description:
Piezo1 was knockout in microglia of 5xFAD mouse
KO_FAD3

value: Piezo1MGKO; FAD


title: Piezo1MGKO; FAD, biological repetition 02.

description:
Piezo1 was knockout in microglia of 5xFAD mouse
KO_FAD2


title: N610M-2 [miRNA-seq]


title: Piezo1MGKO; FAD, biological repetition 01.

description:
Piezo1 was knockout in microglia of 5xFAD mouse
KO_FAD1


title: N610C-8 [miRNA-seq]


title: N610C-7 [miRNA-seq]


title: Rbx1-deficient

city: Hangzhou

first: Di

last: Wu

state: Zhejiang

address: No. 268, Kaixuan Road

institute: Zhejiang University

data_processing:
Raw reads were processed through the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline
The quality-filtered R1 reads were analyzed to identify the cell label sequence (CL), Molecular Identifier sequence (UMI), and poly-dT tail sequence
Putative cells information were combined together with RSEC/DBEC-adjusted molecules to generate a single-cell expression matrix
Raw gene expression matrices from two cartridges were read into R (version 3.6.0) separately and converted to Seurat objects using the Seurat R package (version 3.0.1)
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every single cell

source_name: peripheral lymph nodes

growth_protocol: Female Foxp3cre/wt and Foxp3cre/wt;Rbx1fl/fl mice were maintained in SPF conditions until 10 weeks old.

extract_protocol:
Peripheral lymph nodes were harvested from mice with indicated genotypes, and grinded into single cells, followed by treatment with Dynabeads™ Untouched™ Mouse CD4 Cells Kit (Invitrogen, 11415D) to isolate the CD4+ T cells. The FACS sorting (SONY Cell Sorter, SH800S) was used to isolate the CD4+YFP+ Treg cells with purities > 99%.
Based on BD Rhapsody system Whole transcriptome analysis alpha protocol for single cell whole transcriptome analysis, Microbeads-captured single cell transcriptome were generated into cDNA library containing Cell label and UMI information. Briefly, double strand cDNA were firstly generated from Microbeads-captured single cell transcriptome following several steps including reverse transcription, second strand synthesis, end preparation, adapter ligation and whole transcriptome amplification. Then final cDNA library were generated from double strand full length cDNA by random priming amplification with BD Rhapsody cDNA Kit (BD Biosciences, 633773) and BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (BD Biosciences, 633774). Library was sequenced in a PE150 mode (Pair-End for 150bp read) on the X Ten instrument (Illumina).

value: sorted CD4+YFP+ Treg cells


title: wt

value: wt


title: 60444 FEC 3

type: RNA

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

description: Gene expression data from 60444 FEC

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The scanned images were analyzed with GeneSpring GX (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Manihot esculenta

source_name: friable embryogenic callus (FEC)

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

growth_protocol: For preparation of total RNA, the FEC derived from KU50 was observed at about three months after transferred to FIM. The KU50 FEC was cultured on FIM for an additional 2 months. The FEC derived from 6044 was observed at about one month after cultured to FIM. The FEC was incubated on FIM for an additional 2 months.

extract_protocol: Total RNA was purified according to manual protocol using RNeasy Plant Mini kit protocol (QIAGEN) followed by Plant RNA reagent protocol (Invitrogen). The total RNA quality was evaluated by electrophoresis with the bioanalyzer system (Agilent, USA). The total RNA was stored at -80ºC until further use.

tag: variety

value: friable embryogenic callus (FEC)


title: N610C-4 [miRNA-seq]


title: 60444 FEC 4

description: Gene expression data from 60444 FEC


title: Piezo1fl/fl; FAD; biological repetition 02.

description:
control microglia of 5xFAD mouse
WT_FAD2


title: SW620 (replica 3)

city: Madrid

first: Javier

last: Robles

state: Madrid

address: Calle Ramiro de Maetzu 9

department: Biomedicine

country: Spain

institute: Biological Research Centre Margarita Salas

hyb_protocol: “Clariom™ S Array, human” (Applied Biosystems).

scan_protocol: “GeneChip® Scanner 3000 7G” (Applied Biosystems).

data_processing: Data analysis was performed with Transcriptome Analysis Console (TAC) Software.

label: Biotin

source_name: SW620 human colorectal cancer cell line

label_protocol: Samples were terminal labeled with “GeneChip® WT PLUS Reagent Kit” (Applied Biosystems).

growth_protocol: Cells were grown in DMEM containing 10% FBS (Invitrogen) and antibiotics at 37 °C in a 5% CO2 humidified atmosphere.

extract_protocol: Total RNA was isolated using NucleoSpin RNA kit (Macherey-Nagel). Quality assessment of the RNA was assessed with an Agilent 2100 bio-analyzer.

value: Colorectal cancer


title: SW620 (replica 1)


title: KM12SM (replica 3)

source_name: KM12SM human colorectal cancer cell line


title: SW620 (replica 2)


title: KU50 FEC 3

description: Gene expression data from KU50 FEC


title: SFE1

status: Public on Mar 25 2022

first: Marta

last: Berrocal-Lobo

address: Antonio Nováis 10, s/n

department: System and Natural Resources

institute: School of Forestry Engineering and Natural Resources

data_processing:
Real Time Analysis software (RTA) used for basecalling.
PCR duplicates are removed using Cutadapt software.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
Know genes and transcripts are assembled with StringTie with aligned reads based on reference genome model (SL2.50).
Read count is calculated using featureCounts function from Bioconductor
Genome_build: SGN release version SL2.50
Supplementary_files_format_and_content: Matrix table with raw gene reads counts for every gene and every sample

organism: Solanum lycopersicum

source_name: AEO seed coating + Fusarium inoculated (shoot)

growth_protocol: Hydroponic culture

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tomato seeds were coated with Artemissia Absinthium essential oil (AEO) and inoculated with Fusarium oxysporum sp. Oxysporum radicis lycopersici, data were collected after 12 days

tag: var.

value: marmande

value: Shoot

value: AEO seed coating + Fusarium inoculated


title: SFE2


title: KU50 FEC 2

description: Gene expression data from KU50 FEC


title: 60444 FEC 2

description: Gene expression data from 60444 FEC


title: SFE3


title: KM12SM (replica 1)


title: SF3

source_name: Fuarium inoculated (shoot)

value: Fuarium inoculated


title: SE3

source_name: AEO seed coating (shoot)

value: AEO seed coating


title: SF1


title: SE2


title: SE1


title: SF2


title: KM12SM (replica 2)


title: CS3

source_name: Control (shoot)

value: Control


title: 60444 FEC 1

description: Gene expression data from 60444 FEC


title: CS2


title: CS1


title: RF3

source_name: Fuarium inoculated (root)

value: Root


title: RF2


title: RF1


title: KU50 FEC 1

description: Gene expression data from KU50 FEC


title: KU50 FEC 4

description: Gene expression data from KU50 FEC


title: RFE3

source_name: AEO seed coating + Fusarium inoculated (root)


title: RFE2


title: C.reinhardtii 1000uM Mn rep3

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

data_processing:
Basecalls performed using CASAVA
Alignment of reads to reference genome with STAR --alignIntronMax 3000
FPKMs calculated with cuffdiff (v2.2.1) --multi-read-correct --max-bundle_frags 1000000000 --library-type fr-firststrand
FPKM table prepared with cummeRbund in R.
Genome_build: Chlamydomonas reinhardtii v5.6 (phytozome.net)
Supplementary_files_format_and_content: tab-delimited text file of FPKMs for each gene in each sample

organism: Chlamydomonas reinhardtii

source_name: liquid cultures of microalgae

growth_protocol: Flasks containing 1 L of Tris-Acetate-Phosphate (TAP) medium supplemented with either 6 uM Mn (control) or 1000 uM Mn (experimental) were innoculated with Chlamydomonas reinhardtii (strain CC-4532) at 1x10^4 cells/mL. These cultures were grown on shaking platforms (180 rpm) at 24°C under continuous light (~50 umol * m^-2 * s^-1) until they reached 3x10^6 cells/mL.

extract_protocol:
SDS+proteinase K digestion and phenol/chloroform extraction.
Standard Illumina HiSeq poly-A selected libraries.

treatment_protocol: TAP media with 1000 uM or 6 uM Mn.

tag: growth conditions

value: mid-log photoheterotrophic growth

tag: mn in media


title: RFE1


title: C.reinhardtii 1000uM Mn rep1


title: RE1

source_name: AEO seed coating (root)


title: RE3


title: RE2


title: CR1

source_name: Control (root)


title: C.reinhardtii 1000uM Mn rep2


title: C.reinhardtii 6uM Mn rep2

value: 6 uM


title: CR3


title: CR2


title: C.reinhardtii 6uM Mn rep3


title: C.reinhardtii 6uM Mn rep1


title: ChIPseq.iWAT.GABPa.1

first: Chunjie

last: Jiang

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

library_source: genomic

data_processing:
RNA-seq reads were trimmed using fastp v0.19.5 to remove reads with low quality, too short, or too many N. Trimmed reads were then aligned to human reference genome (mm10) using Hesat2 with default parameters. Only unique mapped reads extracted by SAMtools v1.9 were considered for downstream analyses. Quantification of gene from Ensembl database was estimated using StringTie v1.3.4
ChIP-seq raw reads were trimmed using fastp v0.19.5. Trimmed reads were then aligned to human reference genome (mm10) using Bowtie2 v2.3.0 with default parameters. SAMtools v1.9 was used to extract unique mapped reads and remove duplicated reads following by peak calling and de novo motif analyses using HOMER v4.9 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized abundance measurement was generated using StringTie.Expression profile were extracted using perl script;

molecule: genomic DNA

source_name: Adipose

extract_protocol:
Total RNA was extracted by using Trizol chloroform followed by purification with Qiagen RNeasey Mini kit.
DNA was isolated using phenol/chloroform extraction and NaCl/EtOH precipitated with 20 μg glycogen carrier.
RNA libraries were prepared for sequencing by Novogene (CA).
ChIP-seq library was prepared for sequencing according to the amplification protocol from Illumina.

value: iWAT

tag: chip antibody

value: GABPa antibody (Santa Cruz, sc-22810)


title: ChIPseq.iWAT.GABPa.2


title: mCherry+ siLP eosinophil, biological rep5

first: Wei-Le

last: Wang

address: BJCIH, 8th Floor, Room 8107, 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University

description:
mCherry+5
Gene expression data from sorted mCherry+ or mCherry- eosinophils.

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Mouse Gene 1.0 ST Array or Mouse Gene 2.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G 3000.

data_processing:
The data were processed using the AffySTExpressionFileCreator function of GenePattern using default settings that RMA normalize and background correct data, generating a .gct file of gene expression.
Log2 transformation was removed because data were analyzed using MultiplotStudio, which automatically log2 transforms data.

label: biotin

source_name: siLP eosinophil

label_protocol: Biotinylated cDNA were prepared according to the standard NuGEN WT-Ovation PicoSL RNA Amplification system from 2 ng of total RNA.

extract_protocol: Eosinophil subsets were sorted from the siLP of Clec4a4-KI mCherry mice for identifying Clec4a4+ and Clec4a4− eosinophil-specific genes, WT mice, and Ahr KO mice for identifying AHR-dependent and -independent genes. RNA was extracted using the RNeasy Micro Kit according to the manufacturer instructions.

value: Small intestine

value: mCherry+ siLP eosinophils


title: mCherry- siLP eosinophil, biological rep5

description:
mCherry-5
Gene expression data from sorted mCherry+ or mCherry- eosinophils.

value: mCherry- siLP eosinophils


title: mCherry- siLP eosinophil, biological rep2

description:
mCherry-2
Gene expression data from sorted mCherry+ or mCherry- eosinophils.


title: ChIPseq.iWAT.g2.3

value: Anti-HA Magnetic Beads (Thermo Fisher, Cat #88837)


title: mCherry- siLP eosinophil, biological rep3

description:
mCherry-3
Gene expression data from sorted mCherry+ or mCherry- eosinophils.


title: ChIPseq.iWAT.g2.4


title: mCherry+ siLP eosinophil, biological rep2

description:
mCherry+2
Gene expression data from sorted mCherry+ or mCherry- eosinophils.


title: mCherry- siLP eosinophil, biological rep4

description:
mCherry-4
Gene expression data from sorted mCherry+ or mCherry- eosinophils.


title: ChIPseq.iWAT.g2.2


title: ChIPseq.iWAT.g2.1


title: ChIPseq.iWAT.g1.3


title: ChIPseq.iWAT.g1.4


title: ChIPseq.eWAT.WT

value: eWAT


title: ChIPseq.iWAT.g1.2


title: ChIPseq.iWAT.g1.1


title: mCherry+ siLP eosinophil, biological rep3

description:
mCherry+3
Gene expression data from sorted mCherry+ or mCherry- eosinophils.


title: ChIPseq.eWAT.g2.3


title: mCherry+ siLP eosinophil, biological rep1

description:
mCherry+1
Gene expression data from sorted mCherry+ or mCherry- eosinophils.


title: mCherry+ siLP eosinophil, biological rep4

description:
mCherry+4
Gene expression data from sorted mCherry+ or mCherry- eosinophils.


title: ChIPseq.eWAT.g2.2


title: ChIPseq.eWAT.g2.1


title: ChIPseq.eWAT.g1.3


title: mCherry- siLP eosinophil, biological rep1

description:
mCherry-1
Gene expression data from sorted mCherry+ or mCherry- eosinophils.


title: ChIPseq.BAT.WT

value: BAT


title: ChIPseq.eWAT.g1.2


title: ChIPseq.BAT.g2.4


title: ChIPseq.iWAT.WT


title: ChIPseq.BAT.g2.2


title: ChIPseq.BAT.g2.3


title: ChIPseq.BAT.g1.4


title: ChIPseq.BAT.g2.1


title: ChIPseq.BAT.g1.3


title: ChIPseq.BAT.g1.1


title: ChIPseq.BAT.g1.2


title: ChIPseq.eWAT.g1.1


title: 1000 IUml IFN_2

city: Wako-shi

first: Yutaka

last: Furutani

state: Saitama

address: 2-1 Hirosawa

department: Center for Integrative Medical Sciences

description:
HBV-infected PXB cells
replicate 2

hyb_protocol: The converted cRNA was then labeled and hybridized using the Human HT-12 v4 Expression BeadChip Kit according to the manufacturer’s instruction.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were processed with a package from Bioconductor (lumi) using a free software environment, R (http://www.r-project.org/).

source_name: Primary cultured human hepatocytes (PXB cells)

label_protocol: Five hundred nanograms of total RNA was used for first-stranded cDNA and second-stranded cRNA preparation with the Illumina TotalPrep RNA Amplification Kit (Ambion, USA).

growth_protocol: PXB cells cultured in 24-well plates were not infected or were infected with 3 genome equivalents per cell of HBV C_AT.

extract_protocol: Following treatments, total RNA was purified from the cells using an RNeasy mini kit (Qiagen).

treatment_protocol: After 24 days of infection, the cells were treated with DMSO, 0.3 and 30 microM iCDM-34 or 1000 IU/ml IFNalpha for 7 days (n=3).

value: PXB

tag: infection

value: HBV

value: 1000 IUml IFN


title: 1000 IUml IFN_3

description:
HBV-infected PXB cells
replicate 3


title: 1000 IUml IFN_1

description:
HBV-infected PXB cells
replicate 1


title: 0.3 uM iCDM-34_3

description:
HBV-infected PXB cells
replicate 3

value: 0.3 uM iCDM-34


title: 20_9153-T63_P27

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw data were processed using bcl2fastq Conversion Software (Illumina) to obtain FASTQ files, and the FASTQ files were aligned to the hg38 genome using STAR (Dobin et al., 2013).
Gene expression was quantified with featureCounts (Liao et al., 2014).
Assembly: hg38
Supplementary files format and content: tab delimited file including the counts of reads for all genes and for all samples

source_name: PAXgene blood

growth_protocol: All biosamples were collected in accordance with the guidelines of Institutional Review Boards of Icahn School of Medicine  and  the Naval Medical Research Center (protocol number NMRC.2020.0006) in compliance with all applicable U.S. federal regulations governing the protection of human subjects

extract_protocol:
Total RNA from PAXgene preserved blood was extracted using the Agencourt RNAdvance Blood Kit (Beckman Coulter) on a BioMek FXP Laboratory Automation Workstation (Beckman Coulter). Concentration and integrity (RIN) of isolated RNA were determined using Quant-iT™ RiboGreen™ RNA Assay Kit (Thermo Fisher) and an RNA Standard Sensitivity Kit (DNF-471, Agilent Technologies, Santa Clara, CA, USA) on a Fragment Analyzer Automated CE system (Agilent Technologies), respectively.
cDNA libraries were constructed from total RNA using the Universal Plus mRNA-Seq kit (Tecan Genomics, San Carlos, CA, United States) in a Biomek i7 Automated Workstation (Beckman Coulter). Briefly, mRNA was isolated from purified 300 ng total RNA using oligo-dT beads and used to synthesize cDNA following the manufacturer’s instructions. The transcripts for ribosomal RNA (rRNA) and globin were further depleted using the AnyDeplete kit (Tecan Genomics) prior to the amplification of libraries. Library concentration was assessed fluorometrically using the Qubit dsDNA HS Kit (Thermo Fisher), and quality was assessed with the Genomic DNA 50Kb Analysis Kit (DNF-467, Agilent Technologies). Following library preparation, samples were pooled, preliminary sequencing of cDNA libraries (average read depth of 90,000 reads) was performed using a MiSeq system (Illumina) to confirm library quality and concentration. Deep sequencing was subsequently performed using an S4 flow cell in a NovaSeq sequencing system (Illumina) (average read depth ~30 million pairs of 2×100 bp reads). In addition to the 8-base i5 and i7 barcodes, the i7 adaptor contains 8 random bases immediately following the library index. The additional 8 bases are used for duplicate read determination using the Duplicate Marking Tool. To take advantage of this feature, the libraries were sequenced using 16 cycles for the i7 index read.

treatment_protocol: Whole blood was collected in Paxgene blood collection tubes (BD Biosciences) according to the manufacturer's instructions and stored at -80C until RNA extraction.

value: blood

tag: enrollment batch

value: Later Surveillance

tag: biocollection id

tag: rna-seq plate

tag: participant id

tag: sample collection time point (days since t0)

tag: enrollment date t0

tag: Sex

value: M

tag: age

tag: ethnicity

value: Non-Hispanic

tag: race

value: White

tag: pcr test for sars-cov-2

value: Not

tag: group

value: Post


title: 20_8860-T00_P27

tag: tissue

value: Asian

value: Control


title: 20_9520-T00_P27

value: Initial Outbreak

value: F

value: Hispanic

tag: symptom

value: fatigue

value: Moderate


title: 30 uM iCDM-34_2

description:
HBV-infected PXB cells
replicate 2

tag: cell line

value: PXB

value: HBV

tag: treatment

value: 30 uM iCDM-34


title: 30 uM iCDM-34_3

description:
HBV-infected PXB cells
replicate 3

tag: infection


title: 20_9127-T91_P27

value: blood

tag: enrollment batch


title: DMSO_1

description:
HBV-infected PXB cells
replicate 1

value: DMSO


title: DMSO_2

description:
HBV-infected PXB cells
replicate 2


title: 20_8800-T00_P27

value: Later Surveillance

tag: biocollection id

value: M


title: 20_9127-T00_P27

tag: rna-seq plate

value: Non-Hispanic

value: White


title: DMSO_3

description:
HBV-infected PXB cells
replicate 3


title: 20_9153-T00_P27

tag: participant id

value: Not


title: 20_9719-T91_P27

tag: sample collection time point (days since t0)

value: Post


title: 20_9719-T00_P27

tag: enrollment date t0

value: Control


title: 0.3 uM iCDM-34_2

description:
HBV-infected PXB cells
replicate 2

value: 0.3 uM iCDM-34


title: 30 uM iCDM-34_1

description:
HBV-infected PXB cells
replicate 1


title: 20_9749-T00_P27

tag: Sex

value: F


title: 20_8629-T84_P27

tag: age


title: 20_8629-T00_P27

tag: ethnicity


title: 20_8590-T84_P27

value: Hispanic


title: 20_8590-T74_P27

value: Detected

value: First


title: 20_8359-T56_P27

tag: race

value: Other


title: 20_8991-T00_P27

value: Initial Outbreak

value: Exposed


title: 0.3 uM iCDM-34_1

description:
HBV-infected PXB cells
replicate 1

value: PXB

value: HBV


title: 20_8359-T00_P27

value: blood

value: Later Surveillance

tag: pcr test for sars-cov-2


title: 20_8349-T70_P27

value: M

value: Black

tag: group


title: 20_8349-T00_P27

tag: tissue

value: Not


title: 20_8257-T00_P27

value: Non-Hispanic

value: White

value: Mild


title: 20_8800-T91_P27

value: Post


title: 20_7981-T00_P27

value: Control


title: 20_7981-T91_P27


title: 20_7382-T63_P27

value: Asian

value: Detected

value: Mid


title: 20_7382-T00_P27


title: 20_7382-T74_P27


title: 20_7084-T00_P27

value: Hispanic


title: 20_6957-T77_P27

tag: symptom

value: chill;msk;fatigue;sob;headache


title: 20_7202-T00_P27


title: 20_6215-T74_P27


title: 20_7160-T00_P27

value: F


title: 20_7202-T56_P27


title: 20_7202-T46_P27


title: 20_6636-T00_P27


title: 20_7084-T91_P27


title: 20_6957-T74_P27

value: First


title: 20_6132-T00_P27

value: blood


title: 20_6215-T70_P27

value: Later Surveillance


title: 20_8590-T77_P27

value: M

value: msk;fatigue;cough;headache;taste


title: 20_5765-T91_P27

value: Not


title: 20_5513-T00_P27

value: Initial Outbreak

value: Non-Hispanic

value: Exposed


title: 20_5765-T00_P27

value: White


title: 20_5189-T63_P27

value: Black


title: 20_5189-T00_P27

value: Control


title: 20_9636-T00_P26


title: 20_9614-T91_P26

value: Post


title: 20_9127-T91_P26


title: 20_7620-T00_P27

value: Detected


title: 20_9127-T00_P26


title: 20_8795-T00_P26

value: headache


title: 20_8122-T00_P26


title: 20_9058-T84_P26


title: 20_6586-T91_P26


title: 20_9931-T00_P26

value: Hispanic


title: 20_8122-T91_P26


title: 20_6529-T98_P26


title: 20_6957-T84_P27

value: Mid


title: 20_9058-T00_P26


title: 20_6529-T00_P26


title: 20_6586-T00_P26


title: 20_6228-T91_P26


title: 20_8436-T00_P26


title: 20_7160-T91_P27

value: F


title: 20_6132-T84_P27

value: blood


title: 20_7160-T00_P26

value: Later Surveillance


title: 20_6228-T00_P26

value: M


title: 20_9746-T77_P25


title: 20_5399-T00_P26


title: 20_5011-T00_P26


title: 20_9746-T56_P25


title: 20_9746-T53_P25


title: 20_9931-T77_P26


title: 20_9746-T00_P25


title: 20_9614-T00_P26


title: 20_9704-T46_P25

value: fatigue;cough;sob;nv;headache

value: First


title: 20_7160-T91_P26

value: Not


title: 20_9479-T00_P25

value: Asian


title: 20_9479-T42_P25


title: 20_9571-T28_P25

value: Non-Hispanic


title: 20_7794-T42_P25

value: White


title: 20_9479-T39_P25


title: 20_9746-T49_P25


title: 20_9636-T00_P25

value: Black


title: 20_9704-T49_P25


title: 20_8360-T39_P25


title: 20_7794-T00_P25

value: Control


title: 20_8360-T70_P25

value: Post


title: 20_9479-T35_P25

value: Detected


title: 20_9571-T00_P25


title: 20_9571-T32_P25


title: 20_7794-T35_P25


title: 20_7647-T39_P25


title: 20_7794-T39_P25


title: 20_8360-T00_P25


title: 20_7647-T56_P25


title: 20_7647-T28_P25


title: 20_7647-T35_P25


title: 20_7647-T32_P25


title: 20_7647-T00_P25


title: 20_7013-T46_P25


title: 20_7013-T00_P25


title: 20_9704-T00_P25


title: 20_6250-T77_P25


title: 20_6238-T60_P25


title: 20_6250-T39_P25


title: 20_6250-T35_P25


title: 20_6046-T56_P25


title: 20_5399-T00_P25


title: 20_6046-T32_P25


title: 20_5390-T20_P25


title: 20_5390-T14_P25


title: 20_6238-T56_P25


title: 20_6046-T35_P25


title: 20_6046-T42_P25


title: 20_6250-T00_P25


title: 20_5340-T14_P25

value: Multi-racial


title: 20_6046-T39_P25


title: 20_5281-T46_P25


title: 20_5340-T17_P25


title: 20_5281-T49_P25

value: msk;fatigue;cough;sob;headache;taste


title: 20_5340-T10_P25

value: Mid


title: 20_5390-T10_P25


title: 20_6238-T53_P25

value: Hispanic


title: 20_5281-T00_P25

value: blood

value: F


title: 20_5281-T42_P25

value: Later Surveillance


title: 20_5275-T91_P25

value: M


title: 20_5275-T77_P25


title: 20_5275-T60_P25


title: 20_5275-T56_P25


title: 20_5275-T49_P25


title: 20_9937-T77_P24

value: fatigue;sob;headache;taste;abd


title: 20_5275-T53_P25


title: 20_5275-T00_P25

value: Not


title: 20_9937-T53_P24


title: 20_9937-T56_P24


title: 20_9728-T98_P24


title: 20_9937-T49_P24


title: 20_9937-T00_P24


title: 20_6238-T49_P25

value: First


title: 20_9728-T56_P24

value: Non-Hispanic


title: 20_9728-T42_P24


title: 20_9728-T00_P24


title: 20_9680-T91_P24

value: throat;cough;sob;nv


title: 20_5390-T17_P25

value: White


title: 20_9728-T46_P24


title: 20_9680-T53_P24

value: Black

value: throat;cough;nv;headache


title: 20_9680-T56_P24

value: nv;headache

value: Post


title: 20_9636-T00_P24

value: Control


title: 20_9680-T00_P24


title: 20_9680-T49_P24

value: Detected

value: throat;cough

value: Mid


title: 20_8902-T42_P24

value: blood

value: msk;throat;taste


title: 20_8902-T35_P24

value: Later Surveillance

value: M


title: 20_8902-T39_P24

value: throat;cough;sob;taste


title: 20_8761-T10_P24

value: F

value: headache;taste


title: 20_8902-T00_P24

value: Non-Hispanic

value: Not

value: throat;headache


title: 20_8761-T07_P24

value: Black


title: 20_8491-T49_P24

value: White

value: headache


title: 20_8491-T39_P24


title: 20_8761-T00_P24

value: msk;abd

value: First


title: 20_8491-T42_P24

value: Detected


title: 20_8491-T00_P24

value: Control


title: 20_7992-T10_P24

value: blood

value: Mid


title: 20_7577-T63_P24

value: Later Surveillance

value: Post


title: 20_9728-T70_P24

value: M

value: Multi-racial


title: 20_7577-T56_P24

value: F


title: 20_7992-T00_P24

value: Non-Hispanic


title: 20_7992-T14_P24


title: 20_7121-T60_P24

value: Not


title: 20_7992-T07_P24


title: 20_7121-T56_P24

value: throat


title: 20_9728-T49_P24

value: diarr


title: 20_7121-T53_P24

value: White


title: 20_6864-T39_P24

value: chill;throat;headache


title: 20_7121-T49_P24


title: 20_6864-T35_P24


title: 20_7121-T00_P24


title: 20_8795-T00_P24

value: headache


title: 20_6717-T00_P24

value: Hispanic

value: AI/AN


title: 20_6349-T77_P24

value: msk;fatigue;abd


title: 20_6349-T63_P24

value: blood


title: 20_6349-T56_P24


title: 20_6349-T53_P24

value: Detected

value: Mid


title: 20_6349-T49_P24

value: Later Surveillance


title: 20_6349-T00_P24

value: M

value: Control


title: 20_5983-T00_P24


title: 20_8491-T35_P24


title: 20_5983-T35_P24

value: throat;nv


title: 20_8436-T00_P24


title: 20_5399-T00_P24


title: 20_5748-T00_P24

value: Non-Hispanic


title: 20_5750-T56_P24

value: F


title: 20_9943-T39_P23

value: Not

value: Post


title: 20_5750-T00_P24

value: White

value: First


title: 20_5748-T39_P24


title: 20_7121-T105_P24


title: 20_9918-T00_P23


title: 20_9943-T35_P23


title: 20_9918-T42_P23


title: 20_9918-T49_P23


title: 20_9943-T00_P23


title: 20_9918-T35_P23


title: 20_9918-T63_P23


title: 20_6864-T00_P24


title: 20_9758-T00_P23


title: 20_9636-T00_P23

value: Black


title: 20_9415-T49_P23

value: chill;fatigue;throat;headache


title: 20_9758-T46_P23

value: Hispanic


title: 20_9415-T35_P23


title: 20_9415-T46_P23


title: 20_9415-T00_P23


title: 20_9343-T35_P23


title: 20_9343-T39_P23


title: 20_9343-T42_P23


title: 20_9343-T00_P23


title: 20_9943-T63_P23


title: 20_9027-T00_P23


title: 20_8866-T74_P23

value: Asian


title: 20_8866-T00_P23

value: blood


title: 20_8601-T00_P23


title: 20_8866-T70_P23

value: Detected


title: 20_8436-T00_P23


title: 20_8015-T77_P23


title: 20_7387-T39_P23

value: Mid


title: 20_7387-T35_P23

value: Later Surveillance


title: 20_8015-T63_P23

value: M


title: 20_9918-T39_P23

value: fatigue


title: 20_8015-T00_P23

value: Control


title: 20_8015-T35_P23


title: 20_9758-T49_P23


title: 20_7359-T14_P23

value: Non-Hispanic


title: 20_7387-T00_P23


title: 20_7359-T10_P23


title: 20_9415-T77_P23


title: 20_6444-T00_P23

value: Other


title: 20_6444-T35_P23


title: 20_6444-T39_P23


title: 20_5600-T39_P23


title: 20_5600-T42_P23


title: 20_8601-T35_P23


title: 20_5412-T39_P23


title: 20_5412-T77_P23

value: Not


title: 20_5600-T00_P23


title: 20_5600-T35_P23


title: 20_5412-T00_P23


title: 20_5412-T35_P23


title: 20_5225-T42_P23

value: Post


title: 20_8405-T00_P23

value: White


title: 20_5225-T39_P23


title: 20_9997-T42_P22


title: 20_9636-T00_P22

value: F


title: 20_9997-T56_P22


title: 20_5225-T35_P23

value: Black


title: 20_9997-T00_P22


title: 20_5225-T00_P23


title: 20_9997-T35_P22

value: throat


title: 20_5061-T00_P23


title: 20_5061-T63_P23


title: 20_9249-T77_P22

value: Hispanic


title: 20_9997-T39_P22


title: 20_9249-T39_P22

value: cough


title: 20_8610-T56_P22

value: blood


title: 20_9249-T56_P22


title: 20_9249-T00_P22


title: 20_8610-T77_P22


title: 20_9249-T42_P22

value: Detected


title: 20_8610-T35_P22

value: Mid


title: 20_8610-T39_P22

value: Later Surveillance


title: 20_8795-T00_P22

value: headache


title: 20_8000-T00_P22


title: 20_9249-T35_P22

value: M


title: 20_8610-T00_P22

value: Control


title: 20_6506-T00_P22


title: 20_6207-T56_P22


title: 20_8610-T42_P22


title: 20_8141-T00_P22


title: 20_9997-T91_P22


title: 20_6207-T91_P22


title: 20_8141-T46_P22


title: 20_7916-T53_P22

value: msk


title: 20_8141-T49_P22

value: taste


title: 20_7916-T49_P22

value: msk;abd


title: 20_7916-T00_P22

value: Not


title: 20_7916-T46_P22

value: White

value: Problems:Inconclusive ran twice. New sample required


title: 20_7916-T56_P22


title: 20_6207-T39_P22


title: 20_7916-T91_P22


title: 20_6207-T35_P22


title: 20_6207-T00_P22


title: 20_6037-T00_P22


title: 20_6037-T46_P22


title: 20_6207-T49_P22


title: 20_5932-T91_P22

value: Post


title: 20_6037-T49_P22


title: 20_5932-T56_P22


title: 20_5932-T49_P22


title: 20_5932-T46_P22


title: 20_8436-T00_P22


title: 20_5894-T91_P22


title: 20_5894-T39_P22


title: 20_5894-T35_P22


title: 20_5894-T00_P22


title: 20_5889-T49_P22

value: Non-Hispanic


title: 20_5564-T56_P22

value: Hispanic

value: Asian


title: 20_5889-T00_P22

value: blood


title: 20_5719-T28_P22

value: Detected

value: First


title: 20_5564-T91_P22

value: Later Surveillance


title: 20_5889-T46_P22

value: Mid


title: 20_5719-T00_P22

value: M


title: 20_5564-T00_P22

value: Control


title: 20_5564-T46_P22


title: 20_5399-T00_P22


title: 20_5564-T49_P22

value: chill;msk;fatigue;cough;sob;headache


title: 20_9798-T70_P21

value: Black


title: 20_9690-T88_P21


title: 20_5035-T00_P22


title: 20_9690-T84_P21


title: 20_9690-T00_P21


title: 20_9690-T77_P21

value: fvr;chill;cough;headache


title: 20_9798-T00_P21

value: Not


title: 20_9636-T00_P21

value: F


title: 20_9414-T00_P21


title: 20_9359-T81_P21

value: White


title: 20_9359-T77_P21


title: 20_9359-T74_P21


title: 20_9359-T00_P21


title: 20_9047-T84_P21

value: cough

value: Post


title: 20_5932-T00_P22

value: Hispanic


title: 20_9047-T77_P21


title: 20_9047-T74_P21


title: 20_9047-T00_P21


title: 20_8580-T84_P21


title: 20_8795-T00_P21

value: headache


title: 20_9798-T74_P21

value: blood

value: Non-Hispanic


title: 20_8580-T88_P21

value: Detected


title: 20_8580-T00_P21

value: Later Surveillance


title: 20_8580-T91_P21

value: Mid


title: 20_8845-T00_P21

value: M


title: 20_6803-T00_P21

value: Control


title: 20_6803-T70_P21

value: First


title: 20_7181-T00_P21


title: 20_8436-T00_P21


title: 20_6287-T77_P21

value: Black

value: throat;headache


title: 20_6228-T49_P21


title: 20_6287-T74_P21


title: 20_6665-T00_P21

value: Not


title: 20_6228-T00_P21


title: 20_6287-T00_P21


title: 20_6228-T91_P21


title: 20_9359-T84_P21


title: 20_6195-T74_P21


title: 20_6228-T28_P21

value: msk;sob;headache

value: Pre


title: 20_6195-T00_P21

value: White


title: 20_6195-T81_P21


title: 20_6195-T77_P21


title: 20_6195-T84_P21

value: fatigue;sob


title: 20_5951-T63_P21

value: Hispanic


title: 20_5483-T84_P21

value: Post


title: 20_7738-T00_P21

value: blood


title: 20_5951-T00_P21


title: 20_5220-T00_P21


title: 20_5483-T74_P21

value: Non-Hispanic


title: 20_5108-T74_P21


title: 20_5483-T77_P21


title: 20_5108-T63_P21

value: msk;fatigue


title: 20_9818-T39_P20

value: Later Surveillance

value: Detected

value: msk;fatigue;throat;cough;sob;headache


title: 20_6803-T74_P21

value: M

value: Mid


title: 20_5399-T00_P21

value: Control


title: 20_5108-T67_P21


title: 20_6228-T53_P21


title: 20_5108-T00_P21


title: 20_9995-T00_P20


title: 20_5483-T00_P21


title: 20_9818-T00_P20


title: 20_9729-T39_P20

value: sob;taste


title: 20_9818-T35_P20


title: 20_9729-T00_P20

value: Not


title: 20_9729-T35_P20


title: 20_9636-T00_P20

value: F

value: Black


title: 20_5951-T74_P21

value: White


title: 20_9099-T42_P20


title: 20_9099-T35_P20

value: First


title: 20_8623-T35_P20


title: 20_9099-T00_P20


title: 20_8623-T39_P20


title: 20_8795-T00_P20

value: headache


title: 20_5108-T70_P21

value: Post


title: 20_7386-T39_P20

value: blood

value: taste


title: 20_8495-T35_P20

value: Non-Hispanic


title: 20_8495-T00_P20

value: Later Surveillance


title: 20_8623-T42_P20

value: Detected

value: cough


title: 20_7386-T35_P20

value: M


title: 20_7645-T42_P20

value: Mid


title: 20_8623-T00_P20

value: Control


title: 20_7645-T00_P20


title: 20_9818-T42_P20


title: 20_9995-T35_P20

value: throat;cough;taste


title: 20_8436-T00_P20

value: Hispanic

value: Not


title: 20_7645-T32_P20

value: Black


title: 20_7645-T39_P20


title: 20_7386-T00_P20

value: White


title: 20_7086-T35_P20


title: 20_6769-T35_P20


title: 20_8495-T39_P20


title: 20_5346-T49_P20


title: 20_5346-T42_P20


title: 20_7086-T39_P20


title: 20_6769-T39_P20


title: 20_9198-T56_P19


title: 20_9198-T77_P19


title: 20_6441-T00_P20


title: 20_6441-T35_P20


title: 20_9198-T35_P19


title: 20_9198-T42_P19


title: 20_6769-T00_P20

value: throat


title: 20_5300-T00_P20


title: 20_9636-T00_P19

value: F


title: 20_9198-T46_P19

value: Post


title: 20_9198-T00_P19

value: blood


title: 20_5346-T39_P20


title: 20_9088-T49_P19


title: 20_5399-T00_P20


title: 20_7086-T00_P20


title: 20_5346-T00_P20


title: 20_9088-T39_P19


title: 20_5300-T28_P20

value: First


title: 20_9088-T42_P19

value: Non-Hispanic


title: 20_8739-T49_P19

value: Later Surveillance


title: 20_9099-T39_P20

value: Detected


title: 20_9088-T63_P19


title: 20_8739-T00_P19


title: 20_8656-T77_P19


title: 20_7645-T35_P20


title: 20_8656-T42_P19


title: 20_8656-T35_P19


title: 20_9088-T35_P19


title: 20_8640-T42_P19

value: Other


title: 20_5346-T35_P20

value: M


title: 20_8640-T35_P19

value: Mid


title: 20_8640-T00_P19

value: Control


title: 20_8739-T39_P19

value: msk;fatigue;cough;sob


title: 20_8640-T63_P19

value: Hispanic


title: 20_8739-T35_P19

value: cough;sob


title: 20_7893-T56_P19

value: Not


title: 20_8640-T39_P19

value: msk;throat


title: 20_9088-T00_P19

value: White


title: 20_8656-T46_P19


title: 20_7893-T77_P19


title: 20_8656-T00_P19


title: 20_8656-T39_P19


title: 20_8640-T49_P19


title: 20_7893-T42_P19


title: 20_7893-T35_P19


title: 20_7893-T00_P19


title: 20_6749-T17_P19


title: 20_7893-T46_P19


title: 20_6749-T10_P19


title: 20_8739-T42_P19


title: 20_6749-T14_P19


title: 20_6599-T77_P19


title: 20_6599-T46_P19

value: cough


title: 20_6599-T56_P19

value: Post


title: 20_8656-T56_P19

value: blood


title: 20_6599-T00_P19


title: 20_6599-T42_P19


title: 20_6599-T35_P19

value: fatigue;cough;sob


title: 20_6582-T39_P19

value: Multi-racial

value: headache


title: 20_6453-T77_P19

value: Later Surveillance

value: Non-Hispanic


title: 20_6582-T77_P19

value: M


title: 20_6582-T00_P19


title: 20_6582-T46_P19


title: 20_6453-T56_P19


title: 20_6453-T39_P19

value: Detected

value: Mid


title: 20_6453-T46_P19


title: 20_6453-T35_P19


title: 20_6453-T00_P19

value: Control


title: 20_5913-T56_P19


title: 20_5913-T77_P19


title: 20_6453-T42_P19


title: 20_5913-T42_P19


title: 20_5434-T35_P19

value: First


title: 20_5913-T39_P19


title: 20_5434-T00_P19


title: 20_5399-T00_P19


title: 20_5913-T46_P19


title: 20_5913-T35_P19


title: 20_5124-T63_P19

value: msk;sob


title: 20_5124-T35_P19


title: 20_5124-T00_P19

value: Not


title: 20_5124-T39_P19

value: msk;throat;cough;sob;headache;taste


title: 20_5124-T49_P19

value: White

value: msk;fatigue;throat;sob;headache;taste


title: 20_5124-T42_P19

value: msk;throat;sob;taste


title: 20_6582-T56_P19

value: blood

value: Hispanic

value: Post


title: 20_9192-T42_P18

value: Black


title: 20_9192-T77_P18

value: Later Surveillance


title: 20_9192-T56_P18


title: 20_9636-T00_P18

value: F


title: 20_6599-T39_P19

value: M

value: Non-Hispanic

value: cough


title: 20_9192-T00_P18

value: Control


title: 20_9192-T39_P18


title: 20_8968-T77_P18


title: 20_6582-T35_P19

value: Multi-racial

value: fatigue;taste

value: Mid


title: 20_9192-T35_P18

value: Detected


title: 20_8968-T39_P18

value: White

value: chill;fatigue;throat;cough;sob


title: 20_8292-T39_P18


title: 20_8292-T42_P18

value: Not


title: 20_8968-T46_P18

value: blood


title: 20_5434-T39_P19


title: 20_8968-T42_P18


title: 20_8968-T00_P18


title: 20_8795-T00_P18

value: headache


title: 20_8292-T00_P18


title: 20_7244-T20_P18

value: Post


title: 20_7818-T00_P18


title: 20_8436-T00_P18

value: Hispanic


title: 20_7244-T70_P18

value: Later Surveillance


title: 20_8968-T56_P18


title: 20_7244-T14_P18


title: 20_7244-T00_P18

value: Pre


title: 20_7244-T17_P18

value: M


title: 20_8968-T35_P18

value: Non-Hispanic

value: chill;fatigue;throat;cough;sob;nv;diarr


title: 20_7818-T77_P18


title: 20_6924-T14_P18


title: 20_6924-T17_P18


title: 20_6764-T91_P18


title: 20_6764-T105_P18


title: 20_6764-T77_P18


title: 20_6586-T105_P18


title: 20_6764-T60_P18


title: 20_9099-T35_P18

value: First


title: 20_6764-T53_P18

value: msk;sob


title: 20_6764-T56_P18


title: 20_8292-T35_P18


title: 20_6586-T56_P18


title: 20_6764-T49_P18


title: 20_6586-T91_P18


title: 20_7818-T49_P18


title: 20_6481-T105_P18


title: 20_6586-T77_P18


title: 20_6481-T60_P18


title: 20_6481-T77_P18


title: 20_6481-T91_P18


title: 20_6586-T53_P18


title: 20_7818-T46_P18


title: 20_6586-T49_P18


title: 20_6481-T56_P18


title: 20_6481-T53_P18


title: 20_6586-T00_P18

value: Control


title: 20_6481-T00_P18


title: 20_6924-T00_P18


title: 20_5516-T00_P18


title: 20_5516-T46_P18


title: 20_5399-T00_P18


title: 20_5516-T42_P18

value: fatigue;cough;headache;taste;diarr


title: 20_5316-T56_P18

value: F


title: 20_5316-T77_P18

value: White


title: 20_5316-T42_P18

value: Detected

value: Mid


title: 20_5316-T46_P18

value: blood


title: 20_6764-T00_P18

value: Not


title: 20_5316-T39_P18


title: 20_5316-T35_P18


title: 20_5156-T77_P18

value: cough

value: Post


title: 20_5156-T42_P18

value: Later Surveillance


title: 20_5156-T39_P18


title: 20_5316-T00_P18

value: Hispanic


title: 20_5152-T46_P18

value: M


title: 20_5156-T00_P18


title: 20_5156-T56_P18


title: 20_6586-T60_P18

value: Non-Hispanic


title: 20_5152-T42_P18


title: 20_5156-T35_P18

value: throat;cough


title: 20_5152-T56_P18


title: 20_5152-T39_P18


title: 20_5152-T35_P18


title: 20_5152-T00_P18


title: 20_6481-T49_P18


title: 20_5039-T70_P18

value: Black


title: 20_5039-T84_P18


title: 20_5039-T56_P18


title: 20_5039-T42_P18


title: 20_5516-T77_P18


title: 20_5039-T39_P18

value: sob


title: 20_5039-T35_P18


title: 20_9790-T35_P17


title: 20_9694-T98_P17


title: 20_9694-T84_P17


title: 20_9790-T00_P17

value: Control


title: 20_5039-T32_P18

value: fvr

value: First


title: 20_5039-T00_P18

value: headache


title: 20_9694-T70_P17

value: White


title: 20_9694-T49_P17

value: Detected

value: Mid


title: 20_9694-T56_P17

value: blood

value: Not


title: 20_9388-T63_P17

value: Post


title: 20_9694-T46_P17

value: Later Surveillance

value: fvr;msk;fatigue


title: 20_9388-T35_P17

value: M


title: 20_9388-T77_P17


title: 20_9694-T42_P17


title: 20_9636-T00_P17

value: F

value: Hispanic


title: 20_9694-T00_P17


title: 20_9388-T46_P17


title: 20_9388-T42_P17


title: 20_9388-T00_P17


title: 20_9388-T39_P17


title: 20_8391-T56_P17


title: 20_8391-T49_P17


title: 20_8391-T00_P17

value: fatigue


title: 20_8391-T53_P17


title: 20_8325-T105_P17


title: 20_8325-T91_P17


title: 20_8325-T77_P17


title: 20_8795-T00_P17


title: 20_8325-T49_P17


title: 20_7871-T91_P17

value: Black


title: 20_8325-T00_P17

value: Control


title: 20_8263-T28_P17


title: 20_8263-T35_P17

value: fatigue;throat;cough;sob;headache;taste


title: 20_7871-T77_P17


title: 20_8142-T14_P17

value: Non-Hispanic

value: Asian


title: 20_7871-T56_P17


title: 20_7871-T60_P17


title: 20_7871-T49_P17


title: 20_7871-T00_P17


title: 20_6663-T77_P17

value: White


title: 20_6663-T91_P17


title: 20_7871-T53_P17


title: 20_6663-T63_P17


title: 20_6663-T42_P17


title: 20_6663-T39_P17


title: 20_6663-T00_P17


title: 20_6663-T35_P17

value: Detected


title: 20_6663-T46_P17

value: msk;fatigue;cough;taste


title: 20_8436-T00_P17

value: blood


title: 20_6012-T91_P17

value: Not


title: 20_6012-T60_P17

value: Post


title: 20_6012-T77_P17

value: Later Surveillance


title: 20_6012-T53_P17


title: 20_6012-T49_P17

value: Mid


title: 20_6012-T00_P17

value: M


title: 20_5586-T91_P17


title: 20_5586-T77_P17


title: 20_5586-T60_P17


title: 20_5399-T00_P17


title: 20_5586-T56_P17


title: 20_5586-T53_P17


title: 20_8263-T00_P17

value: First


title: 20_5586-T00_P17


title: 20_5268-T46_P17

value: Hispanic


title: 20_5268-T49_P17


title: 20_5054-T14_P17

value: headache;taste


title: 20_5054-T84_P17


title: 20_5054-T17_P17

value: taste


title: 20_5268-T00_P17

value: Black

value: Control


title: 20_5054-T10_P17

value: Non-Hispanic


title: 20_5054-T00_P17

value: Pre


title: 20_6663-T56_P17

value: White


title: 20_9553-T49_P16


title: 20_9553-T53_P16


title: 20_9553-T60_P16

value: Detected


title: 20_9553-T56_P16


title: 20_9636-T00_P16

value: F


title: 20_9553-T00_P16

value: blood


title: 20_9463-T14_P16

value: Problems:Inconclusive ran twice. New sample required


title: 20_9463-T17_P16


title: 20_9463-T10_P16


title: 20_9463-T00_P16

value: Not


title: 20_9317-T70_P16

value: Later Surveillance

value: chill;fatigue;cough;sob


title: 20_9317-T63_P16

value: M

value: Mid


title: 20_9317-T00_P16

value: Hispanic


title: 20_8671-T98_P16

value: Post


title: 20_8671-T84_P16


title: 20_8671-T56_P16

value: headache


title: 20_8671-T70_P16


title: 20_8671-T46_P16


title: 20_5586-T49_P17


title: 20_8671-T39_P16

value: chill;cough;headache

value: First


title: 20_8671-T42_P16

value: Non-Hispanic


title: 20_8671-T00_P16

value: Control


title: 20_8167-T53_P16

value: Black


title: 20_8167-T91_P16


title: 20_8167-T56_P16


title: 20_8167-T49_P16

value: Detected


title: 20_8088-T70_P16

value: Asian


title: 20_8088-T53_P16

value: blood


title: 20_8088-T56_P16


title: 20_8088-T98_P16


title: 20_8167-T00_P16


title: 20_8167-T28_P16


title: 20_8088-T84_P16


title: 20_8088-T46_P16


title: 20_8088-T00_P16


title: 20_9553-T91_P16

value: White


title: 20_8088-T42_P16


title: 20_7506-T67_P16


title: 20_7506-T63_P16

value: Not


title: 20_6862-T14_P16

value: Later Surveillance


title: 20_6862-T07_P16

value: fvr;headache


title: 20_6682-T98_P16

value: M


title: 20_9317-T67_P16

value: Mid


title: 20_6682-T84_P16

value: Hispanic


title: 20_6862-T00_P16


title: 20_8795-T00_P16

value: F


title: 20_6068-T91_P16

value: Post


title: 20_6682-T00_P16


title: 20_6682-T39_P16


title: 20_6682-T42_P16


title: 20_8671-T49_P16

value: headache


title: 20_6068-T60_P16


title: 20_5447-T00_P16


title: 20_6068-T00_P16


title: 20_5447-T84_P16

value: chill;headache

value: First


title: 20_6068-T77_P16


title: 20_5447-T88_P16


title: 20_5447-T91_P16


title: 20_5399-T00_P16

value: Control


title: 20_5405-T03_P16

value: Black


title: 20_5405-T00_P16

value: Detected


title: 20_5023-T46_P16


title: 20_9920-T70_P15

value: Non-Hispanic


title: 20_9920-T42_P15

value: blood


title: 20_5405-T10_P16


title: 20_9838-T91_P15

value: White

value: throat


title: 20_5405-T17_P16

value: Later Surveillance

value: Reinfection


title: 20_5405-T07_P16

value: M

value: Not


title: 20_9838-T49_P15

value: Mid


title: 20_5023-T77_P16

value: Hispanic


title: 20_7506-T00_P16


title: 20_7506-T74_P16

value: Post


title: 20_9838-T53_P15


title: 20_9920-T00_P15

value: Pre


title: 20_9636-T00_P15

value: F


title: 20_9838-T00_P15


title: 20_9614-T91_P15


title: 20_9614-T77_P15


title: 20_6682-T49_P16


title: 20_9838-T56_P15


title: 20_9614-T00_P15


title: 20_9509-T77_P15

value: fatigue;throat;sob;abd


title: 20_9509-T60_P15


title: 20_6682-T46_P16


title: 20_9838-T60_P15


title: 20_9509-T00_P15

value: Control


title: 20_9454-T70_P15


title: 20_9509-T53_P15

value: throat;nv;headache


title: 20_9614-T60_P15

value: Detected


title: 20_9454-T56_P15


title: 20_9509-T56_P15

value: Non-Hispanic

value: fatigue;throat


title: 20_5405-T21_P16

value: blood

value: Black


title: 20_9920-T56_P15

value: Later Surveillance

value: White


title: 20_5023-T00_P16

value: M


title: 20_9454-T00_P15

value: Not


title: 20_9509-T49_P15

value: msk;fatigue;throat;cough;sob

value: Mid


title: 20_9454-T42_P15

value: Hispanic


title: 20_8969-T53_P15


title: 20_8969-T91_P15

value: Post


title: 20_8969-T00_P15


title: 20_8436-T00_P15


title: 20_7690-T70_P15


title: 20_8969-T60_P15


title: 20_8795-T00_P15

value: F

value: headache


title: 20_8969-T56_P15


title: 20_7690-T28_P15


title: 20_7690-T56_P15


title: 20_7690-T00_P15

value: Pre


title: 20_7589-T77_P15


title: 20_7589-T91_P15


title: 20_7589-T63_P15


title: 20_7589-T56_P15


title: 20_7589-T35_P15


title: 20_9509-T91_P15

value: msk;fatigue;throat;cough


title: 20_7589-T39_P15


title: 20_7364-T91_P15


title: 20_7589-T00_P15

value: Control


title: 20_7364-T53_P15


title: 20_7364-T77_P15


title: 20_7364-T60_P15

value: Detected


title: 20_7364-T49_P15


title: 20_7364-T56_P15


title: 20_7364-T00_P15


title: 20_6529-T60_P15

value: Non-Hispanic

value: msk;fatigue;throat;sob;headache;abd


title: 20_6529-T98_P15

value: blood


title: 20_6529-T77_P15

value: Later Surveillance

value: msk;fatigue;headache


title: 20_6305-T91_P15

value: M

value: White


title: 20_6529-T00_P15

value: Not


title: 20_6305-T60_P15

value: Mid


title: 20_6305-T53_P15


title: 20_6305-T49_P15


title: 20_6305-T56_P15


title: 20_6305-T00_P15


title: 20_5399-T00_P15


title: 20_8969-T49_P15


title: 20_9931-T53_P14

value: Hispanic


title: 20_9931-T56_P14


title: 20_9931-T00_P14


title: 20_9914-T91_P14

value: AI/AN

value: Post


title: 20_9914-T56_P14

value: Reinfection


title: 20_9914-T00_P14


title: 20_7589-T42_P15


title: 20_9914-T39_P14


title: 20_9914-T42_P14


title: 20_9424-T70_P14


title: 20_9914-T35_P14


title: 20_9424-T56_P14


title: 20_9424-T28_P14


title: 20_9424-T10_P14


title: 20_9424-T00_P14

value: Pre


title: 20_9914-T77_P14


title: 20_9058-T53_P14

value: msk;fatigue;throat;cough;sob


title: 20_9058-T49_P14


title: 20_9058-T70_P14


title: 20_9931-T77_P14


title: 20_9058-T46_P14


title: 20_9058-T00_P14

value: Control


title: 20_9058-T42_P14


title: 20_8991-T00_P14

value: Initial Outbreak

value: Exposed


title: 20_8257-T00_P14

value: Non-Hispanic

value: Mild


title: 20_7910-T56_P14

value: blood

value: Later Surveillance


title: 20_7910-T10_P14

value: M

value: Problems:QNS/Leaked in Transit

value: headache


title: 20_7910-T03_P14

value: White

value: Not


title: 20_7910-T00_P14

value: Detected

value: First


title: 20_9931-T60_P14

value: Hispanic

value: Post


title: 20_9931-T49_P14

value: Mid


title: 20_7493-T17_P14


title: 20_7005-T14_P14

value: Reinfection


title: 20_7493-T10_P14


title: 20_7005-T10_P14


title: 20_7005-T07_P14

value: taste


title: 20_7005-T03_P14


title: 20_7005-T00_P14


title: 20_6911-T77_P14

value: Multi-racial


title: 20_6911-T91_P14


title: 20_6911-T56_P14


title: 20_6911-T00_P14

value: Control


title: 20_6911-T35_P14


title: 20_9520-T00_P14

value: Initial Outbreak

value: F

value: fatigue

value: Moderate


title: 20_6544-T91_P14

value: blood

value: Later Surveillance

value: M

value: Non-Hispanic

value: Black


title: 20_6544-T46_P14

value: Detected


title: 20_6376-T91_P14

value: Hispanic

value: White

value: Not


title: 20_6911-T42_P14

value: Mid


title: 20_6544-T00_P14

value: Pre


title: 20_6376-T60_P14


title: 20_6376-T77_P14


title: 20_9058-T84_P14

value: Post


title: 20_6376-T49_P14


title: 20_7910-T07_P14

value: headache


title: 20_5879-T91_P14


title: 20_6376-T00_P14

value: Control


title: 20_5879-T56_P14


title: 20_5879-T77_P14


title: 20_5879-T00_P14


title: 20_5879-T60_P14


title: 20_5879-T49_P14


title: 20_5345-T91_P14


title: 20_7493-T14_P14


title: 20_5345-T60_P14


title: 20_7493-T00_P14


title: 20_5345-T56_P14


title: 20_5345-T53_P14


title: 20_5345-T77_P14


title: 20_5345-T00_P14

value: First


title: 20_5127-T14_P14


title: 20_5127-T70_P14


title: 20_5127-T00_P14


title: 20_5127-T49_P14


title: 20_9880-T63_P13

value: msk;throat;taste


title: 20_9880-T70_P13


title: 20_9880-T00_P13


title: 20_5127-T10_P14


title: 20_6911-T39_P14

value: Multi-racial


title: 20_9770-T70_P13

value: blood


title: 20_6544-T49_P14

value: Later Surveillance


title: 20_9770-T67_P13

value: M


title: 20_5879-T53_P14


title: 20_9636-T00_P13

value: F


title: 20_9634-T56_P13

value: Asian


title: 20_9634-T53_P13

value: Detected


title: 20_9634-T00_P13


title: 20_9634-T49_P13


title: 20_9634-T28_P13


title: 20_9520-T00_P13

value: Initial Outbreak

value: Hispanic

value: fatigue

value: Moderate


title: 20_9181-T67_P13

value: White

value: Not


title: 20_9181-T70_P13

value: Post


title: 20_9181-T63_P13


title: 20_9407-T77_P13

value: Non-Hispanic


title: 20_9181-T00_P13

value: Control


title: 20_9407-T00_P13


title: 20_8795-T00_P13

value: headache


title: 20_9132-T00_P13


title: 20_8989-T00_P13


title: 20_8586-T56_P13

value: Problems:Inconclusive ran twice. New sample required


title: 20_8586-T53_P13

value: blood


title: 20_8586-T49_P13

value: Later Surveillance

value: Mid


title: 20_8586-T42_P13

value: M


title: 20_8586-T46_P13


title: 20_8586-T39_P13

value: First


title: 20_8586-T00_P13


title: 20_5127-T17_P14

value: Detected


title: 20_8586-T28_P13

value: Pre


title: 20_8535-T00_P13

value: F

value: Hispanic


title: 20_9880-T67_P13

value: Black


title: 20_8436-T00_P13

value: White


title: 20_8426-T53_P13

value: Not


title: 20_8426-T49_P13


title: 20_8426-T42_P13

value: fvr;msk;fatigue;throat;cough


title: 20_8426-T46_P13


title: 20_8426-T00_P13


title: 20_8426-T28_P13


title: 20_8257-T00_P13

value: Initial Outbreak

value: Non-Hispanic

value: Mild


title: 20_8122-T56_P13

value: Post


title: 20_9634-T91_P13

value: blood

value: Asian


title: 20_8122-T53_P13

value: Later Surveillance


title: 20_8122-T91_P13

value: M


title: 20_8122-T00_P13

value: Control


title: 20_8122-T49_P13

value: Detected

value: Mid


title: 20_7692-T84_P13

value: F

value: Hawaiian/OPI

value: First


title: 20_7692-T00_P13


title: 20_7222-T42_P13

value: Multi-racial


title: 20_7222-T46_P13


title: 20_7213-T53_P13

value: White

value: Not


title: 20_7222-T35_P13


title: 20_7213-T49_P13


title: 20_7222-T00_P13


title: 20_9132-T77_P13

value: Hispanic

value: chill;cough


title: 20_7149-T53_P13


title: 20_7149-T56_P13


title: 20_7149-T49_P13


title: 20_7149-T91_P13


title: 20_7149-T28_P13

value: Pre


title: 20_7149-T00_P13

value: Immune


title: 20_6016-T39_P13

value: blood

value: Post


title: 20_6016-T42_P13

value: Later Surveillance


title: 20_6016-T35_P13

value: M


title: 20_5601-T00_P13

value: Non-Hispanic

value: Control


title: 20_6016-T00_P13


title: 20_5399-T00_P13


title: 20_5082-T84_P13


title: 20_5082-T00_P13


title: 20_5082-T77_P13

value: Detected


title: 20_9940-T91_P12

value: F


title: 20_9940-T63_P12


title: 20_9940-T49_P12


title: 20_9940-T42_P12

value: msk;fatigue;cough;sob;taste


title: 20_9940-T28_P12

value: Problems:Inconclusive ran twice. New sample required


title: 20_9365-T39_P12

value: Mid


title: 20_9520-T00_P12

value: Initial Outbreak

value: White

value: fatigue

value: Moderate


title: 20_9365-T35_P12

value: Hispanic


title: 20_9234-T91_P12

value: Black

value: Not


title: 20_9365-T00_P12

value: blood


title: 20_9234-T56_P12

value: Later Surveillance

value: Post


title: 20_9940-T00_P12