title: blood_covid+_CB0134_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0134-02


title: blood_covid+_CB0133_timepoint 6

status: Public on Sep 30 2023

type: RNA

city: Seattle

first: Fang Yun

last: Lim

state: WA

address: 1100 Eastlake Ave E

department: Vaccine and Infectious Disease Division

country: USA

institute: Fred Hutchinson Cancer Center

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0133-06

data_processing: nCounter RCC files of all samples were pre-processed on the nSolverTM software (nanoString) to obtain normalized expression counts. Quality control (QC) measures were applied to all participant samples.  Imaging QC was assessed by measuring the percent field of view (FOV) successfully scanned within each sample. Samples with scanned FOV < 75% were flagged for removal. Binding density QC was assessed by measuring the density of the reporter probe on the cartridge surface within each sample. Samples with binding density outside of 0.1 - 2.25 spots/square micron were flagged for removal. The correlations between the observed counts for all six positive ERCC control probes (Positives A – F) and their spike-in synthetic nucleic acids (0.125 fM – 128 fM) were used to determine a sample’s positive control linearity. Samples with positive control linearity of < 0.95 were flagged for removal. Gene expression count normalization was performed on all samples that passed the QC metrics above. For normalization, all samples were subjected to i) positive control normalization, ii) codeset content normalization, and iii) panel standard normalization. Nine reference genes (ABCF1, GUSB, HRPT1, MRPS7, NMT1, NRDE2, PGK1, SDHA, TBP) were used in codeset content normalization.

label: Molecular barcode with using 4 fluorophores (Alexa 488, Alexa 594, Alexa 647, Cy3) in 7 positions: https://www.nature.com/articles/nbt1385

molecule: total RNA

organism: Homo sapiens

source_name: acute phase COVID-19+ participants-longitudinal

label_protocol: color-coded reporter and capture probes from manufacturer (nCounter codeset chemistry): https://nanostring.com/wp-content/uploads/MAN-10056-05-Gene-Expression-Hybridization-Protocol.pdf

growth_protocol: Capillary blood was self-collected and immediately stabilized using a home-use blood collection kit (homeRNA). Stabilized blood were mailed back to the lab and samples stored at -80ºC until ready for RNA extraction.

tag: disease status

tag: participant id

tag: Sex

value: male

tag: age

tag: covid-19 vaccination history

value: vaccinated

tag: day post symptom onset

tag: study day

tag: ncounter host response codeset


title: blood_covid+_CB0133_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0133-01


title: blood_covid+_CB0133_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0133-05


title: blood_covid+_CB0133_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0133-02


title: LKSupMillipore2

type: SRA

city: La Jolla

first: Louise

middle: C

last: Laurent

state: CA

address: SCRM, 2880 Torrey Pines Scenic Drive

department: Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

library_source: transcriptomic

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: neoplastic cell

extract_protocol:
RNA Isolation kit was miRNeasy (Qiagen).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were multiplexed. Type of Starting Material was total RNA.

tag: condition

value: Cholangiocarcinoma

tag: anatomical location

value: Bile duct structure

tag: rna source

value: extracellular vesicle

tag: rna isolation kit

value: miRNeasy (Qiagen)


title: D4_M.ONC.D4.3.200124

city: Sendai

first: Kota

last: Sato

state: Miyagi

address: 1-1, Seiryo-machi, Aoba-ku

department: Ophthalmology

country: Japan

institute: Tohoku University

data_processing:
RNA-seq libraries were sequenced using paired end reads (50 nt for read 1 and 25 nt for read 2) on a NextSeq 500 instrument (Illumina). The obtained reads were mapped to the mouse GRCm38.p6 (mm10) genome with STAR software (version 2.7.2b). Reads of annotated genes were counted using featureCounts software (version 1.6.1). FPKM values were calculated from mapped reads by normalizing to total counts and the transcript.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

organism: Mus musculus

source_name: retina

extract_protocol:
Total RNA were directly extracted with lysis buffer inculding Rnase inhibitor from single cell sorted with FACS.
RNA sequence library preparation, sequencing, mapping, gene expression, and gene ontology (GO) enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). cDNA synthesis and amplification of RNA derived from lysed cell was sequentially conducted in a same PCR tube. After purification, amplified cDNA was validated and quantified. Following tagmentation of cDNA, adapter addition and PCR amplification were conducted using Nextera XT DNA Library Prep Kit (Illumina).

tag: cell type

value: microglia

tag: tissue

value: retina

tag: strain

value: 13 weeks old

tag: treatment

value: optic nerve crush day 4


title: D4_M.ONC.D4.4.200124


title: PKSupMillipore1


title: D4_M.ONC.D4.2.191126


title: blood_covid+_CB0132_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0132-07

value: female


title: blood_covid+_CB0133_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0133-04


title: blood_covid+_CB0132_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0132-05


title: blood_covid+_CB0132_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0132-04


title: blood_covid+_CB0135_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0135-02


title: blood_covid+_CB0132_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0132-03


title: blood_covid+_CB0132_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0132-02


title: D4_M.ONC.D4.1.191126


title: LhSupExoQuick1

source_name: embryonic stem cell

value: Healthy Subject

value: Entire embryo

value: SeraMir Kit (System Biosciences)


title: blood_covid+_CB0135_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0135-04


title: LKSupExoRNeasy1


title: LKSupUltra1


title: DKSupUltra2


title: D2_F.ONC.D2.4.200122

value: optic nerve crush day 2


title: blood_covid+_CB0132_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0132-06


title: blood_covid+_CB0131_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0131-07


title: DhSupExoquick2


title: D2_F.ONC.D2.3.200122


title: LKSupExoQuick2


title: blood_covid+_CB0131_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0131-05


title: blood_covid+_CB0131_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0131-04


title: PKSupExoQuick1


title: blood_covid+_CB0131_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0131-01


title: blood_covid+_CB0131_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0131-02


title: blood_covid+_CB0130_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0130-07


title: blood_covid+_CB0132_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0132-01


title: H7_20200930, 26-SDD00481

city: NEW YORK

first: Hyomin

last: Seo

state: NY

address: 1 Gustave L. Levy Pl

department: Neurosciences

institute: Icahn school of medicine at Mount Sinai

description:
Raw_Counts.txt
Raw_TPM.txt

data_processing:
Samples were sequenced with a depth of 30 million 150-bp paired-end reads using Illumina HiSeq 4000 platform
RAPID-nf was used to. Rocess FASTQ files. After adapter trimming with trimmomatic(v0.36), STAR(2.7.2a) was used to align samples to hg38 build.
For gene expression quantification, RSEM(1.3.1) was used. Sequencing quality and technical metrics were assessed with FASTQC (0.11.8) before alignment, and Picard(2.20) and Samtools(v1.9) post-alignment.
Multidimensional reduction using principal component analysis and multidimensional scaling before and after regressing covariates were used for the identification of outliers.
Individual gene counts and transcripts per million used for downstream analyses were generated using RSEM and assembled to a matrix via the tximport R package
Assembly: Hg 38 build
Supplementary files format and content: tsv file includes raw counts for each Sample
Supplementary files format and content: tsv file includes raw TPM for each Sample
Supplementary files format and content: tsv file includes Metadata associated with each Sample

growth_protocol: Monocytes were isolated from cryopreserved PBMCs through CD14+ magnetic bead sorting, yielding a concentration of 1 million cells/ml in supplemented RPMI media

extract_protocol:
RNA was isolated using RNeasy Mini kit (Qiagen), following the manufacturer’s instruction and including the optional DNase treatment
Library preparation and sequencing was performed at Genewiz Inc. using the SMART-Seq v4 Ultra Low input library preparation protocol, which uses poly-A selection

treatment_protocol: After 24 hours of culture with LPS-EK ultrapure(10ng/ml) or IFNg(20ng/ml) stimuli, cells were washed, preserved in RLT with 2-Mercaptoethanol, and stored at -80C.

tag: cell line

value: Microglia

tag: genotype

value: LRRK2 G2019S mutation (Hom)

value: IFNg


title: H7_20200930, 27-SDD00482

description:
Raw_Counts.txt
Raw_TPM.txt

value: LPS


title: D0_M.ONC.D0.3.200122

value: 15 weeks old

value: no treatment


title: blood_covid+_CB0130_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0130-04

tag: disease status

tag: participant id

value: male

value: vaccinated


title: blood_covid+_CB0131_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0131-06

tag: Sex

tag: age


title: D0_M.ONC.D0.2.191126

value: microglia


title: blood_covid+_CB0130_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0130-03

tag: covid-19 vaccination history

tag: day post symptom onset


title: H7_20200930, 25-SDD00480

description:
Raw_Counts.txt
Raw_TPM.txt

value: Basal


title: D2_M.ONC.D2.2.191127

value: retina

value: 13 weeks old


title: blood_covid+_CB0131_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0131-03

tag: study day

tag: ncounter host response codeset


title: D2_M.ONC.D2.1.191127


title: blood_covid+_CB0130_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0130-01


title: blood_covid+_CB0129_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0129-07

value: female


title: H7_20200928, 24-SDD00479

description:
Raw_Counts.txt
Raw_TPM.txt


title: blood_covid+_CB0129_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0129-06


title: blood_covid+_CB0130_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0130-06


title: NC.D4_Plate3.H6

library_source: transcriptomic single cell

data_processing:
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software. Trimmed reads were then mapped to the mouse GRCm38.p6 (mm10) genome with STAR software (version 2.7.2b). Reads on annotated genes were counted using featureCounts (version 1.6.1). FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

value: 16 weeks old

value: nerve crush day 4


title: D0_M.ONC.D0.4.200122


title: H7_20200928, 23-SDD00478

description:
Raw_Counts.txt
Raw_TPM.txt


title: blood_covid+_CB0130_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0130-05


title: H7_20200928, 22-SDD00477

description:
Raw_Counts.txt
Raw_TPM.txt


title: NC.D4_Plate3.H5


title: NC.D4_Plate3.H4


title: H7_20200926, 21-SDD00476

description:
Raw_Counts.txt
Raw_TPM.txt


title: blood_covid+_CB0129_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0129-02


title: blood_covid+_CB0129_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0129-04


title: blood_covid+_CB0129_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0129-01


title: D0_M.ONC.D0.1.191126


title: blood_covid+_CB0130_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0130-02


title: blood_covid+_CB0129_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0129-03


title: blood_covid+_CB0128_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0128-07


title: H7_20200926, 19-SDD00474

description:
Raw_Counts.txt
Raw_TPM.txt


title: H7_20200926, 20-SDD00475

description:
Raw_Counts.txt
Raw_TPM.txt


title: NC.D4_Plate3.H3


title: NC.D4_Plate3.H2


title: blood_covid+_CB0129_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0129-05


title: blood_covid+_CB0128_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0128-05


title: blood_covid+_CB0128_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0128-01


title: blood_covid+_CB0128_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0128-06


title: blood_covid+_CB0128_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0128-02


title: A9_20200930, 18-SDD00473

description:
Raw_Counts.txt
Raw_TPM.txt

value: LRRK2 G2019S mutation (Het)


title: LhSupExoQuick3

tag: condition

value: Healthy Subject

tag: anatomical location

value: Entire embryo

value: extracellular vesicle

value: SeraMir Kit (System Biosciences)


title: NC.D4_Plate3.H1


title: A9_20200930, 17-SDD00472

description:
Raw_Counts.txt
Raw_TPM.txt

value: Microglia

value: IFNg


title: blood_covid+_CB0125_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0125-07


title: blood_covid+_CB0125_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0125-05


title: blood_covid+_CB0125_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0125-06


title: NC.D4_Plate3.G5


title: NC.D4_Plate3.G6


title: A9_20200930, 16-SDD00471

description:
Raw_Counts.txt
Raw_TPM.txt


title: blood_covid+_CB0125_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0125-04


title: A9_20200928, 15-SDD00470

description:
Raw_Counts.txt
Raw_TPM.txt

value: LPS


title: A9_20200928, 14-SDD00469

description:
Raw_Counts.txt
Raw_TPM.txt


title: blood_covid+_CB0125_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0125-03


title: NC.D4_Plate3.G3


title: NC.D4_Plate3.G4


title: blood_covid+_CB0125_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0125-02


title: A9_20200928, 13-SDD00468

description:
Raw_Counts.txt
Raw_TPM.txt


title: NC.D4_Plate3.G2


title: A9_20200926, 12-SDD00467

description:
Raw_Counts.txt
Raw_TPM.txt


title: blood_covid+_CB0125_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0125-01


title: blood_covid+_CB0124_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0124-05

value: unvaccinated


title: blood_covid+_CB0124_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0124-06


title: blood_covid+_CB0124_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0124-04


title: blood_covid+_CB0124_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0124-03


title: blood_covid+_CB0124_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0124-02


title: NC.D4_Plate3.G1


title: blood_covid+_CB0123_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0123-07


title: blood_covid+_CB0124_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0124-01


title: NC.D4_Plate2.H6


title: blood_covid+_CB0123_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0123-06


title: A9_20200926, 10-SDD00465

description:
Raw_Counts.txt
Raw_TPM.txt


title: NC.D4_Plate2.H5


title: WT_20200930, 9-SDD00464

description:
Raw_Counts.txt
Raw_TPM.txt

source_name: WT

value: WT

value: LRRk2 (Wt)


title: blood_covid+_CB0123_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0123-05


title: blood_covid+_CB0123_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0123-03


title: blood_covid+_CB0123_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0123-02


title: blood_covid+_CB0123_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0123-04


title: NC.D4_Plate2.H4

value: microglia


title: NC.D4_Plate2.H3

value: retina


title: WT_20200930, 8-SDD00463

description:
Raw_Counts.txt
Raw_TPM.txt


title: WT_20200930, 7-SDD00462

description:
Raw_Counts.txt
Raw_TPM.txt

value: Basal


title: blood_covid+_CB0122_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0122-07

value: female


title: blood_covid+_CB0122_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0122-03


title: A9_20200926, 11-SDD00466

description:
Raw_Counts.txt
Raw_TPM.txt


title: blood_covid+_CB0122_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0122-04


title: WT_20200928, 6-SDD00461

description:
Raw_Counts.txt
Raw_TPM.txt


title: blood_covid+_CB0122_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0122-02


title: NC.D4_Plate2.H2

value: 16 weeks old


title: NC.D4_Plate2.H1

value: nerve crush day 4


title: blood_covid+_CB0122_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0122-01


title: NC.D4_Plate2.G6


title: blood_covid+_CB0121_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0121-06

value: partial


title: blood_covid+_CB0121_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0121-05


title: blood_covid+_CB0121_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0121-07


title: NC.D4_Plate2.G5


title: NC.D4_Plate2.G4


title: WT_20200926, 3-SDD00458

description:
Raw_Counts.txt
Raw_TPM.txt


title: blood_covid+_CB0121_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0121-03


title: blood_covid+_CB0121_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0121-04


title: blood_covid+_CB0121_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0121-02


title: WT_20200926, 2-SDD00457

description:
Raw_Counts.txt
Raw_TPM.txt


title: blood_covid+_CB0121_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0121-01


title: NC.D4_Plate2.G3


title: NC.D4_Plate2.G2


title: blood_covid+_CB0120_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0120-05


title: blood_covid+_CB0120_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0120-06


title: blood_covid+_CB0120_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0120-07


title: WT_20200926, 1-SDD00456

description:
Raw_Counts.txt
Raw_TPM.txt


title: NC.D4_Plate2.G1


title: Donor 5 pRNA stimulated BDCA3

city: Nijmegen

first: Johannes

last: Textor

address: Geert Groteplein 26-28

country: Netherlands

institute: Radboud University Medical Center

data_processing:
FASTQ files provided by BGI were mapped to the human genome version GRCH38 using hisat2 version 2.1.0 with parameter --phred64 and default parameters otherwise. Alignments were saved as BAM files.
Feature counts were extracted from BAM files using the Bioconductor package "Rsubread" version 2.4.3 (Liao et al, doi 10.1093/nar/gkz114)
Entrez IDs were converted to gene symbols using the Bioconductor packages "org.Hs.eg.db" version 3.12.0 and "annotate" version 1.68.0.
Assembly: hg38
Supplementary files format and content: counts.csv is a CSV file containing a matrix of feature counts per sample

source_name: Blood

growth_protocol: Cells were obtained from aphaeresis of 5 different donors. Peripheral blood mononuclear cells (PBMCs) were isolated by using Ficoll density centrifugation (Lymphoprep; Axis-Shield PoC AS, Oslo, Anti-Human Lineage Cocktail 1 in FITC (LIN1) (BD Bioscience Pharmingen, San Jose, CA) containing antibodies for CD3, CD14, CD16, CD19, CD20, CD56 receptors, together with the anti-FITC conjugated magnetic microbeads of Miltenyi Biotec (Bergisch-Gladbach, Germany) were used to deplete the LIN1+ cell fraction, by following manufacturer’s instructions. Next, CDC1were further purified by sorting (flowcytometry) using anti–BDCA-3–APC combined with anti-HLA-DR-PE-Vio770 (Miltenyi Biotec) to a purity of 99.9%. DCs were cultured in X-VIVO-15 medium (Lonza, Basel, Switzerland) supplemented with 2% human serum (Sanquin).

extract_protocol:
RNA was harvested using Trizol (Invitrogen, MA, USA), following the standard protocol. Quality control of the isolated RNA (concentration, RIN, 28S/18S and size) was performed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).
After extraction of total RNA and treatment with with DNase I, Oligo(dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA are fragmented. ThencDNAis synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for thePCRamplification. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-TimePCRSystem are used in quantification and qualification of the sample library. Then the library is sequenced using Illumina HiSeq 4000 or other sequencer when necessary.

treatment_protocol: DCs were stimulated with: pRNA (15μg/ ml) and Hiltonol (10 μg/ml) for 16 hours.

value: Blood

value: cDC1 (BDCA3+ DC)

value: pRNA


title: Donor 5 Hiltonol+pRNA stimulated BDCA3

value: Hiltonol+pRNA


title: blood_covid+_CB0120_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0120-04


title: blood_covid+_CB0120_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0120-02


title: blood_covid+_CB0120_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0120-03


title: NC.D4_Plate1.H6


title: blood_covid+_CB0120_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0120-01


title: WT_20200928, 4-SDD00459

description:
Raw_Counts.txt
Raw_TPM.txt

value: Microglia


title: blood_covid+_CB0119_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0119-07


title: Donor 5 Hiltonol stimulated BDCA3

value: Hiltonol


title: blood_covid+_CB0119_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0119-06


title: NC.D4_Plate1.H5


title: blood_covid+_CB0119_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0119-04


title: Donor 5 unstimulated BDCA3


title: blood_covid+_CB0119_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0119-05


title: blood_covid+_CB0119_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0119-03


title: NC.D4_Plate1.H4


title: blood_covid+_CB0119_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0119-02


title: Donor 4 Hiltonol+pRNA stimulated BDCA3


title: NC.D4_Plate1.H3


title: blood_covid+_CB0119_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0119-01


title: blood_covid+_CB0118_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0118-07


title: NC.D4_Plate1.H2


title: intact-TAS

city: Sagamihara

first: Makoto

last: Kashima

state: Kanagawa

address: 5-1-16, Fuchinobe

institute: Aoyama Gakuinn University

description: BD Rhapsody

data_processing:
First, a whitelist of cell barcodes was prepared using umi_tools (version 1.1.2) (Smith, Heger, and Sudbery 2017) with the following command: “umi_tools whitelist –stdin Read1.fastq.gz –method=umis –extract-method=regex –bc-pattern=”(?P<cell_1>.{9})(?P<discard_1>.{12})(?P<cell_2>.{9})(?P<discard_2>.{13})(?P<cell_3>.{9})(?P<umi_1>.{8}).*” –set-cell-number=10000 –ed-above-threshold=correct > whitelist.txt”. The information of cell barcodes and UMI (unique molecular identifier) was added to read ID in Read2.fastq with the following command: “umi_tools extract  --stdin Read1.fastq.gz --read2-in Read2.fastq.gz --read2-stdout --extract-method=regex --bc-pattern="(?P<cell_1>.{9})(?P<discard_1>.{12})(?P<cell_2>.{9})(?P<discard_2>.{13})(?P<cell_3>.{9})(?P<umi_1>.{8}).*" --error-correct-cell --whitelist=whitelist.txt > Read2-umi.fastq.gz”. Low quality bases and adapter sequences of read2 were removed using fastp (version 0.21.0) (S. Chen et al. 2018) with the following command: “fastp --trim_poly_x -w 20 -o Read2-trimmed.fastp.gz  --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -i Read2-umi.fastq.gz -l 31”. The trimmed reads were mapped on a D. japonica transcriptome reference (An et al. 2018) using bwa mem (version 0.7.17-r1188) (W. Chen et al. 2013). PCR-duplicated reads harboring same UMIs were removed using umi_tools with the following command: “umi_tools dedup -I input bam --out-sam --log2stderr --per-contig --per-gene --umi-separator="_" -S input.sam”. Then, the non-redundant mapping results were split into each cell barcodes using a homemade ruby script “sam_demutiplexing.rb” and “sam2bam.rb” (github). Finally, For each cell-barcode, the read count for each gene was calculated with salmon  (version v0.12.0) (Patro et al. 2017) using -l IU, which specifies the library type.
Assembly: D. japonica transcriptome reference (An et al. 2018)
Supplementary files format and content: Comma-separated values of count matrix.
Supplementary files format and content: Comma-separated values of metadata matrix (nCount_RNA, nFeature_RNA, major.cell.type, and minor.cell.type).

organism: Dugesia japonica

source_name: whole body

growth_protocol: A clonal strain of planarian D. japonica, sexualizing super planarian (SSP) (2n=16), was used in this study (Shibata et al. 2012). The planarians were maintained in deionized water containing 0.05 g/L Instant Ocean Sea Salt (Instant Ocean, Blacksburg, VA, USA) and fed with chicken liver once or twice a week. The planarians that are approximately 5 mm in length were starved for at least one week prior to the following experiments.

extract_protocol:
Planarian was placed on a filter paper on ice and cut into small pieces using a surgical knife. The cell suspension was incubated in 1/7 × PBS(-) (NACALAI TESQUE, INC, Kyoto, Japan) containing 25 µg/mL Liberase TL (Merck, Darmstadt, Germany) or 0.25% (v/w) Trypsin (NACALAI TESQUE, INC, Kyoto, Japan) at 22℃ for 5 min. After the incubation, the cell suspension was gently pipetted at least 60 times to completely dissociate it into single cells. In order to wash out the enzymes, the dissociated cell solution was centrifuged at 200 x g for 10 minutes, followed by discarding the supernatant and re-suspension with 500 μL of 1/7 × PBS(-). After another round of the wash step, the cells were re-suspended in 1 mL of 1/7 × PBS(-) containing 1 µg/mL of Calcein AM (DOJINDO LABORATORIES, Kumamoto, Japan) and 1 µg/mL PI (DOJINDO LABORATORIES, Kumamoto, Japan), and were passed through pluriStrainer-Mini 40 μm, 20 μm, and 10 μm (pluriselect, Leipzig, Germany) to remove debris or cell aggregations. The numbers of living and dead cells were counted with a hemocytometer and fluorescence microscope BX53 (Olympus, Tokyo, Japan).
The dissociated cells of D. japonica (Chiba, Japan) were subjected to a BD Rhapsody system with BD Rhapsody™ Whole Transcriptome Analysis (WTA) Amplification Kit (BD Biosciences, New Jersey, USA) following the manufacturer’s instructions except for using 1/7 × PBS(-) instead of Sample Buffer. The reverse-transcribed, Exonuclease I-treated BD Rhapsody beads were subjected to TAS-Seq workflow according to the protocols described previously (Shichino et al. 2022) by ImmunoGeneTeqs, Inc (Chiba, Japan).

value: whole body


title: NC.D4_Plate1.H1


title: Donor 4 pRNA stimulated BDCA3


title: smeg_PAP_m3

city: Lodz

first: Przemysław

middle: Adam

last: Płociński

state: lodzkie

address: Lodowa 106

department: Mycobacterium Physiology and Genetics

country: Poland

institute: Institute of Medical Biology of the Polish Academy of Sciences

description: This sample was used for polyadenylation rates estimation in comparison to the other samples in this study. Quantified gene expression not performed for this sample.

data_processing:
unzipping the .gz file with gunzip function with Ubuntu Linux command line
seqencing adapter removal with Cutadapt software with parameters set cutadapt -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -g TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -G AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -A TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15 && cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -g GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -G TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15
quality trimming was done with Sickle -pe script setting variable parameters as -t sanger -q 20 -l 20
mapping reads to the reference genome with BWA-mem software with -t 30 -k 20 settings
sorting and indexing of the alignemnt files with Samtools
samtools view -b -F 4 step was included whenever extraction of mappable reads was required
bazam -bam *.bam (-L bed.bed) -o *.fastq was then used to convert the data format to fastq, which could be serached with bbduk.sh -Xmx5g -literal ARGUMENT, whenever required
samtools view -h *.bam | samclip --ref H37Rv_v4.fasta --max 3 --invert | samtools sort > *.bam was used to calculate the softclipping statistics presented in the manuscript associated with this data submission
counting reads to features with HTSeq.count -t CDS -i Locus -m intersection-nonempty
count matrix was build in excel by merging the HTSeq.count output files
Assembly: NC_000962.3 (Mycobacterium tuberculosis, H37Rv_v4.fasta) or NC_008596.1 (Mycolicibacterium smegmatis, MC2_v4.fasta) were used for mapping.

molecule: polyA RNA

organism: Mycolicibacterium smegmatis MC2 155

source_name: strain carrying Cas9 plasmid for targeted PAP (Rv3907c) depletion grown in 7H9/10% OADC medium

growth_protocol: The Mycobacterium tuberculosis H37Rv wild-type strain and ∆rv3143 mutant were grown in 7H9 broth (Becton-Dickinson) supplemented with 10% OADC enrichment (Becton-Dickinson). For RNA sequencing, the Mtb wild-type and ∆rv3143 mutant were grown to mid-logarythmic phase of growth. Bacteria were cultured in triplicate. 100 ml of each culture was spun down and subjected directly to total RNA isolation.

extract_protocol:
RNA was isolated using TRIzol LS reagent (Invitrogen). Cells were lysed by bead beating with the MP FastPrep system (MP Biomedicals) using lysing matrix B. DNA contamination of the RNA samples was removed by DNase I turbo (Invitrogen) digestion according to the manufacturer’s protocol. The quantity and integrity of the DNase I-treated RNA was assessed using an Agilent 2100 BioAnalyzer according to the manufacturer's instructions (Agilent RNA 6000 Nano Kit).
1mg of crude isolated RNA was used for preparation of each small RNA libraries with TruSeq kit and detailed protocol provided by the manufacturer (Illumina). For total RNA-Seq, RNA samples were purified using AMPure XP magnetic beads (Becton Dickinson) with a 2.2:1 bead-to-RNA ratio. 2mgs of the purified RNA was used for total RNA library. The ribosomal RNA was removed with the riboPools Pan-Bacteria (siTools) according to the manufacturer’s protocol. The Illumina-compatible RNA/cDNA sequencing libraries were prepared with the use of KAPA Stranded RNA-Seq kit (Roche) according to the detailed instructions provided by the manufacturer. For polyA selected libraries, the total RNA was incubated with poly(dT) beads, than washed extensively before recovering the enriched polyA fraction for further processing with VAHTS mRNA-seq V3 Library Prep Kit for Illumina® (Vazyme).

treatment_protocol: No treatment was applied. Wild type and mutant strain grown under the same conditions are compared.

value: Cas9 mutant

value: anhydrotetracycline 100ng/ml

tag: growth phase

value: grown to mid-exponential phase


title: NC.D4_Plate1.G6

tag: cell type

value: microglia


title: Donor 4 unstimulated BDCA3

tag: tissue


title: Donor 3 Hiltonol+pRNA stimulated BDCA3


title: blood_covid+_CB0118_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0118-05

value: unvaccinated


title: blood_covid+_CB0118_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0118-06


title: smeg_PAP_m2


title: smeg_PAP_m1


title: blood_covid+_CB0118_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0118-04


title: NC.D4_Plate1.G5

value: retina

tag: strain


title: Donor 4Hiltonol stimulated BDCA3

tag: treatment


title: smeg_Cas9_3

source_name: strain carrying an empty Cas9 plasmid (pLJR965, Rock et al.2017) grown in 7H9/10% OADC  medium

value: Cas9 control


title: Donor 3 pRNA stimulated BDCA3


title: blood_covid+_CB0118_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0118-03

value: female


title: NC.D4_Plate1.G4

value: 16 weeks old

value: nerve crush day 4


title: smeg_Cas9_2


title: NC.D4_Plate1.G3


title: Donor 3 unstimulated BDCA3

value: Blood


title: Donor 3 Hiltonol stimulated BDCA3

value: cDC1 (BDCA3+ DC)


title: blood_covid+_CB0118_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0118-01


title: NC.D4_Plate1.G2


title: smeg_Cas9_1


title: blood_covid+_CB0117_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0117-07

value: male


title: Donor 2 pRNA stimulated BDCA3

value: pRNA


title: NC.D4_Plate1.G1


title: D_VP2

city: Hangzhou

first: Wang

last: Shuang

address: 666 Wusujie Linan

country: China

institute: Zhejiang A & F University

description: Short photoperiod treatment_20d

data_processing:
Samples are sequenced by using NovaSeq 6000 platform (Illumina) by Shanghai Personal Biotechnology Cp. Ltd to get image files .
Cutadapt (v1.15) software was used to filter the sequencing data to get high quality sequence（Clean   Data）for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.0.5.
we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression. Then difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.  At the same time, We used R language Pheatmap(1.0.8) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
we mapped all the genes to Terms in the Gene Ontology database and calculated the numbers of differentially enriched genes in each Term. Using topGO to perform GO enrichment analysis on the differential genes, calculate P-value by hypergeometric distribution method (the standard of significant enrichment is P-value <0.05), and find the GO term with significantly enriched differential genes to determine the main biological functions performed by differential genes. ClusterProfiler (3.4.4) software was used to carry out the enrichment analysis of the KEGG pathway of differential genes, focusing on the significant enrichment pathway with P-value <0.05.
Assembly: Reference genome ASM126359v1 BGI-SZ (2015).
Supplementary files format and content: Text files include FPKM values for each Sample

organism: Phalaenopsis amabilis

source_name: leaf

growth_protocol: 120 healthy Phalaenopsis plants were cultured in a photoperiod of 12 h per day, a day/night temperature range of 28/25℃, and relative humidity of 70±5%.

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies),1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared usingusing the NEBNext Ultra II RNA Library Prep Kit for Illumina.

treatment_protocol: 120 healthy Phalaenopsis plants were averagely distributed to LD and SD. The experiment started with a temperature of 25/18℃ with a cycle of light and dark consisting of 16/8 h and 8/16 h.

value: leaf

value: Short photoperiod treatment_20d


title: Donor 2 Hiltonol stimulated BDCA3

value: Hiltonol


title: D_VP3

description: Short photoperiod treatment_20d


title: blood_covid+_CB0117_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0117-06


title: D_VP1

description: Short photoperiod treatment_20d


title: Donor 2 unstimulated BDCA3


title: NC.D2_Plate3.F6

value: nerve crush day 2


title: NC.D2_Plate3.F5


title: blood_covid+_CB0117_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0117-05


title: D_RP3

description: Short photoperiod treatment_40d

value: Short photoperiod treatment_40d


title: blood_covid+_CB0117_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0117-04


title: blood_covid+_CB0134_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0134-03

value: vaccinated


title: D_RP2

description: Short photoperiod treatment_40d


title: blood_covid+_CB0118_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0118-02


title: NC.D2_Plate3.F4

value: microglia


title: blood_covid+_CB0117_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0117-03

value: unvaccinated


title: MKN45_sh-NR2F1

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: FileincludeCount and FPKM valuesforeachsample

growth_protocol: The gastric cancer cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 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.

treatment_protocol: The established GC cell lines were grown as usual in 6-well plates.

tag: cell line

value: gastric cancer cell


title: MKN45_sh-NC


title: blood_covid+_CB0117_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0117-02


title: NC.D2_Plate3.F3

value: retina


title: SGC7901_OE_NR2F1


title: CK3

description: Control

value: Control


title: D_RP1

description: Short photoperiod treatment_40d


title: NC.D2_Plate3.F2

value: 16 weeks old


title: SGC7901_OE_NC


title: NC.D2_Plate3.F1


title: CK2

description: Control


title: GM12878-SMC1A-ChIA-PET

city: FARMINGTON

first: Yijun

last: Ruan

state: CT

address: 10 DISCOVERY DR

department: Ruan

institute: The Jackson Laboratory

description:
Sample 66
nuclear chromatin
SMC1A-ChIA-PET
LHG0051H_0104V.e500.clusters.cis.BE3
LHG0051H_0104V.for.BROWSER.sorted.bedgraph
LHG0051H_0104V.for.BROWSER.spp.z6.broadPeak
ChIA-PET_hg38_GM12878_Cohesin_LHG0051H_0104V_pooled_pairs.hic

library_source: genomic

data_processing:
Library strategy: ChIA-PET
ChIA-Drop fastq files were mapped by longranger (version 2.1.5, 10X Genomics) with wgs command. ChIP-seq fastq files were mapped by BWA (version 0.7.7) with mem command. ChIA-PET fastq files were mapped by our in-house ChIA-PET processing pipeline, available in github (ChIA-PIPE).
After mapping and identifying barcords of ChIA-Drop using longranger, our in-house processing pipeline (available in github, ChIA-DropBox) generated putative complexes. These data sets were further filtered by MIA-Sig (available in github), and then generated tab-delimited txt file.
DNA-binding protein coverage files (bedgraph) were generated by bedtools (version 2.26.0) with genomecov command. Coverage files were sorted by chromosome and coordinate.
ChIA-PET loop files (bedpe) were generated by our in-house ChIA-PET processing pipeline, available in github (ChIA-PIPE).
Peaks (broadPeak, bed file type) were called by SPP (version 1.13) with our input control file (sample# 63, library ID: CHG0033).
2D contact map files (hic) were generated by Juicer Tools (Version 1.7.5) using chromatin interaction data from ChIA-PET and ChIA-Drop. In ChIA-Drop, we used all pairwise interactions from each GEM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt format of ChIA-Drop, containing GEM_ID, GEM_coordinate, GEM_span, Fragment_number, List_of_fragment_coordinates. Each row represents one GEM.
Supplementary_files_format_and_content: bedgraph format of ChIA-Drop, ChIP-seq, and ChIA-PET, containing a DNA-binding protein coverage
Supplementary_files_format_and_content: bedpe format of ChIA-PET, containing ChIA-PET loop (long-range interaction data) data
Supplementary_files_format_and_content: broadPeak format of ChIP-seq and ChIA-PET, containing peaks called by SPP software
Supplementary_files_format_and_content: hic format of ChIA-Drop and ChIA-PET, 2D contact map file, visualized by Juicebox software

molecule: genomic DNA

extract_protocol:
The overall chromatin sample preparation for ChIA-Drop is very similar to Hi-C, except without the proximity ligation step in ChIA-Drop.  Similarly, CTCF, cohesin, and RNAPII ChIA-Drop chromatin samples are prepared as they are for respective ChIA-PET experiments but omitting proximity ligation step.
Fragmented chromatin sample was mixed with BSA to prevent chromatin aggregation. About 0.5ng of chromatin DNA material was loaded to microfluidics device, Chromium Controller with reagents from Chromium Genome v2 Library Kit & Gel Bead Kit for partitioning of single chromatin complex into individual droplets with unique gel beads according to the manufacturer’s protocol with modification. The barcoded DNA amplicons of each chromatin complex were released from all droplets.The purified DNA fragments were subjected for end repair, A-tailing, adaptor ligation, Sample Index PCR and size selection.  The final ChIA-Drop library was sequenced (2× 150 bp) by NextSeq, HiSeq, or NovaSeq runs.
We applied microfluidics-based strategy for genome-wide analysis of multiplex chromatin interactions with single-molecule precision (ChIA-Drop). Here, individual chromatin complexes are isolated in droplets that contain a gel bead with unique DNA barcode, in which tethered chromatin DNA fragments are barcoded and amplified for sequencing and mapping to demarcate chromatin contacts.

tag: method

tag: antibody

value: SMC1 (Bethyl Laboratories, catalog# A300-055A)


title: blood_covid+_CB0117_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0117-01

tag: disease status

tag: participant id


title: NC.D2_Plate3.E6

tag: age


title: blood_covid+_CB0116_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0116-07

tag: Sex

tag: covid-19 vaccination history


title: NC.D2_Plate3.E5


title: CK1

description: Control


title: GM12878-CTCF-ChIA-PET

description:
Sample 64
nuclear chromatin
CTCF-ChIA-PET
LHG0052H.e500.clusters.cis.BE3
LHG0052H.for.BROWSER.sorted.bedgraph
LHG0052H.for.BROWSER.spp.z6.broadPeak
ChIA-PET_hg38_GM12878_CTCF_LHG0052H_hiseq_pairs.hic

value: CTCF-ChIA-PET

value: CTCF (Abclonal, catalog# A1133)


title: C_VP3

description: Long photoperiod treatment_20d

value: Long photoperiod treatment_20d


title: blood_covid+_CB0116_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0116-06

value: male

tag: day post symptom onset

tag: study day


title: GM12878-RNAPII-ChIA-Drop-Rep9

description:
Sample 46
nuclear chromatin
RNAPII-ChIA-Drop
GM12878-RNAPII-pooledv2_comp.txt
GM12878-RNAPII-pooledv2.bedgraph
GM12878-RNAPII-pooledv2.hic

data_processing:
Library strategy: ChIA-Drop
ChIA-Drop fastq files were mapped by longranger (version 2.1.5, 10X Genomics) with wgs command. ChIP-seq fastq files were mapped by BWA (version 0.7.7) with mem command. ChIA-PET fastq files were mapped by our in-house ChIA-PET processing pipeline, available in github (ChIA-PIPE).
After mapping and identifying barcords of ChIA-Drop using longranger, our in-house processing pipeline (available in github, ChIA-DropBox) generated putative complexes. These data sets were further filtered by MIA-Sig (available in github), and then generated tab-delimited txt file.
DNA-binding protein coverage files (bedgraph) were generated by bedtools (version 2.26.0) with genomecov command. Coverage files were sorted by chromosome and coordinate.
ChIA-PET loop files (bedpe) were generated by our in-house ChIA-PET processing pipeline, available in github (ChIA-PIPE).
Peaks (broadPeak, bed file type) were called by SPP (version 1.13) with our input control file (sample# 63, library ID: CHG0033).
2D contact map files (hic) were generated by Juicer Tools (Version 1.7.5) using chromatin interaction data from ChIA-PET and ChIA-Drop. In ChIA-Drop, we used all pairwise interactions from each GEM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt format of ChIA-Drop, containing GEM_ID, GEM_coordinate, GEM_span, Fragment_number, List_of_fragment_coordinates. Each row represents one GEM.
Supplementary_files_format_and_content: bedgraph format of ChIA-Drop, ChIP-seq, and ChIA-PET, containing a DNA-binding protein coverage
Supplementary_files_format_and_content: bedpe format of ChIA-PET, containing ChIA-PET loop (long-range interaction data) data
Supplementary_files_format_and_content: broadPeak format of ChIP-seq and ChIA-PET, containing peaks called by SPP software
Supplementary_files_format_and_content: hic format of ChIA-Drop and ChIA-PET, 2D contact map file, visualized by Juicebox software

value: RNAPII-ChIA-Drop

value: RNAPII (BioLegend, catalog# 664912)


title: NC.D2_Plate3.E4


title: GM12878-RNAPII-ChIA-Drop-Rep8

description:
Sample 45
nuclear chromatin
RNAPII-ChIA-Drop
GM12878-RNAPII-pooledv2_comp.txt
GM12878-RNAPII-pooledv2.bedgraph
GM12878-RNAPII-pooledv2.hic


title: blood_covid+_CB0116_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0116-04

tag: ncounter host response codeset


title: blood_covid+_CB0116_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0116-05


title: NC.D2_Plate3.E3


title: C_VP1

description: Long photoperiod treatment_20d

value: leaf


title: blood_covid+_CB0116_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0116-03


title: GM12878-RNAPII-ChIA-Drop-Rep7

description:
Sample 44
nuclear chromatin
RNAPII-ChIA-Drop
GM12878-RNAPII-pooledv2_comp.txt
GM12878-RNAPII-pooledv2.bedgraph
GM12878-RNAPII-pooledv2.hic


title: GM12878-RNAPII-ChIA-Drop-Rep6

description:
Sample 43
nuclear chromatin
RNAPII-ChIA-Drop
GM12878-RNAPII-pooledv2_comp.txt
GM12878-RNAPII-pooledv2.bedgraph
GM12878-RNAPII-pooledv2.hic


title: C_RP3

description: Long photoperiod treatment_40d

value: Long photoperiod treatment_40d


title: NC.D2_Plate3.E2

value: nerve crush day 2


title: blood_covid+_CB0116_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0116-02


title: NC.D2_Plate3.E1


title: C_RP2

description: Long photoperiod treatment_40d


title: GM12878-RNAPII-ChIA-Drop-Rep5

description:
Sample 42
nuclear chromatin
RNAPII-ChIA-Drop
GM12878-RNAPII-pooledv2_comp.txt
GM12878-RNAPII-pooledv2.bedgraph
GM12878-RNAPII-pooledv2.hic


title: NC.D2_Plate3.D6


title: C_RP1

description: Long photoperiod treatment_40d


title: NC.D2_Plate3.D5


title: C_VP2

description: Long photoperiod treatment_20d


title: NC.D2_Plate3.D4


title: blood_covid+_CB0115_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0115-06


title: GM12878-RNAPII-ChIA-Drop-Rep4

description:
Sample 41
nuclear chromatin
RNAPII-ChIA-Drop
GM12878-RNAPII-pooledv2_comp.txt
GM12878-RNAPII-pooledv2.bedgraph
GM12878-RNAPII-pooledv2.hic


title: NC.D2_Plate3.D3


title: blood_covid+_CB0115_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0115-05


title: blood_covid+_CB0115_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0115-07


title: GM12878-RNAPII-ChIA-Drop-Rep3

description:
Sample 40
nuclear chromatin
RNAPII-ChIA-Drop
GM12878-RNAPII-pooledv2_comp.txt
GM12878-RNAPII-pooledv2.bedgraph
GM12878-RNAPII-pooledv2.hic


title: MSU 24h rep2

first: Chengyu

last: Yin

state: Zhejiang

address: 548 Binwen Road, Binjiang District, Hangzhou

department: The Third Clinical Medical College

institute: Zhejiang Chinese Medical University

description: GA ankle seq.txt

data_processing:
The fragments were enriched by PCR amplification to construct a library ready for sequencing using BGISEQ-500 by BGI Group (Shenzhen, China).
Primary sequencing data produced by RNA-Seq (raw reads) were subjected to quality control (QC).
Raw reads were filtered into clean reads by internal software SOAPnuke (version 1.5.2), followed by: Remove reads in which unknown bases (N) are more than 10%; Remove reads with adaptors; Remove low quality reads (we define the low quality read as the percentage of base which quality is < 15 and > 50% in a read).
QC of alignment was performed to determine if re-sequencing was needed. If the alignment result passed QC, downstream analysis including gene expression, differentially expressed genes, cluster analysis, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Set Enrichment Analysis (GSEA) analysis, etc. was then performed.
Assembly: mm11
Supplementary files format and content: Matrix table with raw gene TPM for every gene and every sample

source_name: Ankle joint

growth_protocol: Mice were randomly allocated, and 5 mice were housed per cage(12 hour light–dark cycles and 24 ± 2 ℃). Food and water were provided ad libitum.

extract_protocol:
At 8 h or 24 h after injection, mice were deeply anesthetized and were perfused transcardially with 20 mL 0.9% saline (4℃). After the perfusion, the right ankle joints were collected and were immediately preserved in the RNA later solution (Thermo Fisher, USA). Total RNA was extracted using the Trizol reagent (Thermo Fisher, USA) following the manufacturer’s instructions.  DNase I was used to degrade contaminating DNA. The purity and concentration of the samples was assessed by Nanodrop Spectrophotometer (NanoDrop Products, USA) and the RNA integrity was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
RNA libraries were prepared for sequencing using standard BGI-SEQ500 protocols

treatment_protocol: The gout arthritis model was established through intra-articular (i.a.) injection of MSU crystals (500 μg) suspended in endotoxin-free PBS (20 μl) into ankle joints of mice under isoflurane anesthesia. Control mice were injected (i.a.) with an equal volume of sterile PBS.

value: Ankle joint

tag: genotype

value: WT

value: 24 h after MSU injected


title: blood_covid+_CB0115_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0115-04

value: unvaccinated


title: MSU 24h rep3

description: GA ankle seq.txt


title: GM12878-RNAPII-ChIA-Drop-Rep1

description:
Sample 38
nuclear chromatin
RNAPII-ChIA-Drop
GM12878-RNAPII-pooledv2_comp.txt
GM12878-RNAPII-pooledv2.bedgraph
GM12878-RNAPII-pooledv2.hic


title: MSU 24h rep1

description: GA ankle seq.txt


title: NC.D2_Plate3.D2

value: microglia

value: retina


title: Con 24h rep3

description: GA ankle seq.txt

value: 24 h after Vehicle injected


title: blood_covid+_CB0116_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0116-01


title: blood_covid+_CB0115_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0115-03


title: Con 24h rep2

description: GA ankle seq.txt


title: GM12878-CTCF-ChIA-Drop-Rep18

description:
Sample 18
nuclear chromatin
CTCF-ChIA-Drop
GM12878-CTCF-pooled_comp.txt
GM12878-CTCF-pooled.bedgraph
GM12878-CTCF-pooled.hic

value: CTCF-ChIA-Drop


title: NC.D2_Plate3.D1

value: 16 weeks old


title: GM12878-CTCF-ChIA-Drop-Rep16

description:
Sample 16
nuclear chromatin
CTCF-ChIA-Drop
GM12878-CTCF-pooled_comp.txt
GM12878-CTCF-pooled.bedgraph
GM12878-CTCF-pooled.hic

value: CTCF (Abclonal, catalog# A1133)


title: blood_covid+_CB0115_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0115-02


title: Con 24h rep1

description: GA ankle seq.txt


title: GM12878-RNAPII-ChIA-Drop-Rep2

description:
Sample 39
nuclear chromatin
RNAPII-ChIA-Drop
GM12878-RNAPII-pooledv2_comp.txt
GM12878-RNAPII-pooledv2.bedgraph
GM12878-RNAPII-pooledv2.hic


title: GM12878-CTCF-ChIA-Drop-Rep15

description:
Sample 15
nuclear chromatin
CTCF-ChIA-Drop
GM12878-CTCF-pooled_comp.txt
GM12878-CTCF-pooled.bedgraph
GM12878-CTCF-pooled.hic


title: NC.D2_Plate2.F5


title: MSU 8h rep3

description: GA ankle seq.txt

value: 8 h after MSU injected


title: GM12878-CTCF-ChIA-Drop-Rep14

description:
Sample 14
nuclear chromatin
CTCF-ChIA-Drop
GM12878-CTCF-pooled_comp.txt
GM12878-CTCF-pooled.bedgraph
GM12878-CTCF-pooled.hic


title: NC.D2_Plate2.F4


title: blood_covid+_CB0113_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0113-07

value: female

value: partial


title: MSU 8h rep2

description: GA ankle seq.txt


title: blood_covid+_CB0113_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0113-06


title: NC.D2_Plate2.F2


title: MSU 8h rep1

description: GA ankle seq.txt


title: GM12878-CTCF-ChIA-Drop-Rep11

description:
Sample 11
nuclear chromatin
CTCF-ChIA-Drop
GM12878-CTCF-pooled_comp.txt
GM12878-CTCF-pooled.bedgraph
GM12878-CTCF-pooled.hic


title: GM12878-CTCF-ChIA-Drop-Rep12

description:
Sample 12
nuclear chromatin
CTCF-ChIA-Drop
GM12878-CTCF-pooled_comp.txt
GM12878-CTCF-pooled.bedgraph
GM12878-CTCF-pooled.hic


title: blood_covid+_CB0113_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0113-05


title: NC.D2_Plate2.F1


title: blood_covid+_CB0113_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0113-04


title: NC.D2_Plate2.F6


title: blood_covid+_CB0115_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0115-01

value: male


title: GM12878-CTCF-ChIA-Drop-Rep6

description:
Sample 6
nuclear chromatin
CTCF-ChIA-Drop
GM12878-CTCF-pooled_comp.txt
GM12878-CTCF-pooled.bedgraph
GM12878-CTCF-pooled.hic


title: Con 8h rep1

description: GA ankle seq.txt

value: 8 h after Vehcile injected


title: blood_covid+_CB0113_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0113-03


title: blood_covid+_CB0113_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0113-02


title: NC.D2_Plate2.E5


title: GM12878-CTCF-ChIA-Drop-Rep5

description:
Sample 5
nuclear chromatin
CTCF-ChIA-Drop
GM12878-CTCF-pooled_comp.txt
GM12878-CTCF-pooled.bedgraph
GM12878-CTCF-pooled.hic


title: Clone-8_5

city: san francisco

first: Akiko

last: Hata

state: CALIFORNIA

address: 555 Mission Bay Blvd. South, CVRI, ucsf, Room 252T

department: Cardiovascular Research Institute

institute: University of California San Francisco

data_processing:
fastq_quality_filter to filter out the sequenceing data with low quality
The sequence was trimmed with fastx_trimmer to keep the first 27 bp sequence of each read
The indexfile was build with GRch38 (ensemble) by bowtie
the sequencing was aligned to the index file to generate the reads
Assembly: GRch38
Supplementary files format and content: single tab-delimited text file include normalized counts for each Sample

growth_protocol: HEK293T cells were cultured in DMEM (high glucose) with 10% FCS, 1% penicillin/streptomycin at 37 ˚C and 5% CO2. Drosha ∆N-Drosha clones were maintained in the same media except containing 5 nM puromycin.

extract_protocol: RNA was harvested using Rneasy mini kit (Qiagen). The quality of RNAs was evaluated by 2100 Bioanalyzer Instrument (Agilent Technologies).

value: human embryonic kidney cell

value: [delta]N-Drosha


title: GM12878-CTCF-ChIA-Drop-Rep13

description:
Sample 13
nuclear chromatin
CTCF-ChIA-Drop
GM12878-CTCF-pooled_comp.txt
GM12878-CTCF-pooled.bedgraph
GM12878-CTCF-pooled.hic


title: NC.D2_Plate2.F3

value: nerve crush day 2


title: NC.D2_Plate2.E4


title: blood_covid+_CB0113_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0113-01


title: Clone-8_4


title: ERM_H3

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
DESeq2 was used for differential expression analysis between the control and treatments.
Supplementary files format and content: AVS vs ERM excel files containing read count, fpkm, log2 fold change, p-value
Supplementary files format and content: Afid vs ERM excel files containing read count, fpkm, log2 fold change, p-value

organism: Danio rerio

source_name: larvae

extract_protocol:
Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library"
Total RNA was used for mRNA isolation using the NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490). RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 (Illumina Inc., CA, U.S.A). Sequencing was performed by Novogene.

value: whole larvae

value: Control


title: Con 8h rep3

description: GA ankle seq.txt

value: Ankle joint

value: WT


title: NC.D2_Plate2.E3

value: microglia

value: retina


title: Con 8h rep2

description: GA ankle seq.txt


title: NC.D2_Plate2.E6


title: Clone-8_3


title: WT C57BL/6J Circadian Time 8 rep3

city: Istanbul

first: Halil

last: Kavakli

address: Rumelifeneri Yolu, Sariyer

department: Chemical and Biological Engineering

country: Turkey

institute: Koc University

data_processing:
Quality of sequencing reads was evaluated by using FastQC (Babraham Bioinformatics, UK) program. Trimmomatic (v0.35) was used to clean low-quality bases and adaptor contaminations
Star aligner program (v2.5.3) was used to align clean reads to reference mouse genome (GRCm39). To determine differentially expressed genes (DEGs) among genetically different mice and time points, DESeq2 function (adjusted p value < 0.05 ) in R was used
Sorted reads by the STAR aligner were counted by using HTSeq (htseq-count v. 1.99.2)
DEGs were calculated by using DESeq2 to construct distance-distance matrix and to perform principle component analysis (PCA).
Assembly: mm39
Supplementary files format and content: tab-delimited text files includes read counts
Supplementary files format and content: normalized reads obtained from deseq2

source_name: Liver

growth_protocol: All mice received a standard diet, and food and water were provided ad libitum.

extract_protocol:
Total RNA from liver samples (WT and CRYDKO mice treated with oxaliplatin at CT8 and CT16) were isolated by using RNeasy Mini Kit (QIAGEN, Germany). Quality of amount of RNA were assessed by using Qubit (Thermo Fisher Scientific, USA).
High quality RNA samples (OD260/280 1.8-2.0) were used to prepare library for RNA Sequencing analysis. Briefly, adenylated mRNAs were isolated by using Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, US). Then mRNAs were fragmented, converted to cDNA and second strand synthesis was performed.

treatment_protocol: Oxaliplatin (Alfa Aesar, Germany) was diluted in 5% dextrose solution to a final concentration of 12 mg/kg before each injection. Oxaliplatin (12 mg/kg, i.p.) was given to wild-type and Cry DKO male mice at two circadian times (CT8, CT16) for three consecutive days.

value: Liver

value: Wild Type

value: Oxaliplatin


title: blood_covid+_CB0112_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0112-06

value: unvaccinated


title: NC.D2_Plate2.E1

value: 16 weeks old


title: Clone-8_1


title: AVS_L5

value: AVS low dose


title: Clone-7_2

value: het-Drosha


title: NC.D2_Plate2.D6


title: AVS_L4


title: blood_covid+_CB0112_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0112-04

value: male


title: blood_covid+_CB0112_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0112-05


title: blood_covid+_CB0112_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0112-07


title: blood_covid+_CB0112_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0112-03


title: Clone-7_1

value: human embryonic kidney cell


title: AVS_L2


title: NC.D2_Plate2.D5


title: AVS_L1


title: blood_covid+_CB0112_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0112-02


title: ERM_H2


title: NC.D2_Plate2.E2


title: Clone-4_3


title: NC.D2_Plate2.D3


title: Clone-8_2

value: [delta]N-Drosha


title: NC.D2_Plate2.D2

value: nerve crush day 2


title: ERM_H1

value: whole larvae


title: AVS_H4

value: AVS high dose


title: Clone-4_2


title: blood_covid+_CB0112_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0112-01


title: blood_covid+_CB0111_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0111-07

value: female


title: blood_covid+_CB0111_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0111-06


title: AVS_H3


title: ERM_H4

value: Control


title: Clone-4_4

value: WT


title: NC.D2_Plate2.D4

value: microglia

value: retina


title: NC.D2_Plate1.F5


title: AVS_H1


title: NC.D2_Plate1.F4


title: Afid_L4

value: Afid low dose


title: blood_covid+_CB0111_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0111-04


title: Afid_L2


title: Afid_L1


title: NC.D2_Plate1.F3


title: NC.D2_Plate1.F2


title: blood_covid+_CB0111_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0111-03


title: blood_covid+_CB0111_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0111-01


title: Clone-4_1


title: NC.D2_Plate2.D1


title: blood_covid+_CB0111_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0111-05


title: AVS_H2


title: NC.D2_Plate1.F6


title: blood_covid+_CB0111_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0111-02


title: NC.D2_Plate1.F1


title: blood_covid+_CB0107_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0107-07

value: partial


title: NC.D2_Plate1.E6


title: blood_covid+_CB0107_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0107-06


title: Afid_H2

value: Afid high dose


title: NC.D2_Plate1.E5

value: 16 weeks old


title: blood_covid+_CB0107_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0107-04


title: Afid_H4


title: Donor 5 Hiltonol+pRNA stimulated BDCA3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: According to the standard Affymetrix protocol by ThermoFisher (Clariom D Expression Analysis Technical Manual revision B.0, ThermoFisher).

data_processing: Expression intensities from CEL files were converted to an expression matrix using the bioconductor packages affycoretools, version 1.70.0, and oligo, version 1.62.2.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol by ThermoFisher (Clariom D Expression Analysis Technical Manual revision B.0, ThermoFisher).

extract_protocol: RNA was harvested using Trizol (Invitrogen, MA, USA), following the standard protocol. Quality control of the isolated RNA (concentration, RIN, 28S/18S and size) was performed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

value: cDC1 (BDCA3+ DC)

value: Hiltonol+pRNA


title: Donor 5 pRNA stimulated BDCA3

value: pRNA


title: Donor 4 Hiltonol+pRNA stimulated BDCA3


title: blood_covid+_CB0107_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0107-05

data_processing: nCounter RCC files of all samples were pre-processed on the nSolverTM software (nanoString) to obtain normalized expression counts. Quality control (QC) measures were applied to all participant samples.  Imaging QC was assessed by measuring the percent field of view (FOV) successfully scanned within each sample. Samples with scanned FOV < 75% were flagged for removal. Binding density QC was assessed by measuring the density of the reporter probe on the cartridge surface within each sample. Samples with binding density outside of 0.1 - 2.25 spots/square micron were flagged for removal. The correlations between the observed counts for all six positive ERCC control probes (Positives A – F) and their spike-in synthetic nucleic acids (0.125 fM – 128 fM) were used to determine a sample’s positive control linearity. Samples with positive control linearity of < 0.95 were flagged for removal. Gene expression count normalization was performed on all samples that passed the QC metrics above. For normalization, all samples were subjected to i) positive control normalization, ii) codeset content normalization, and iii) panel standard normalization. Nine reference genes (ABCF1, GUSB, HRPT1, MRPS7, NMT1, NRDE2, PGK1, SDHA, TBP) were used in codeset content normalization.


title: Donor 5 Hiltonol stimulated BDCA3

value: Hiltonol


title: NC.D2_Plate1.E4


title: Afid_H3


title: NC.D2_Plate1.E3


title: Afid_H1


title: NC.D2_Plate1.E2


title: xenograft_control, 43

city: Dallas

first: Jiwoong

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality and adapter trimming. STAR (v2.7.2b) (Dobin et al., 2013) was employed to align the reads onto the mouse genome, SAMtools (v1.9) (Li et al., 2009) was employed to sort the alignments, and HTSeq Python package (Anders et al., 2015) was employed to count reads per gene.
The mouse reference genome sequence and gene annotation data, mm10, were downloaded from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). The qualities of RNA sequencing libraries were estimated by mapping the reads onto mouse transcript and ribosomal RNA sequences (Ensembl release 89) using Bowtie (v2.3.4.3). STAR (v2.7.2b) was sed to align the reads onto the mouse genome. SAMtools (v1.9) was used to sort the alignments, and HTSeq Python package was used to count reads per gene. DESeq2 R Bioconductor package was used to normalize read counts and identify differentially expressed (DE) genes. KEGG pathway data was downloaded using KEGG API (https://www.kegg.jp/kegg/rest/keggapi.html) and gene ontology (GO) data was downloaded from NCBI FTP (ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz). The enrichment of DE genes to pathways and GOs were calculated by Fisher's exact test in R statistical package. The reads were aligned to mouse RefSeq RNA sequences using Burrows-Wheeler Aligner (BWA, v0.7.17) with MEM algorithm and the options, -T 19 -h 200 -Y, and primary alignments with proper read pairs were selected by SAMtools with the options, -f 3 -F 2316, to count the reads aligned to ribosomal RNA sequences defined by the sequence descriptions containing the keyword of ribosomal RNA or rRNA. The reads were aligned to human MYC RNA isoform 1 sequence (NM_002467.6) using BWA with MEM algorithm. The alignments were compared with the alignments to mouse genomic and RNA sequences from NCBI Assembly, GRCm38.p6, using a custom Perl script named REMOCON (https://github.com/jiwoongbio/REMOCON) and the reads with better alignments to human MYC were counted.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene read counts for each sample
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample

source_name: mouse liver cancer

growth_protocol: MYC-driven liver tumor model was generated by crossing TRE-MYC with LAP-tTA mouse. Male breeders with 2 copies of LAP-tTA and single copy of TRE-MYC was crossed with WT FVB females to generate LAP-tTA/TRE-MYC mice used for experiments. The breeders were maintained on doxycycline water (1 mg/mL). The females with the litters were transferred to a fresh cage on the day of birth to activate MYC overexpression. Animals were maintained on a regular chow diet. For comparison between WT and MYC overexpression, FVB WT males were used. Both the WT males and MYC overexpression males were 45 days old.

extract_protocol: RNA-seq was performed by Genewiz and the data processing was done using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality and adapter trimming

treatment_protocol: For the experiments with different Trp diet, the mice were transferred to either the control diet, or No-Trp diet for 21 days

value: mouse liver cancer

tag: injected cell_type

value: mouse primary liver tumor cells generated from Myc that are knock out for p53 and overexpress mutant NRAS in hepatocytes

tag: host mouse_genotype

value: NOD-SKID

tag: cancer cell_genotype

value: FVB MYC ON

value: Complete diet


title: Donor 5 unstimulated BDCA3

tag: cell type


title: xenograft_control, 40

tag: tissue

tag: treatment


title: blood_covid+_CB0107_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0107-03

value: female


title: blood_covid+_CB0107_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0107-02


title: blood_covid+_CB0107_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0107-01


title: NC.D2_Plate1.E1

tag: strain

value: nerve crush day 2


title: blood_covid+_CB0106_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0106-07

value: male

value: unvaccinated


title: xenograft_NoTrp, 37

value: No Trp Diet


title: xenograft_control, 41


title: Donor 4Hiltonol stimulated BDCA3


title: Donor 4 pRNA stimulated BDCA3


title: NC.D2_Plate1.D6

value: microglia

value: retina


title: Donor 3 Hiltonol+pRNA stimulated BDCA3


title: xenograft_NoTrp, 36


title: WT_20200928, 5-SDD00460

description:
Raw_Counts.txt
Raw_TPM.txt

tag: cell line

value: WT

value: Microglia

value: LRRk2 (Wt)

value: IFNg


title: Donor 4 unstimulated BDCA3

value: cDC1 (BDCA3+ DC)


title: NC.D2_Plate1.D5

value: 16 weeks old


title: blood_covid+_CB0106_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0106-06

tag: disease status


title: NC.D2_Plate1.D4


title: xenograft_NoTrp, 35

value: mouse liver cancer

value: mouse primary liver tumor cells generated from Myc that are knock out for p53 and overexpress mutant NRAS in hepatocytes