title: HT29_BatchC_Vehicle(DMSO)_rep1

description:
sample C1-1-1
RCM_tonifying_HT29.txt


title: biol rep 4 : Ifnar1-/-_PBS_d4_4

status: Public on Jun 21 2024

type: SRA

city: Tianjin

first: Henan

last: XU

address: No.94 Weijin Road

department: immunology

country: China

institute: Nankai University

library_source: transcriptomic

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp 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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted from the blood using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.Cells were homogenized for 2 minutes then added 0.3 mL chloroform. The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

tag: tissue

value: Peripheral blood

tag: cell type

value: whole blood

tag: genotype

tag: treatment

value: PBS/priatane induced day4


title: HT29_BatchB_water extract of Samul-tang (Low dose)_rep3

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description:
sample 7-3-6
RCM_tonifying_HT29.txt

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

organism: Homo sapiens

growth_protocol: Human colorectal adenocarcinoma cell line, HT29 (HTB-38) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). HT29 cells were maintained in DMEM medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 5% CO2 incubator. The cell was subcultured every 3 or 4 days, depending on the cell density.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: Dulbecco's Modified Eagle Medium (DMEM), phosphate-buffered saline (PBS), TrypLE Express, penicillin-streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO) and QIAzol lysis reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA) and Qiagen (Germantown, MD, USA), respectively. The dried medicinal plants, prepared in compliance with the Korean Pharmacopoeia, were supplied from Kwangmyung-dang Medicinal Herbs Co. (Ulsan, Republic of Korea). The samples used in the experiment underwent organoleptic examination by Dr. Choi Goya, an herbal medicine organoleptic examination expert appointed by the Korea Food and Drug Administration, and were additionally identified at the species level by analyzing the DNA barcode region sequences. Voucher specimen were deposited in the Korean Herbarium of Standard Herbal Resources, Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Republic of Korea . All herbs and extracts can be obtained from the Oriental Medicine Resources Research Center (KIOM, https://oasis.kiom.re.kr/herblib). A hot water and 70% ethanol extract of each plant was prepared and supplied by KOC Biotech Co. (Daejeon, Republic of Korea). Briefly, dried plants (1,000 g) were pulverized and extracted in hot distilled water (10 L) for 3 h under a reflux extraction system (MS-DM609; MTOPS, Seoul, Republic of Korea) or in 70% ethanol (15L) for 1 h under ultrasonication system (VCP-20, Lab companion, Dajeon, Republic of Korea) twice. The extract solution was filtered through a 5 µm cartridge filter, concentrated in a rotary evaporator (Ev-1020, SciLab, Seoul, Republic of Korea), and then lyophilized in a freeze dryer (LP-20, Ilshin-Bio-Base, Dongduchen, Republic of Korea) to obtain the final extract. The extract was finely homogenized and packed in a glass bottle containing a desiccant silica gel. The decoction was prepared by mixing each extract, considering the composition ratio and extract yield of a single medicinal herb, and homogenized, according to the Korean Pharmacopoeia. For the in vitro treatment, extracts (100 mg) were vigorously vortexed for 30 min in 10 mL phosphate-buffered saline (PBS; Thermo Fisher Scientific, Rockford, IL, USA) containing 2% DMSO and then sterilized by filtering through a 0.22 µm membrane to obtain a stock solution (10 mg/mL); the stock solution was aliquoted in small volumes and stored at -80°C until use.

tag: cell line

value: Samul-tang water extract 20 μg/mL

tag: time


title: 414C2, iPSC-derived motor neurons from healthy control, ROPI, 6h

city: Kanagawa

first: Satoru

last: Morimoto

address: 3－25－10, Tonomachi, Kawasaki-ku, Kawasaki-shi

department: Keio Regenerative Medicine Research Center (KRM)

country: Japan

institute: Keio University

description: SMART-seq

data_processing:
Quality Control of the sequences was performed by fastp (version 0.23.2).
Read counts were calculated by salmon (version 1.7.0), and the read count data outputs by salmon were processed by tximport (version 1.22.0).
The processed data were subjected to Transcripts Per Million (TPM) normalization among groups.

extract_protocol:
RNA was harvested using Rneasy Micro Kit (Qiagen). 0.2 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Nextera XT DNA Library Prep Kit following manufacturer's protocols.

value: WT

value: ROPI


title: HT29_BatchB_water extract of Samul-tang (Medium dose)_rep3

description:
sample 7-3-5
RCM_tonifying_HT29.txt

value: Samul-tang water extract 100 μg/mL


title: biol rep 3 : Ifnar1-/-_PBS_d4_3


title: HT29_BatchB_water extract of Samul-tang (High dose)_rep3

description:
sample 7-3-4
RCM_tonifying_HT29.txt

value: Samul-tang water extract 500 μg/mL


title: HT29_BatchB_water extract of Sagunja-tang (Low dose)_rep3

description:
sample 7-3-3
RCM_tonifying_HT29.txt

value: Sagunja-tang water extract 20 μg/mL


title: 414C2, iPSC-derived motor neurons from healthy control, non, 72h

description: SMART-seq

value: non


title: biol rep 3 : Ifnar1-/-_PBS_d6_3

value: PBS/priatane induced day6


title: biol rep 2 : Ifnar1-/-_PBS_d4_2


title: HT29_BatchB_water extract of Sagunja-tang (Medium dose)_rep3

description:
sample 7-3-2
RCM_tonifying_HT29.txt

value: Sagunja-tang water extract 100 μg/mL


title: biol rep 1 : Ifnar1-/-_PBS_d4_1


title: HT29_BatchB_water extract of Samul-tang (Low dose)_rep2

description:
sample 7-2-6
RCM_tonifying_HT29.txt


title: 414C2, iPSC-derived motor neurons from healthy control, non, 60h

description: SMART-seq


title: 414C2, iPSC-derived motor neurons from healthy control, non, 48h

description: SMART-seq


title: HT29_BatchB_water extract of Samul-tang (High dose)_rep2

description:
sample 7-2-4
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Sagunja-tang (High dose)_rep3

description:
sample 7-3-1
RCM_tonifying_HT29.txt

value: Sagunja-tang water extract 500 μg/mL


title: biol rep 6 :  Ifnar1+/+_spm_d6_6

value: Spermine/priatane induced day6


title: HT29_BatchB_water extract of Samul-tang (Medium dose)_rep2

description:
sample 7-2-5
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Sagunja-tang (Low dose)_rep2

description:
sample 7-2-3
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Sagunja-tang (Medium dose)_rep2

description:
sample 7-2-2
RCM_tonifying_HT29.txt


title: biol rep 5 :  Ifnar1+/+_spm_d6_5


title: 414C2, iPSC-derived motor neurons from healthy control, non, 36h

description: SMART-seq


title: HT29_BatchB_water extract of Sagunja-tang (High dose)_rep2

description:
sample 7-2-1
RCM_tonifying_HT29.txt


title: biol rep 3 :  Ifnar1+/+_spm_d6_3


title: HT29_BatchB_water extract of Samul-tang (Low dose)_rep1

description:
sample 7-1-6
RCM_tonifying_HT29.txt


title: biol rep 4 :  Ifnar1+/+_spm_d6_4


title: HT29_BatchB_water extract of Samul-tang (Medium dose)_rep1

description:
sample 7-1-5
RCM_tonifying_HT29.txt


title: 414C2, iPSC-derived motor neurons from healthy control, non, 84h

description: SMART-seq


title: 414C2, iPSC-derived motor neurons from healthy control, non, 24h

description: SMART-seq


title: HT29_BatchB_water extract of Samul-tang (High dose)_rep1

description:
sample 7-1-4
RCM_tonifying_HT29.txt


title: biol rep 2 :  Ifnar1+/+_spm_d6_2


title: 414C2, iPSC-derived motor neurons from healthy control, non, 0h

description: SMART-seq


title: HT29_BatchB_water extract of Sagunja-tang (High dose)_rep1

description:
sample 7-1-1
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Sagunja-tang (Low dose)_rep1

description:
sample 7-1-3
RCM_tonifying_HT29.txt


title: biol rep 1 :  Ifnar1+/+_spm_d6_1


title: HT29_BatchB_water extract of Astragali Radix (Low dose)_rep3

description:
sample 6-3-6
RCM_tonifying_HT29.txt

value: Astragali Radix water extract 20 μg/mL


title: HT29_BatchB_water extract of Astragali Radix (Medium dose)_rep3

description:
sample 6-3-5
RCM_tonifying_HT29.txt

value: Astragali Radix water extract 100 μg/mL


title: HT29_BatchB_water extract of Cinnamomi Cortex (Low dose)_rep3

description:
sample 6-3-3
RCM_tonifying_HT29.txt

value: Cinnamomi Cortex water extract 20 μg/mL


title: 201B7, iPSC-derived motor neurons from healthy control, ROPI, 12h

description: SMART-seq


title: biol rep 4 :  Ifnar1+/+_spm_d4_4

value: Peripheral blood

value: Spermine/priatane induced day4


title: HT29_BatchB_water extract of Astragali Radix (Medium dose)_rep2

description:
sample 6-2-5
RCM_tonifying_HT29.txt


title: 414C2, iPSC-derived motor neurons from healthy control, non, 12h

description: SMART-seq


title: 201B7, iPSC-derived motor neurons from healthy control, ROPI, 36h

description: SMART-seq


title: biol rep 5 :  Ifnar1+/+_spm_d4_5

value: whole blood


title: biol rep 6 :  Ifnar1+/+_spm_d4_6


title: biol rep 3 :  Ifnar1+/+_spm_d4_3


title: HT29_BatchB_water extract of Cinnamomi Cortex (Medium dose)_rep3

description:
sample 6-3-2
RCM_tonifying_HT29.txt

value: Cinnamomi Cortex water extract 100 μg/mL


title: HT29_BatchB_water extract of Cinnamomi Cortex (Low dose)_rep2

description:
sample 6-2-3
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Astragali Radix (High dose)_rep3

description:
sample 6-3-4
RCM_tonifying_HT29.txt

value: Astragali Radix water extract 500 μg/mL


title: HT29_BatchB_water extract of Astragali Radix (Low dose)_rep2

description:
sample 6-2-6
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Sagunja-tang (Medium dose)_rep1

description:
sample 7-1-2
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Cinnamomi Cortex (Medium dose)_rep2

description:
sample 6-2-2
RCM_tonifying_HT29.txt


title: 201B7, iPSC-derived motor neurons from healthy control, non, 84h

description: SMART-seq

value: WT


title: 201B7, iPSC-derived motor neurons from healthy control, ROPI, 84h

description: SMART-seq

value: ROPI


title: 201B7, iPSC-derived motor neurons from healthy control, non, 72h

description: SMART-seq


title: biol rep 1 :  Ifnar1+/+_spm_d4_1


title: HT29_BatchB_water extract of Astragali Radix (Low dose)_rep1

description:
sample 6-1-6
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Astragali Radix (Medium dose)_rep1

description:
sample 6-1-5
RCM_tonifying_HT29.txt


title: biol rep 6 :  Ifnar1+/+_PBS_d6_6


title: HT29_BatchB_water extract of Cinnamomi Cortex (High dose)_rep2

description:
sample 6-2-1
RCM_tonifying_HT29.txt

value: Cinnamomi Cortex water extract 500 μg/mL


title: biol rep 2 :  Ifnar1+/+_spm_d4_2


title: HT29_BatchB_water extract of Astragali Radix (High dose)_rep1

description:
sample 6-1-4
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Cinnamomi Cortex (High dose)_rep3

description:
sample 6-3-1
RCM_tonifying_HT29.txt


title: 201B7, iPSC-derived motor neurons from healthy control, ROPI, 6h

description: SMART-seq


title: HT29_BatchB_water extract of Cinnamomi Cortex (Low dose)_rep1

description:
sample 6-1-3
RCM_tonifying_HT29.txt


title: biol rep 5 :  Ifnar1+/+_PBS_d6_5


title: HT29_BatchB_water extract of Astragali Radix (High dose)_rep2

description:
sample 6-2-4
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Cinnamomi Cortex (High dose)_rep1

description:
sample 6-1-1
RCM_tonifying_HT29.txt


title: biol rep 4 :  Ifnar1+/+_PBS_d6_4


title: 201B7, iPSC-derived motor neurons from healthy control, non, 36h

description: SMART-seq


title: HT29_BatchB_water extract of  Rehmanniae Radix Preparata (Low dose)_rep3

description:
sample 5-3-6
RCM_tonifying_HT29.txt

value: Rehmanniae Radix Preparata water extract 20 μg/mL


title: biol rep 3 :  Ifnar1+/+_PBS_d6_3


title: HT29_BatchB_water extract of  Rehmanniae Radix Preparata (High dose)_rep3

description:
sample 5-3-4
RCM_tonifying_HT29.txt

value: Rehmanniae Radix Preparata water extract 500 μg/mL


title: HT29_BatchB_water extract of Cnidii Rhizoma (Low dose)_rep3

description:
sample 5-3-3
RCM_tonifying_HT29.txt

value: Cnidii Rhizoma water extract 20 μg/mL


title: 201B7, iPSC-derived motor neurons from healthy control, non, 0h

description: SMART-seq

value: non


title: HT29_BatchB_water extract of Cnidii Rhizoma (High dose)_rep3

description:
sample 5-3-1
RCM_tonifying_HT29.txt

value: Cnidii Rhizoma water extract 500 μg/mL


title: biol rep 1 :  Ifnar1+/+_PBS_d6_1

value: PBS/priatane induced day6


title: 201B7, iPSC-derived motor neurons from healthy control, non, 12h

description: SMART-seq


title: 201B7, iPSC-derived motor neurons from healthy control, non, 60h

description: SMART-seq


title: 201B7, iPSC-derived motor neurons from healthy control, non, 48h

description: SMART-seq


title: HT29_BatchB_water extract of  Rehmanniae Radix Preparata (Medium dose)_rep3

description:
sample 5-3-5
RCM_tonifying_HT29.txt

value: Rehmanniae Radix Preparata water extract 100 μg/mL


title: HT29_BatchB_water extract of  Rehmanniae Radix Preparata (Low dose)_rep2

description:
sample 5-2-6
RCM_tonifying_HT29.txt


title: biol rep 6 : Ifnar1+/+_PBS_d4_6

value: PBS/priatane induced day4


title: HT29_BatchB_water extract of  Rehmanniae Radix Preparata (High dose)_rep2

description:
sample 5-2-4
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Cnidii Rhizoma (Low dose)_rep2

description:
sample 5-2-3
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Cinnamomi Cortex (Medium dose)_rep1

description:
sample 6-1-2
RCM_tonifying_HT29.txt


title: biol rep 5 : Ifnar1+/+_PBS_d4_5


title: sample3_glioma

city: Chengdu

first: Yi

last: Wang

state: Please Select

address: 32 West Frist Ring Rd.,

institute: Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital

description: 10 x Genomics Chromium system

library_source: transcriptomic single cell

data_processing:
Using droplet-based single-cell transcriptome profiling through the Cell Ranger software pipeline (version 3.1.0) provided by the 10 x Genomics Chromium system. The number of high-quality cells in each sample after Cell Ranger quantitative quality control ranged from 2419 to 10733. Following the removal of low-quality cells such as doublets, multiplets, and apoptotic cells, the final number of cells collected varies from 1606 to 9744, the average number of UMIs (Unique molecular identifiers) in each cell is 7325 to 15424, the average number of genes in each cell is 2424 to 3858, and the average ratio of mitochondrial genes in each cell is 0.0569 0.1190.
Used the R package Seurat (version 3.1.1) to process the filtered unique molecular identifier (UMI) count matrix. The algorithm provided by Macosko et al was used to identify the top variable genes across single cells.
Principal component analysis (PCA) was used in Seurat to reduce dimensionality using the RunPCA function (PC num = 15). We used the FindClusters function to analyze cell groups using graph-based clustering according to their gene expression profiles, the RunTSNE function to display clusters using a 2-dimensional t-distributed stochastic neighbor embedding (t-SNE) method, and the FindAllMarkers function to find marker genes in each cluster in Seurat.
Used the R package SingleR, an automated annotation method for unbiased scRNA-seq cell type detection, with Human Primary Cell Atlas from Mabbott et al as the reference transcriptome datasets, to infer the cell types.
The FindMarkers function in Seurat was used to identify differentially expressed genes (DEGs). The criterion for substantially different expression was established at P.Value = 0.05 and |log2foldchange| > 0.58. The hypergeometric distribution was used to perform GO (Gene Ontology) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes pathway enrichment) analyses of DEGs.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: temporal lobe

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: temporal lobe

value: human brain

value: glioma


title: sample4_glioma

description: 10 x Genomics Chromium system


title: HT29_BatchB_water extract of Cnidii Rhizoma (Medium dose)_rep2

description:
sample 5-2-2
RCM_tonifying_HT29.txt

value: Cnidii Rhizoma water extract 100 μg/mL


title: sample2_glioma

description: 10 x Genomics Chromium system


title: 201B7, iPSC-derived motor neurons from healthy control, non, 24h

description: SMART-seq


title: HT29_BatchB_water extract of Cnidii Rhizoma (High dose)_rep2

description:
sample 5-2-1
RCM_tonifying_HT29.txt


title: biol rep 4 : Ifnar1+/+_PBS_d4_4

value: Peripheral blood

value: whole blood


title: HT29_BatchB_water extract of  Rehmanniae Radix Preparata (Low dose)_rep1

description:
sample 5-1-6
RCM_tonifying_HT29.txt


title: sample1_normal

description: 10 x Genomics Chromium system

value: normal


title: HT29_BatchB_water extract of  Rehmanniae Radix Preparata (Medium dose)_rep1

description:
sample 5-1-5
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Cnidii Rhizoma (Medium dose)_rep3

description:
sample 5-3-2
RCM_tonifying_HT29.txt


title: biol rep 2 :  Ifnar1+/+_PBS_d6_2


title: HT29_BatchB_water extract of  Rehmanniae Radix Preparata (High dose)_rep1

description:
sample 5-1-4
RCM_tonifying_HT29.txt


title: biol rep 2 : Ifnar1+/+_PBS_d4_2


title: HT29_BatchB_water extract of Cnidii Rhizoma (Medium dose)_rep1

description:
sample 5-1-2
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of  Rehmanniae Radix Preparata (Medium dose)_rep2

description:
sample 5-2-5
RCM_tonifying_HT29.txt


title: HT29_BatchB_water extract of Cnidii Rhizoma (Low dose)_rep1

description:
sample 5-1-3
RCM_tonifying_HT29.txt


title: PDX model, control_3

city: Hangzhou

first: Sheyu

last: Zhang

address: Dongfang Road 150

institute: Hangzhou Institute of Medicine Chinese Academy of Sciences

description:
counts_PDX.txt
NC_3

data_processing:
Sequencing was done as paired end reads with a read length of 126 bases. Raw sequencing information was collected in the form ofFASTQ files. The raw trimmed reads were aligned to the reference genome UCSC hg19.
Assembly: hg19
Supplementary files format and content: For cell line, CSV file includes raw counts for each sample. For PDX model, txt file includes raw counts for each sample.

source_name: breast cancer(PDX)

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104) with on-column DNase digestion using the RNase-free DNase set (Qiagen, 79254)
RNA-seq libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit (NEB, #E7760), following the manufacturer’s instructions.

value: breast cancer(PDX)

value: control


title: HT29_BatchB_water extract of Cnidii Rhizoma (High dose)_rep1

description:
sample 5-1-1
RCM_tonifying_HT29.txt


title: PDX model, control_2

description:
counts_PDX.txt
NC_2


title: biol rep 1 : Ifnar1+/+_PBS_d4_1


title: HT29_BatchB_water extract of Paeoniae Radix (Medium dose)_rep3

description:
sample 4-3-5
RCM_tonifying_HT29.txt

value: Paeoniae Radix water extract 100 μg/mL


title: biol rep 3 : Ifnar1-/-_uni_3

value: priatane uninduced


title: PDX model, control_1

description:
counts_PDX.txt
NC_1


title: HT29_BatchB_water extract of Paeoniae Radix (High dose)_rep3

description:
sample 4-3-4
RCM_tonifying_HT29.txt

value: Paeoniae Radix water extract 500 μg/mL


title: HT29_BatchB_Vehicle(DMSO)_rep2

description:
sample B1-2-1
RCM_tonifying_HT29.txt

value: 0.1% DMSO


title: biol rep 2:  Ifnar1-/-_uni_2


title: HT29_BatchB_Vehicle(DMSO)_rep3

description:
sample B1-3-1
RCM_tonifying_HT29.txt


title: PDX model, LLY283_3

description:
counts_PDX.txt
LLY283_3


title: HT29_BatchA_water extract of Angelicae Gigantis Radix (Low dose)_rep3

description:
sample 4-3-3
RCM_tonifying_HT29.txt

value: Angelicae Gigantis Radix water extract 20 μg/mL


title: biol rep 1 : Ifnar1-/-_uni_1


title: HT29_BatchB_Vehicle(DMSO)_rep1

description:
sample B1-1-1
RCM_tonifying_HT29.txt


title: PDX model, LLY283_1

description:
counts_PDX.txt
LLY283_1


title: biol rep 3 : Ifnar1+/+_PBS_d4_3


title: HT29_BatchA_water extract of Angelicae Gigantis Radix (High dose)_rep3

description:
sample 4-3-1
RCM_tonifying_HT29.txt

value: Angelicae Gigantis Radix water extract 500 μg/mL


title: biol rep 3 : Ifnar1+/+_uni_3


title: HT29_BatchA_water extract of Angelicae Gigantis Radix (Medium dose)_rep3

description:
sample 4-3-2
RCM_tonifying_HT29.txt

value: Angelicae Gigantis Radix water extract 100 μg/mL


title: HT29_BatchA_water extract of Paeoniae Radix (Low dose)_rep2

description:
sample 4-2-6
RCM_tonifying_HT29.txt

value: Paeoniae Radix water extract 20 μg/mL


title: HCT116 cells, shDusp18_3

city: Zhengzhou

first: Xiaojun

last: Zhou

state: Henan

address: 100 Lianhua Street

department: College of Bioengineering

institute: Henan University of Technology

description: gene.counts.matrix.txt

data_processing:
For analysis of RNA-seq results, RNA-seq reads quality was evaluated using FastQC (v0.11.9, https:// www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the mouse genome GRCm38 by HISAT2 (v2.2.1, https://daehwankimlab.github.io/hisat2/).
FeatureCounts (v2.0.1, http://subread.sourceforge.net/) was used to quantitate the transcriptome using the GTF annotation files. Differential analyses were performed to the count files using the R packages DESeq2 (v1.28.1, https://bioconductor.org/ packages/release/bioc/html/DESeq2.html), following standard normalization procedures.
Differential analyses were performed to the count files using the R packages DESeq2 (v1.28.1, https://bioconductor.org/ packages/release/bioc/html/DESeq2.html), following standard normalization procedures. The differentially expressed genes (DEGs) were identified with adjusted pvalue < 0.05 and absolute log2 fold-change > 1 and plotted with R packages ggplot2 (v3.3.2, https://cran.r-project.org/web/packages/ggplot2/index.html). Heatmaps were generated using pheatmap package (v1.0.12, https://cran.r-project.org/web/ packages/pheatmap/index.html) in R (v4.0.2, https://cran.r-project.org). Gene Ontology (GO) enrichment analysis was performed by the R packages clusterProfiler (v3.16.1, https://bioconductor.org/packages/3.13/bioc/html/ clusterProfiler.html). Gene-set enrichment analysis was performed using the GSEA software (v4.1.0, https://www.gsea-msigdb.org/gsea/index.jsp). The RNA-seq data from Usp8 WT and KO CT26 cells will be deposited in the Gene Expression Omnibus (GEO) database.
Assembly: hg38/GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: MC38 and HCT116 cells are mantained in  high-glucose DMEM  supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
Extract total RNA from cell samples and assess the concentration and purity using the Nanodrop2000. Evaluate the integrity of the RNA through agarose gel electrophoresis. The RNA Integrity Number (RIN) is determined using an Agilent2100. For constructing a single library, a minimum of 1 µg of RNA is required, with a concentration of at least 50 ng/µL and an OD260/280 ratio between 1.8 and 2.2. 1.5μg of total RNA was used for the construction of sequencing libraries.
The RNA library for sequencing was meticulously prepared in accordance with the manufacturer's guidelines using the TruSeq™ RNA Sample Preparation Kit.

value: CRC cells

value: DUSP 18 knockdown


title: biol rep 2 : Ifnar1+/+_uni_2


title: HT29_BatchB_water extract of Paeoniae Radix (Low dose)_rep3

description:
sample 4-3-6
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Paeoniae Radix (High dose)_rep2

description:
sample 4-2-4
RCM_tonifying_HT29.txt


title: biol rep 1 : Ifnar1+/+_uni_1


title: HCT116 cells, shDusp18_1

description: gene.counts.matrix.txt


title: HT29_BatchA_water extract of Paeoniae Radix (Medium dose)_rep2

description:
sample 4-2-5
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Angelicae Gigantis Radix (Medium dose)_rep2

description:
sample 4-2-2
RCM_tonifying_HT29.txt


title: M_Myo2

city: Chongqing

first: yong

middle: can

last: liu

address: No.1, Yi-Xue-Yuan Road, Yu-zhong District, Chongqing 400016, China.

institute: Chongqing medical university

data_processing:
The sequencing data was filtered with SOAPnuke  by  Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
The reaction system is configured for reverse transcription. First-strand cDNA is synthesized with SMART-SeqII. The reaction system is configured for PCR amplification to process preamplification of cDNAs,Qualified amplified cDNAs use transposon-based method for further library construction

value: Lung

value: fibroblasts

value: lung fibroblasts from  mice with lung metastasis


title: HT29_BatchA_water extract of Angelicae Gigantis Radix (Low dose)_rep2

description:
sample 4-2-3
RCM_tonifying_HT29.txt


title: PDX model, LLY283_2

description:
counts_PDX.txt
LLY283_2


title: HCT116 cells, shCt_3

description: gene.counts.matrix.txt

value: WT


title: HCT116 cells, shDusp18_2

description: gene.counts.matrix.txt


title: M_Myo3


title: HCT116 cells, shCt_1

description: gene.counts.matrix.txt


title: HT29_BatchA_water extract of Paeoniae Radix (High dose)_rep1

description:
sample 4-1-4
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Angelicae Gigantis Radix (High dose)_rep2

description:
sample 4-2-1
RCM_tonifying_HT29.txt


title: HCT116 cells, shCt_2

description: gene.counts.matrix.txt


title: HT29_BatchA_water extract of Paeoniae Radix (Medium dose)_rep1

description:
sample 4-1-5
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Angelicae Gigantis Radix (High dose)_rep1

description:
sample 4-1-1
RCM_tonifying_HT29.txt


title: M_Myo1


title: M_MF2


title: HT29_BatchA_water extract of Paeoniae Radix (Low dose)_rep1

description:
sample 4-1-6
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Panax Ginseng (Medium dose)_rep3

description:
sample 3-3-5
RCM_tonifying_HT29.txt

value: Panax Ginseng water extract 100 μg/mL


title: HT29_BatchA_water extract of Angelicae Gigantis Radix (Low dose)_rep1

description:
sample 4-1-3
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Angelicae Gigantis Radix (Medium dose)_rep1

description:
sample 4-1-2
RCM_tonifying_HT29.txt


title: M_MF3


title: HT29_BatchA_water extract of Panax Ginseng (Low dose)_rep3

description:
sample 3-3-6
RCM_tonifying_HT29.txt

value: Panax Ginseng water extract 20 μg/mL


title: CD8Tn+NaCl 5' Gene expression

city: Jena

first: Christina

last: Zielinski

address: Beutenbergstrasse 11a

department: Department of Infection Immunology, Leibniz Institute for Natural Product Research and Infection Biology

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the  multi pipeline from CellRanger v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi#cellranger-multi)
Assembly: GRCh38 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation)
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
CD8 memory and naive T cells were freshly isolated from Peripheral blood mononuclear cells by positive selection with CD8 MicroBeads (Miltenyi Biotec) with autoMACS Pro Separator and by antibodies cell sorting with CD8+ CD45RA- lymphocytes with BD FACSAria III. Fresh PBMCs were labelled with CD8 MicroBeads at RT for 15min. PBMCs were washed and resuspended with MACS buffer (PBS, 1% v/v FCS, 2 mM EDTA). Beads labelled PBMCs proceeded with autoMACS program positive selection in sensitive mode. MACS-purified CD8 cells were stained with fluorochrome-conjugated antibodies, washed and resuspended in MACS buffer. CD8 T cells were sorted using BD FACSAria III (BD Biosciences) according to the presence of CD8 and the absence of CD45RA antibodies. The sorted CD8 T cell subsets were washed in FCS-contained PBS (10% v/v FCS).
Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index)

value: 3days TCR activation+3hr PMA/Iono+NaCl

tag: Sex

value: female

tag: age


title: CD8Tn 5' Gene expression

description: 10x Genomics

value: 3days TCR activation+3hr PMA/Iono


title: HT29_BatchA_water extract of Glycyrrhizae Radix (Low dose)_rep3

description:
sample 3-3-3
RCM_tonifying_HT29.txt

value: Glycyrrhizae Radix water extract 20 μg/mL


title: M_MF1


title: HT29_BatchA_water extract of Panax Ginseng (High dose)_rep3

description:
sample 3-3-4
RCM_tonifying_HT29.txt

value: Panax Ginseng water extract 500 μg/mL


title: C42-DEC1-KD-SAL-R3

first: Mehdi

last: Heidari Horestani

state: Thüringen

address: Am klinikum1

institute: Jena University Hospital

data_processing:
FastQC software version 0.11.5 was used for quality control and adaptors were trimmed with skewer version 0.2.1 .
hg38 as a reference genome was used for alignment using Rhisat2 aligner algorithm
Read counting was carried out by using GenomicAlignments R package
Normalization was performed by using DESeq2 R package
Assembly: hg38 (BSgenome.Hsapiens.UCSC.hg38)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

growth_protocol: C4-2 cells were seeded 24 h prior transfection with siRNA tarrgeting BHLHE40 and relevant Sicontrol. siRNAs were transfected by the DharmaFECT reagent (Dharmacon) according to the manufacturer’s protocol. Transfection was performed 24 h prior treatment.

extract_protocol:
RNA was harvested from the cells using peqGOLD TriFast (Peqlab, Erlangen, Germany) according to the manufacturer’s protocol and sent for RNA-sequencing to macrogen Europe.
Libraries were produced using the TruSeq stranded total RNA (with Ribo-Zero) kit by Macrogen

treatment_protocol: Cells were treated in DMEM with 1nM R1881 (SAL) or 0.1% DMSO for 72 h.

value: castration resistant prostate cancer

value: KD

value: SAL


title: HT29_BatchA_water extract of Glycyrrhizae Radix (High dose)_rep3

description:
sample 3-3-1
RCM_tonifying_HT29.txt

value: Glycyrrhizae Radix water extract 500 μg/mL


title: HT29_BatchA_water extract of Glycyrrhizae Radix (Medium dose)_rep3

description:
sample 3-3-2
RCM_tonifying_HT29.txt

value: Glycyrrhizae Radix water extract 100 μg/mL


title: N_Myo3

value: lung fibroblasts from normal mice


title: HT29_BatchC_ethanol extract of Poria Cocos (Low dose)_rep1

description:
sample 9-1-3
RCM_tonifying_HT29.txt

value: Poria Cocos ethanol extract 20 μg/mL


title: C42-DEC1-KD-SAL-R2


title: N_Myo2

value: Lung

value: fibroblasts


title: HT29_BatchA_water extract of Panax Ginseng (Medium dose)_rep2

description:
sample 3-2-5
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Panax Ginseng (Low dose)_rep2

description:
sample 3-2-6
RCM_tonifying_HT29.txt


title: C42-DEC1-KD-SAL-R1


title: HT29_BatchA_water extract of Glycyrrhizae Radix (Low dose)_rep2

description:
sample 3-2-3
RCM_tonifying_HT29.txt


title: C42-DEC1-KD-DMSO-R3

value: DMSO


title: HT29_BatchA_water extract of Glycyrrhizae Radix (Medium dose)_rep2

description:
sample 3-2-2
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Panax Ginseng (High dose)_rep2

description:
sample 3-2-4
RCM_tonifying_HT29.txt


title: N_Myo1


title: N_MF3


title: C42-DEC1-KD-DMSO-R2


title: HT29_BatchA_water extract of Glycyrrhizae Radix (High dose)_rep2

description:
sample 3-2-1
RCM_tonifying_HT29.txt


title: C42-DEC1-KD-DMSO-R1


title: HT29_BatchA_water extract of Glycyrrhizae Radix (Medium dose)_rep1

description:
sample 3-1-2
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Glycyrrhizae Radix (Low dose)_rep1

description:
sample 3-1-3
RCM_tonifying_HT29.txt


title: N_MF1


title: HT29_BatchA_water extract of Panax Ginseng (Medium dose)_rep1

description:
sample 3-1-5
RCM_tonifying_HT29.txt

value: Panax Ginseng water extract 100 μg/mL


title: N_MF2


title: C42-control-SAL-R3

value: control


title: C42-control-SAL-R2


title: HT29_BatchA_water extract of Glycyrrhizae Radix (High dose)_rep1

description:
sample 3-1-1
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Atractylodis Rhizoma (Medium dose)_rep3

description:
sample 2-3-5
RCM_tonifying_HT29.txt

value: Atractylodis Rhizoma water extract 100 μg/mL


title: HT29_BatchA_water extract of Atractylodis Rhizoma (Low dose)_rep3

description:
sample 2-3-6
RCM_tonifying_HT29.txt

value: Atractylodis Rhizoma water extract 20 μg/mL


title: C42-control-SAL-R1


title: HT29_BatchA_water extract of Atractylodis Rhizoma (High dose)_rep3

description:
sample 2-3-4
RCM_tonifying_HT29.txt

value: Atractylodis Rhizoma water extract 500 μg/mL


title: C42-control-DMSO-R3


title: HT29_BatchA_water extract of Poria Cocos (Medium dose)_rep3

description:
sample 2-3-2
RCM_tonifying_HT29.txt

value: Poria Cocos water extract 100 μg/mL


title: batch2_S047

type: RNA

city: Nagoya

first: Masahiro

last: Nakatochi

state: Aichi

address: 1-1-20 Daiko-Minami, Higashi-ku

institute: Nagoya University

hyb_protocol: Hybridization buffer and washing protocol were attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The following criteria were used for the quality control of the microarray data. First, the reliability of the spots was evaluated by imaging, and only reliable miRNAs were extracted. Next, background (BG) subtraction was performed by taking the mean value of the BLANK (DNA not detected) portion as the BG value and subtracting the BG value from measurements greater than the BG value (mean) + 2SD. Measurements below the BG value (mean) + 2SD were defined as missing values. The BG subtraction value, in which NA was substituted for the missing value, was used as the conversion value.  The missing percentage was calculated for each miRNA with a ratio >0.95, which was excluded from the BG subtraction and conversion value data and analysed totaly 1928 miRNAs. And, we processed bellow preprocessing (pipeline 4). Using the converted value, (1) missing values were imputed using the missForest method. (2) After imputation A, the data were log-transformed (base = 2).(3) Quantile normalization was performed on the log-transformed data. This normalization sorts the values for each sample, averages the sorted values across the samples of each rank, and assigns these averages to the original order of each sample. (4) Batch effect correction was performed using the combat function in the sva package (ver. 3.48.0). R is using version 4.3.1 (R Foundation for Statistical Computing, http://www.R-project.org).

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

extract_protocol: Total RNA was extracted using 3D-Gene RNA Extraction Reagent with EVs isolated from the serum of subjects with ALS (Toray Industries Inc., Tokyo, Japan).

tag: subject status

value: ALS patient

tag: age at time of blood collection

value: Male


title: batch2_S046

source_name: EVs isolated from the serum of subjects with ALS


title: HT29_BatchA_water extract of Atractylodis Rhizoma (Medium dose)_rep2

description:
sample 2-2-5
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Poria Cocos (High dose)_rep3

description:
sample 2-3-1
RCM_tonifying_HT29.txt

value: Poria Cocos water extract 500 μg/mL


title: HT29_BatchA_water extract of Panax Ginseng (Low dose)_rep1

description:
sample 3-1-6
RCM_tonifying_HT29.txt

value: Panax Ginseng water extract 20 μg/mL


title: HT29_BatchA_water extract of Panax Ginseng (High dose)_rep1

description:
sample 3-1-4
RCM_tonifying_HT29.txt

value: Panax Ginseng water extract 500 μg/mL


title: C42-control-DMSO-R2

value: castration resistant prostate cancer


title: HT29_BatchA_water extract of Atractylodis Rhizoma (Low dose)_rep2

description:
sample 2-2-6
RCM_tonifying_HT29.txt


title: batch2_S045


title: HT29_BatchA_water extract of Atractylodis Rhizoma (High dose)_rep2

description:
sample 2-2-4
RCM_tonifying_HT29.txt


title: C42-control-DMSO-R1


title: HT29_BatchA_water extract of Poria Cocos (Medium dose)_rep2

description:
sample 2-2-2
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Poria Cocos (Low dose)_rep2

description:
sample 2-2-3
RCM_tonifying_HT29.txt

value: Poria Cocos water extract 20 μg/mL


title: batch2_S043


title: HT29_BatchA_water extract of Poria Cocos (High dose)_rep2

description:
sample 2-2-1
RCM_tonifying_HT29.txt


title: Patient 18  Posttreatment #2

city: St. Louis

first: David

last: DeNardo

state: MO

address: 425 S Euclid Ave

department: Department of Medicine

country: USA

institute: Washington University in St. Louis

data_processing:
The generated libraries were sequenced by a NovaSeq 6000 sequencing system (Illumina) to an average of 50,000 mean reads per cell. FASTQ files from each sample were processed and aligned with BD Rhapsody WTA Analysis Pipeline (SevenBridges) using reference genome (GRCh38-PhiX-gencodev29.tar.gz) to generate a feature barcode matrix. Feature barcode matrices were loaded into R Seurat and analyzed
Assembly: GRCh38-PhiX-gencodev29.tar.gz
Supplementary files format and content: csv

source_name: humanPancreaticTumors

extract_protocol:
PDAC tissue was then isolated, minced with scissors, and digested in ~15-25mL Dulbecco’s Modified Eagle Medium (DMEM) with 2mg/mL Collagenase A and 1x DNase I for 25 minutes at 37°C with constant stirring. Digestion buffer was quenched with 3mL fetal bovine serum (FBS) and filtered through 100uM Nylon mesh, pelleted by centrifugation (2000rmp for 5 min) and resuspended in FACS buffer (1% BSA in PBS). Following tissue digestion, processed cells from each sample were encapsulated into droplets and libraries using BD Rhapsody Single-Cell Capture and cDNA Synthesis Analysis System (BD Biosciences) according to the manufacturer’s protocol.
Biopsy tissues were processed and digested to single cell suspensions as described above. Samples were negatively selected for viable cells using a magnetic bead live/dead kit (Miltenyi). Sample count and viability (>85%) were assessed using the BD Rhapsody Single Cell System (BD Biosciences). Up to 10000 cells per sample were encapsulated into droplets and libraries using the BD Rhapsody Single Cell System according to manufacturer protocols. The generated libraries were sequenced by a NovaSeq 6000 sequencing system (Illumina) to an average of 50,000 mean reads per cell.

treatment_protocol: PDAC tissues were taken from patients using ultrasound-guided biopsies and details of the trial design are available on clincaltrials.gov (NCT04331041) and briefly here. Patients received SBRT with a total of 50Gy given in 5 fractions. FAKi (VS-6063) was given at a dose of 400mg BID starting the end of day 2 post-SBRT and continued up to one year. Tissues were obtained pre-treatment and after 12-14 weeks post-SBRT.

value: humanPancreaticTumors


title: Patient 18  Posttreatment #1


title: batch2_S042

value: Female


title: HT29_BatchA_water extract of Atractylodis Rhizoma (Low dose)_rep1

description:
sample 2-1-6
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Atractylodis Rhizoma (High dose)_rep1

description:
sample 2-1-4
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Poria Cocos (Low dose)_rep3

description:
sample 2-3-3
RCM_tonifying_HT29.txt


title: HT29_BatchA_water extract of Atractylodis Rhizoma (Medium dose)_rep1

description:
sample 2-1-5
RCM_tonifying_HT29.txt


title: Patient 13 Posttreatment


title: HT29_BatchA_water extract of Poria Cocos (Low dose)_rep1

description:
sample 2-1-3
RCM_tonifying_HT29.txt


title: Patient 18  Pretreatment


title: batch2_S041


title: batch2_S044


title: HT29_BatchA_water extract of Poria Cocos (Medium dose)_rep1

description:
sample 2-1-2
RCM_tonifying_HT29.txt


title: batch2_S040


title: HT29_BatchA_water extract of Poria Cocos (High dose)_rep1

description:
sample 2-1-1
RCM_tonifying_HT29.txt


title: Patient 13 Pretreatment


title: HT29_BatchA_LY294002_rep3

description:
sample 1-3-3
RCM_tonifying_HT29.txt


title: HT29_BatchA_Wortmannin_rep3

description:
sample 1-3-2
RCM_tonifying_HT29.txt

value: wortmannin 10 uM


title: batch2_S039


title: Patient 12  Posttreatment #1


title: HT29_BatchA_Wortmannin_rep2

description:
sample 1-2-2
RCM_tonifying_HT29.txt


title: batch2_S038


title: HT29_BatchA_LY294002_rep2

description:
sample 1-2-3
RCM_tonifying_HT29.txt


title: HT29_BatchA_Wortmannin_rep1

description:
sample 1-1-2
RCM_tonifying_HT29.txt


title: batch2_S037


title: Patient 12  Pretreatment


title: batch2_S036


title: Patient 11  Posttreatment#2

description: processed data merged with rep1


title: HT29_BatchA_Vehicle(DMSO)_rep2

description:
sample A1-2-1
RCM_tonifying_HT29.txt

value: 0.1% DMSO


title: HT29_BatchA_Vehicle(DMSO)_rep3

description:
sample A1-3-1
RCM_tonifying_HT29.txt


title: batch2_S035


title: HT29_BatchA_Vehicle(DMSO)_rep1

description:
sample A1-1-1
RCM_tonifying_HT29.txt


title: Patient 11  Posttreatment#1


title: batch2_S034


title: A549_BatchE_ethanol extract of Sibjeondaebo-tang (Low dose)_rep3

description:
sample 15-3-6
RCM_tonifying_A549.txt

growth_protocol: Human non-small cell lung carcinoma, A549 (CCL-185) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). A549 cells were maintained in RPMI medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 5% CO2 incubator. The cell was subcultured every 3 or 4 days, depending on the cell density.

treatment_protocol: Roswell Park Memorial Institute (RPMI) 1640 medium, phosphate-buffered saline (PBS), TrypLE Express, penicillin-streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO) and QIAzol lysis reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA) and Qiagen (Germantown, MD, USA), respectively. The dried medicinal plants, prepared in compliance with the Korean Pharmacopoeia, were supplied from Kwangmyung-dang Medicinal Herbs Co. (Ulsan, Republic of Korea). The samples used in the experiment underwent organoleptic examination by Dr. Choi Goya, an herbal medicine organoleptic examination expert appointed by the Korea Food and Drug Administration, and were additionally identified at the species level by analyzing the DNA barcode region sequences. Voucher specimen were deposited in the Korean Herbarium of Standard Herbal Resources, Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Republic of Korea . All herbs and extracts can be obtained from the Oriental Medicine Resources Research Center (KIOM, https://oasis.kiom.re.kr/herblib). A hot water and 70% ethanol extract of each plant was prepared and supplied by KOC Biotech Co. (Daejeon, Republic of Korea). Briefly, dried plants (1,000 g) were pulverized and extracted in hot distilled water (10 L) for 3 h under a reflux extraction system (MS-DM609; MTOPS, Seoul, Republic of Korea) or in 70% ethanol (15L) for 1 h under ultrasonication system (VCP-20, Lab companion, Dajeon, Republic of Korea) twice. The extract solution was filtered through a 5 µm cartridge filter, concentrated in a rotary evaporator (Ev-1020, SciLab, Seoul, Republic of Korea), and then lyophilized in a freeze dryer (LP-20, Ilshin-Bio-Base, Dongduchen, Republic of Korea) to obtain the final extract. The extract was finely homogenized and packed in a glass bottle containing a desiccant silica gel. The decoction was prepared by mixing each extract, considering the composition ratio and extract yield of a single medicinal herb, and homogenized, according to the Korean Pharmacopoeia. For the in vitro treatment, extracts (100 mg) were vigorously vortexed for 30 min in 10 mL phosphate-buffered saline (PBS; Thermo Fisher Scientific, Rockford, IL, USA) containing 2% DMSO and then sterilized by filtering through a 0.22 µm membrane to obtain a stock solution (10 mg/mL); the stock solution was aliquoted in small volumes and stored at -80°C until use.

value: Sibjeondaebo-tang ethanol extract 20 μg/mL


title: A549_BatchE_ethanol extract of Sibjeondaebo-tang (High dose)_rep3

description:
sample 15-3-4
RCM_tonifying_A549.txt

value: Sibjeondaebo-tang ethanol extract 500 μg/mL


title: A549_BatchE_ethanol extract of Palmul-tang (Low dose)_rep3

description:
sample 15-3-3
RCM_tonifying_A549.txt

value: Palmul-tang ethanol extract 20 μg/mL


title: A549_BatchE_ethanol extract of Sibjeondaebo-tang (Medium dose)_rep3

description:
sample 15-3-5
RCM_tonifying_A549.txt

value: Sibjeondaebo-tang ethanol extract 100 μg/mL


title: Patient 11  Pretreatment


title: Patient 9  Posttreatment#2

description: processed data merged with rep1


title: HT29_BatchA_LY294002_rep1

description:
sample 1-1-3
RCM_tonifying_HT29.txt


title: batch2_S033


title: batch2_S032


title: Patient 12  Posttreatment #2


title: Patient 9  Posttreatment#1


title: A549_BatchE_ethanol extract of Palmul-tang (High dose)_rep3

description:
sample 15-3-1
RCM_tonifying_A549.txt

value: Palmul-tang ethanol extract 500 μg/mL


title: A549_BatchE_ethanol extract of Sibjeondaebo-tang (Low dose)_rep2

description:
sample 15-2-6
RCM_tonifying_A549.txt


title: A549_BatchE_ethanol extract of Sibjeondaebo-tang (High dose)_rep2

description:
sample 15-2-4
RCM_tonifying_A549.txt


title: A549_BatchE_ethanol extract of Palmul-tang (Low dose)_rep2

description:
sample 15-2-3
RCM_tonifying_A549.txt


title: A549_BatchE_ethanol extract of Sibjeondaebo-tang (Medium dose)_rep2

description:
sample 15-2-5
RCM_tonifying_A549.txt


title: Patient 9  Pretreatment


title: A549_BatchE_ethanol extract of Palmul-tang (Medium dose)_rep2

description:
sample 15-2-2
RCM_tonifying_A549.txt

value: Palmul-tang ethanol extract 100 μg/mL


title: batch2_S031

value: ALS patient


title: A549_BatchE_ethanol extract of Palmul-tang (High dose)_rep2

description:
sample 15-2-1
RCM_tonifying_A549.txt


title: Patient 8  Posttreatment


title: A549_BatchE_ethanol extract of Sibjeondaebo-tang (Low dose)_rep1

description:
sample 15-1-6
RCM_tonifying_A549.txt


title: batch2_S029

value: Male


title: batch2_S028


title: batch2_S030


title: Patient 8  Pretreatment


title: A549_BatchE_ethanol extract of Sibjeondaebo-tang (Medium dose)_rep1

description:
sample 15-1-5
RCM_tonifying_A549.txt


title: A549_BatchE_ethanol extract of Palmul-tang (Medium dose)_rep3

description:
sample 15-3-2
RCM_tonifying_A549.txt


title: batch2_S027


title: A549_BatchE_ethanol extract of Sibjeondaebo-tang (High dose)_rep1

description:
sample 15-1-4
RCM_tonifying_A549.txt


title: A549_BatchE_ethanol extract of Palmul-tang (Low dose)_rep1

description:
sample 15-1-3
RCM_tonifying_A549.txt


title: A549_BatchE_ethanol extract of Palmul-tang (Medium dose)_rep1

description:
sample 15-1-2
RCM_tonifying_A549.txt


title: Patient 7  Pretreatment


title: A549_BatchE_ethanol extract of Palmul-tang (High dose)_rep1

description:
sample 15-1-1
RCM_tonifying_A549.txt


title: A549_BatchE_ethanol extract of Samul-tang (Low dose)_rep3

description:
sample 14-3-6
RCM_tonifying_A549.txt

value: Samul-tang ethanol extract 20 μg/mL


title: Patient 6  Posttreatment


title: A549_BatchE_ethanol extract of Samul-tang (Medium dose)_rep3

description:
sample 14-3-5
RCM_tonifying_A549.txt

value: Samul-tang ethanol extract 100 μg/mL


title: Patient 6  Pretreatment


title: batch2_S025


title: A549_BatchE_ethanol extract of Sagunja-tang (Medium dose)_rep3

description:
sample 14-3-2
RCM_tonifying_A549.txt

value: Sagunja-tang ethanol extract 100 μg/mL


title: A549_BatchE_ethanol extract of Sagunja-tang (Low dose)_rep3

description:
sample 14-3-3
RCM_tonifying_A549.txt

value: Sagunja-tang ethanol extract 20 μg/mL


title: A549_BatchE_ethanol extract of Sagunja-tang (High dose)_rep3

description:
sample 14-3-1
RCM_tonifying_A549.txt

value: Sagunja-tang ethanol extract 500 μg/mL


title: batch2_S024


title: Patient 4 Posttreatment

value: humanPancreaticTumors


title: A549_BatchE_ethanol extract of Samul-tang (Medium dose)_rep2

description:
sample 14-2-5
RCM_tonifying_A549.txt


title: Patient 4 Pretreatment


title: A549_BatchE_ethanol extract of Samul-tang (High dose)_rep2

description:
sample 14-2-4
RCM_tonifying_A549.txt

value: Samul-tang ethanol extract 500 μg/mL


title: Patient 3 Pretreatment #2


title: A549_BatchE_Vehicle(DMSO)_rep3

description:
sample E1-3-1
RCM_tonifying_A549.txt


title: batch2_S021

value: Female


title: Patient 7  Posttreatment


title: batch2_S022


title: batch2_S026


title: A549_BatchE_Vehicle(DMSO)_rep2

description:
sample E1-2-1
RCM_tonifying_A549.txt

value: 0.1% DMSO


title: A549_BatchE_Vehicle(DMSO)_rep1

description:
sample E1-1-1
RCM_tonifying_A549.txt


title: Patient 3 Pretreatment #1


title: batch2_S023


title: Patient 2 Pretreatment #2


title: A549_BatchD_ethanol extract of Sagunja-tang (Low dose)_rep2

description:
sample 14-2-3
RCM_tonifying_A549.txt


title: A549_BatchE_ethanol extract of Samul-tang (High dose)_rep3

description:
sample 14-3-4
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Sagunja-tang (Medium dose)_rep2

description:
sample 14-2-2
RCM_tonifying_A549.txt


title: Patient 2 Pretreatment #1


title: A549_BatchE_ethanol extract of Samul-tang (Low dose)_rep2

description:
sample 14-2-6
RCM_tonifying_A549.txt


title: batch2_S019


title: A549_BatchD_ethanol extract of Samul-tang (Low dose)_rep1

description:
sample 14-1-6
RCM_tonifying_A549.txt


title: batch2_S020


title: A549_BatchD_ethanol extract of Samul-tang (Medium dose)_rep1

description:
sample 14-1-5
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Samul-tang (High dose)_rep1

description:
sample 14-1-4
RCM_tonifying_A549.txt


title: batch2_S017


title: A549_BatchD_ethanol extract of Sagunja-tang (Low dose)_rep1

description:
sample 14-1-3
RCM_tonifying_A549.txt


title: batch2_S018


title: Patient 1  Posttreatment #1


title: A549_BatchD_ethanol extract of Sagunja-tang (Medium dose)_rep1

description:
sample 14-1-2
RCM_tonifying_A549.txt


title: batch2_S016


title: A549_BatchD_ethanol extract of Cinnamomi Cortex (Low dose)_rep3

description:
sample 13-3-6
RCM_tonifying_A549.txt

value: Cinnamomi Cortex ethanol extract 20 μg/mL


title: Patient 1  Pretreatment #2


title: A549_BatchD_ethanol extract of Cinnamomi Cortex (Medium dose)_rep3

description:
sample 13-3-5
RCM_tonifying_A549.txt

value: Cinnamomi Cortex ethanol extract 100 μg/mL


title: batch2_S015


title: A549_BatchD_ethanol extract of Cinnamomi Cortex (High dose)_rep3

description:
sample 13-3-4
RCM_tonifying_A549.txt

value: Cinnamomi Cortex ethanol extract 500 μg/mL


title: A549_BatchD_ethanol extract of Sagunja-tang (High dose)_rep2

description:
sample 14-2-1
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Astragali Radix (Low dose)_rep3

description:
sample 13-3-3
RCM_tonifying_A549.txt

value: Astragali Radix ethanol extract 20 μg/mL


title: PDO_13

city: Nanjing

first: Yanling

state: Jiangsu

address: NO.136 Hanzhong Road

institute: Nanjing Medical University

data_processing:
Trim seuqence reads using trimmomatic v 0.39 (parameters: -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Trimmed seuqence reads were mapped to hg38 using hisat2 v 2.2.1 (parameters: --very-sensitive --avoid-pseudogene --rna-standness RF --dta -t)
Raw readcounts were extracted by using featureCounts v 2.0.6 (parameters: -s 2 -p -t exon -g gene_id)
Assembly: hg38
Supplementary files format and content: tab-demlimited text file includes raw counts for each Sample

source_name: head neck squamous cell carcinoma PDO

extract_protocol:
RNA was isolated using Trizol reagent. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: head neck squamous cell carcinoma PDO


title: Patient 1  Pretreatment #1


title: A549_BatchD_ethanol extract of Astragali Radix (Medium dose)_rep3

description:
sample 13-3-2
RCM_tonifying_A549.txt

value: Astragali Radix ethanol extract 100 μg/mL


title: batch2_S014

value: ALS patient


title: A549_BatchD_ethanol extract of Astragali Radix (High dose)_rep3

description:
sample 13-3-1
RCM_tonifying_A549.txt

value: Astragali Radix ethanol extract 500 μg/mL


title: A549_BatchD_ethanol extract of Cinnamomi Cortex (Low dose)_rep2

description:
sample 13-2-6
RCM_tonifying_A549.txt


title: Patient 1  Posttreatment #2


title: PDO_11


title: PDO_12


title: A549_BatchD_ethanol extract of Cinnamomi Cortex (High dose)_rep2

description:
sample 13-2-4
RCM_tonifying_A549.txt


title: batch2_S012

value: Male


title: batch2_S013


title: A549_BatchD_ethanol extract of Sagunja-tang (High dose)_rep1

description:
sample 14-1-1
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Astragali Radix (Low dose)_rep2

description:
sample 13-2-3
RCM_tonifying_A549.txt


title: batch2_S011


title: PDO_10


title: A549_BatchD_ethanol extract of Astragali Radix (High dose)_rep2

description:
sample 13-2-1
RCM_tonifying_A549.txt


title: batch2_S010


title: A549_BatchD_ethanol extract of Astragali Radix (Medium dose)_rep2

description:
sample 13-2-2
RCM_tonifying_A549.txt


title: PDO_9


title: batch2_S009


title: A549_BatchD_ethanol extract of Cinnamomi Cortex (Low dose)_rep1

description:
sample 13-1-6
RCM_tonifying_A549.txt


title: batch2_S008


title: batch2_S007


title: PDO_7


title: A549_BatchD_ethanol extract of Astragali Radix (Medium dose)_rep1

description:
sample 13-1-2
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Cinnamomi Cortex (Medium dose)_rep1

description:
sample 13-1-5
RCM_tonifying_A549.txt


title: PDO_8


title: A549_BatchD_ethanol extract of Astragali Radix (Low dose)_rep1

description:
sample 13-1-3
RCM_tonifying_A549.txt


title: PDO_6


title: batch2_S006


title: A549_BatchD_ethanol extract of Cinnamomi Cortex (Medium dose)_rep2

description:
sample 13-2-5
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Rehmanniae Radix Preparata (Low dose)_rep3

description:
sample 12-3-6
RCM_tonifying_A549.txt

value: Rehmanniae Radix Preparata ethanol extract 20 μg/mL


title: A549_BatchD_ethanol extract of Rehmanniae Radix Preparata (High dose)_rep3

description:
sample 12-3-4
RCM_tonifying_A549.txt

value: Rehmanniae Radix Preparata ethanol extract 500 μg/mL


title: A549_BatchD_ethanol extract of Rehmanniae Radix Preparata (Medium dose)_rep3

description:
sample 12-3-5
RCM_tonifying_A549.txt

value: Rehmanniae Radix Preparata ethanol extract 100 μg/mL


title: PDO_5


title: A549_BatchD_ethanol extract of Cnidii Rhizoma (High dose)_rep3

description:
sample 12-3-1
RCM_tonifying_A549.txt

value: Cnidii Rhizoma ethanol extract 500 μg/mL


title: PDO_4


title: A549_BatchD_ethanol extract of Cnidii Rhizoma (Medium dose)_rep3

description:
sample 12-3-2
RCM_tonifying_A549.txt

value: Cnidii Rhizoma ethanol extract 100 μg/mL


title: A549_BatchD_ethanol extract of Rehmanniae Radix Preparata (Medium dose)_rep2

description:
sample 12-2-5
RCM_tonifying_A549.txt


title: batch2_S005


title: PDO_3


title: A549_BatchD_ethanol extract of Rehmanniae Radix Preparata (Low dose)_rep2

description:
sample 12-2-6
RCM_tonifying_A549.txt


title: PDO_2


title: A549_BatchD_ethanol extract of Cinnamomi Cortex (High dose)_rep1

description:
sample 13-1-4
RCM_tonifying_A549.txt


title: batch2_S003


title: A549_BatchD_ethanol extract of Rehmanniae Radix Preparata (High dose)_rep2

description:
sample 12-2-4
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Astragali Radix (High dose)_rep1

description:
sample 13-1-1
RCM_tonifying_A549.txt


title: batch2_S002


title: batch2_S004


title: A549_BatchD_ethanol extract of Cnidii Rhizoma (Low dose)_rep2

description:
sample 12-2-3
RCM_tonifying_A549.txt

value: Cnidii Rhizoma ethanol extract 20 μg/mL


title: batch2_S001

value: Female


title: PDO_1


title: A549_BatchD_ethanol extract of Cnidii Rhizoma (Low dose)_rep3

description:
sample 12-3-3
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Cnidii Rhizoma (Medium dose)_rep2

description:
sample 12-2-2
RCM_tonifying_A549.txt


title: P5_RSV_M

city: Vienna

first: Lukas

last: Wisgrill

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

data_processing:
The nfcore/rnaseq pipeline (https://nf-co.re/rnaseq) was used for reference genome alignment (GRCh38) using the STAR aligner.
Data filtering, normalization as well as differentially expression was conducted using the DESeq2 package (1.34.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include counts per sample/gene

source_name: Nasal Epithelial Cells at Air-Liquid-Interface

growth_protocol: Nasal biopsy sampling, nasal epithelial cell passaging, and ALI-differentiation was conducted according to our previously published protocol with step-by-step instructions (doi: 10.1038/s41598-019-56737-9).

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit Plus (Qiagen, Hilden, GER). RNA concentrations and integrity were measured using an Agilent Bioanalyzer and only samples with a RIN-value > 9 were included for sequencing
Libraries were prepared using Illumina TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) for poly-A selected strand-specific sequencing according to the manufacturers instructions.
Sequencing was performed using Illumina NovaSeq 6000 (Illumina) with 'NovaSeqXp' workflow in 'S4' mode flowcell which generated 150 bp paired-end reads with a mean sequencing depth of about 83 million reads per sample.

value: Primary nasal cells

value: Epithelial cells

value: WT

value: MOCK


title: A549_BatchD_ethanol extract of Rehmanniae Radix Preparata (Medium dose)_rep1

description:
sample 12-1-5
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Rehmanniae Radix Preparata (High dose)_rep1

description:
sample 12-1-4
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Cnidii Rhizoma (Low dose)_rep1

description:
sample 12-1-3
RCM_tonifying_A549.txt


title: P4_RSV_S

value: Nasal Epithelial Cells at Air-Liquid-Interface

value: Respiratory Syncytial Virus


title: batch1_S026


title: batch1_S027


title: A549_BatchD_ethanol extract of Cnidii Rhizoma (Medium dose)_rep1

description:
sample 12-1-2
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Angelicae Gigantis Radix (Low dose)_rep3

description:
sample 11-3-3
RCM_tonifying_A549.txt

value: Angelicae Gigantis Radix ethanol extract 20 μg/mL


title: batch1_S028

value: ALS patient


title: batch1_S025


title: P3_RSV_S


title: A549_BatchD_ethanol extract of Paeoniae Radix (High dose)_rep3

description:
sample 11-3-4
RCM_tonifying_A549.txt

value: Paeoniae Radix ethanol extract 500 μg/mL


title: A549_BatchD_ethanol extract of Angelicae Gigantis Radix (Medium dose)_rep3

description:
sample 11-3-2
RCM_tonifying_A549.txt

value: Angelicae Gigantis Radix ethanol extract 100 μg/mL


title: P3_RSV_M


title: A549_BatchD_ethanol extract of Paeoniae Radix (Medium dose)_rep3

description:
sample 11-3-5
RCM_tonifying_A549.txt

value: Paeoniae Radix ethanol extract 100 μg/mL


title: A549_BatchD_ethanol extract of Cnidii Rhizoma (High dose)_rep2

description:
sample 12-2-1
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Paeoniae Radix (Low dose)_rep3

description:
sample 11-3-6
RCM_tonifying_A549.txt

value: Paeoniae Radix ethanol extract 20 μg/mL


title: batch1_S022

value: Male


title: batch1_S023


title: A549_BatchD_ethanol extract of Rehmanniae Radix Preparata (Low dose)_rep1

description:
sample 12-1-6
RCM_tonifying_A549.txt

value: Rehmanniae Radix Preparata ethanol extract 20 μg/mL


title: P5_RSV_S


title: P4_RSV_M


title: A549_BatchD_ethanol extract of Angelicae Gigantis Radix (High dose)_rep3

description:
sample 11-3-1
RCM_tonifying_A549.txt

value: Angelicae Gigantis Radix ethanol extract 500 μg/mL


title: batch1_S024


title: A549_BatchD_ethanol extract of Cnidii Rhizoma (High dose)_rep1

description:
sample 12-1-1
RCM_tonifying_A549.txt

value: Cnidii Rhizoma ethanol extract 500 μg/mL


title: P1_RSV_S


title: A549_BatchD_ethanol extract of Paeoniae Radix (Medium dose)_rep2

description:
sample 11-2-5
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Paeoniae Radix (Low dose)_rep2

description:
sample 11-2-6
RCM_tonifying_A549.txt


title: P2_RSV_M


title: A549_BatchD_ethanol extract of Paeoniae Radix (High dose)_rep2

description:
sample 11-2-4
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Angelicae Gigantis Radix (Medium dose)_rep2

description:
sample 11-2-2
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Angelicae Gigantis Radix (High dose)_rep2

description:
sample 11-2-1
RCM_tonifying_A549.txt


title: batch1_S021


title: A549_BatchD_Vehicle(DMSO)_rep2

description:
sample D1-2-1
RCM_tonifying_A549.txt

value: 0.1% DMSO


title: batch1_S020

value: Female


title: batch1_S019


title: T5_RSV_S

value: Primary nasal cells

value: Epithelial cells


title: A549_BatchD_Vehicle(DMSO)_rep1

description:
sample D1-1-1
RCM_tonifying_A549.txt


title: P1_RSV_M

value: WT

value: MOCK


title: A549_BatchC_ethanol extract of Paeoniae Radix (Low dose)_rep1

description:
sample 11-1-6
RCM_tonifying_A549.txt


title: A549_BatchD_ethanol extract of Angelicae Gigantis Radix (Low dose)_rep2

description:
sample 11-2-3
RCM_tonifying_A549.txt


title: T5_RSV_M

value: Nasal Epithelial Cells at Air-Liquid-Interface


title: A549_BatchC_ethanol extract of Paeoniae Radix (Medium dose)_rep1

description:
sample 11-1-5
RCM_tonifying_A549.txt


title: batch1_S018


title: batch1_S017


title: A549_BatchD_Vehicle(DMSO)_rep3

description:
sample D1-3-1
RCM_tonifying_A549.txt


title: T4_RSV_S

value: Respiratory Syncytial Virus


title: batch1_S016

value: ALS patient


title: A549_BatchC_ethanol extract of Paeoniae Radix (High dose)_rep1

description:
sample 11-1-4
RCM_tonifying_A549.txt

value: Paeoniae Radix ethanol extract 500 μg/mL


title: A549_BatchC_ethanol extract of Angelicae Gigantis Radix (Medium dose)_rep1

description:
sample 11-1-2
RCM_tonifying_A549.txt

value: Angelicae Gigantis Radix ethanol extract 100 μg/mL


title: A549_BatchC_ethanol extract of Angelicae Gigantis Radix (Low dose)_rep1

description:
sample 11-1-3
RCM_tonifying_A549.txt

value: Angelicae Gigantis Radix ethanol extract 20 μg/mL


title: T4_RSV_M


title: A549_BatchC_ethanol extract of Angelicae Gigantis Radix (High dose)_rep1

description:
sample 11-1-1
RCM_tonifying_A549.txt


title: T3_RSV_S


title: A549_BatchC_ethanol extract of Panax Ginseng (Low dose)_rep3

description:
sample 10-3-6
RCM_tonifying_A549.txt

value: Panax Ginseng ethanol extract 20 μg/mL


title: batch1_S015

value: Male


title: A549_BatchC_ethanol extract of Panax Ginseng (Medium dose)_rep3

description:
sample 10-3-5
RCM_tonifying_A549.txt

value: Panax Ginseng ethanol extract 100 μg/mL


title: batch1_S014


title: P2_RSV_S


title: A549_BatchC_ethanol extract of Panax Ginseng (High dose)_rep3

description:
sample 10-3-4
RCM_tonifying_A549.txt

value: Panax Ginseng ethanol extract 500 μg/mL


title: batch1_S013


title: A549_BatchC_ethanol extract of Glycyrrhizae Radix (Medium dose)_rep3

description:
sample 10-3-2
RCM_tonifying_A549.txt

value: Glycyrrhizae Radix ethanol extract 100 μg/mL


title: batch1_S012


title: A549_BatchC_ethanol extract of Glycyrrhizae Radix (High dose)_rep3

description:
sample 10-3-1
RCM_tonifying_A549.txt

value: Glycyrrhizae Radix ethanol extract 500 μg/mL


title: T2_RSV_S


title: A549_BatchC_ethanol extract of Panax Ginseng (Low dose)_rep2

description:
sample 10-2-6
RCM_tonifying_A549.txt


title: batch1_S011


title: A549_BatchC_ethanol extract of Panax Ginseng (Medium dose)_rep2

description:
sample 10-2-5
RCM_tonifying_A549.txt


title: A549_BatchC_ethanol extract of Panax Ginseng (High dose)_rep2

description:
sample 10-2-4
RCM_tonifying_A549.txt


title: T2_RSV_M


title: batch1_S010

value: Female


title: A549_BatchC_ethanol extract of Glycyrrhizae Radix (Low dose)_rep2

description:
sample 10-2-3
RCM_tonifying_A549.txt

value: Glycyrrhizae Radix ethanol extract 20 μg/mL


title: T1_RSV_S

value: Primary nasal cells

value: Epithelial cells


title: T1_RSV_M

value: WT

value: MOCK


title: A549_BatchC_ethanol extract of Panax Ginseng (Low dose)_rep1

description:
sample 10-1-6
RCM_tonifying_A549.txt


title: A549_BatchC_ethanol extract of Glycyrrhizae Radix (High dose)_rep2

description:
sample 10-2-1
RCM_tonifying_A549.txt


title: A549_BatchC_ethanol extract of Panax Ginseng (Medium dose)_rep1

description:
sample 10-1-5
RCM_tonifying_A549.txt


title: A5_RSV_S

value: Nasal Epithelial Cells at Air-Liquid-Interface

value: Respiratory Syncytial Virus


title: T3_RSV_M


title: A549_BatchC_ethanol extract of Glycyrrhizae Radix (Medium dose)_rep2

description:
sample 10-2-2
RCM_tonifying_A549.txt


title: A549_BatchC_ethanol extract of Glycyrrhizae Radix (Low dose)_rep3

description:
sample 10-3-3
RCM_tonifying_A549.txt


title: batch1_S009

value: ALS patient


title: A549_BatchC_ethanol extract of Panax Ginseng (High dose)_rep1

description:
sample 10-1-4
RCM_tonifying_A549.txt


title: A5_RSV_M


title: A549_BatchC_ethanol extract of Glycyrrhizae Radix (Medium dose)_rep1

description:
sample 10-1-2
RCM_tonifying_A549.txt


title: A4_RSV_S


title: batch1_S008


title: batch1_S007


title: A549_BatchC_ethanol extract of Atractylodis Rhizoma (Low dose)_rep3

description:
sample 9-3-6
RCM_tonifying_A549.txt

value: Atractylodis Rhizoma ethanol extract 20 μg/mL


title: batch1_S006


title: A549_BatchC_ethanol extract of Glycyrrhizae Radix (Low dose)_rep1

description:
sample 10-1-3
RCM_tonifying_A549.txt


title: A4_RSV_M


title: A549_BatchC_ethanol extract of Atractylodis Rhizoma (Medium dose)_rep3

description:
sample 9-3-5
RCM_tonifying_A549.txt

value: Atractylodis Rhizoma ethanol extract 100 μg/mL


title: batch1_S005


title: A549_BatchC_ethanol extract of Atractylodis Rhizoma (High dose)_rep3

description:
sample 9-3-4
RCM_tonifying_A549.txt

value: Atractylodis Rhizoma ethanol extract 500 μg/mL


title: A549_BatchC_ethanol extract of Glycyrrhizae Radix (High dose)_rep1

description:
sample 10-1-1
RCM_tonifying_A549.txt


title: A3_RSV_S


title: A549_BatchC_ethanol extract of Poria Cocos (Low dose)_rep3

description:
sample 9-3-3
RCM_tonifying_A549.txt

value: Poria Cocos ethanol extract 20 μg/mL


title: batch1_S004

value: Male


title: batch1_S003


title: A3_RSV_M


title: A549_BatchC_ethanol extract of Poria Cocos (Medium dose)_rep3

description:
sample 9-3-2
RCM_tonifying_A549.txt

value: Poria Cocos ethanol extract 100 μg/mL


title: A549_BatchC_ethanol extract of Poria Cocos (High dose)_rep3

description:
sample 9-3-1
RCM_tonifying_A549.txt

value: Poria Cocos ethanol extract 500 μg/mL


title: A549_BatchC_ethanol extract of Atractylodis Rhizoma (Low dose)_rep2

description:
sample 9-2-6
RCM_tonifying_A549.txt


title: A549_BatchC_ethanol extract of Atractylodis Rhizoma (Medium dose)_rep2

description:
sample 9-2-5
RCM_tonifying_A549.txt


title: A2_RSV_S


title: batch1_S002


title: A549_BatchC_ethanol extract of Atractylodis Rhizoma (High dose)_rep2

description:
sample 9-2-4
RCM_tonifying_A549.txt


title: A549_BatchC_ethanol extract of Poria Cocos (Low dose)_rep2

description:
sample 9-2-3
RCM_tonifying_A549.txt


title: A2_RSV_M


title: A549_BatchC_ethanol extract of Poria Cocos (High dose)_rep2

description:
sample 9-2-1
RCM_tonifying_A549.txt


title: A1_RSV_S


title: sehA-OH-ara-positive

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

description: OH / arabinose

data_processing:
At first, we demultiplexed and trimmed the ligated RNA linker using ultraplex with the parameter '-m5 0 -l 50'. The barcodes for each sample was supplied in the specific file.
Trimmed reads were mapped to reference genome using hisat2 v.2.2.1 with modified parameters (-k 1 --no-spliced-alignment).
The mapping result was converted to BAM format and split to have a stranded specificity with SAM flag information by samtools.
Resulted data was further modified to bedGraph format for reporting the depth of 5′ site in the mapped read position using genomeCoverageBed with changed parameters (-5 -dz).
Each bedGraph file were normalized to have 10 millions of sequence tags.
Assembly: GCF_000022165.1
Supplementary files format and content: forward and reverse strand bedGraph file includes TSS peaks for each sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

growth_protocol: Bacteria were grown at 37°C in N-minimal media (30) supplemented with 0.1% casamino acids, 38 mM glycerol, and the 10 mM MgCl2.

extract_protocol:
Total RNA was isolated using RNeasy Kit (Qiagen), according to the manufacturer’s instructions.
5'-ends of hydroxylated or mono-phosphorylated RNA were identified using modified EMOTE protocol (Redder, 2015). 1 µg of total RNA was processed by Ribo-Zero Magnetic Kit (Bacteria). Resulting rRNA-depleted mRNA was phosphorylated by T4 polynucleotide kinase. Mono-phosphorylated transcripts was ligated to the synthesized RNA oligo Rp6. Ligated RNA was purified and reverse-transcribed using the DROAA primer, which contains sequencing barcode. Resulting cDNA was proceeded to PCR amplification using linker- (D6X) and DROAA-specific (B-PE-PCR20) primers. After 5 cycles, A-PE-PCR10 primer was added and continue 25 cycles to amplify PCR products.

treatment_protocol: L-arabinose at 0.2% (w/v) was used for overexpression of sehA.

tag: strain

value: sehA mutant

value: OH / arabinose


title: A549_BatchC_ethanol extract of Atractylodis Rhizoma (Medium dose)_rep1

description:
sample 9-1-5
RCM_tonifying_A549.txt


title: A1_RSV_M


title: sehA-mono-P-ara-negative

description: mono phosphate / no arabinose

value: mono phosphate / no arabinose


title: A549_BatchC_ethanol extract of Atractylodis Rhizoma (Low dose)_rep1

description:
sample 9-1-6
RCM_tonifying_A549.txt


title: sehA-OH-ara-negative

description: OH / no arabinose

value: OH / no arabinose


title: P5_INF_S

value: Primary nasal cells

value: Epithelial cells

value: INFLUENZA A (H3N2)


title: sehA-mono-P-ara-positive

description: mono phosphate / arabinose

value: mono phosphate / arabinose


title: batch1_S001

value: Female


title: A549_BatchC_ethanol extract of Poria Cocos (Low dose)_rep1

description:
sample 9-1-3
RCM_tonifying_A549.txt


title: PsaOmpR-2

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

library_source: genomic

data_processing:
ChIP-seq reads were mapped to the P. syringae 1448A genome (NC_005773.3), DC3000 (NC_004578.1), B728a (NC_007005.1) and C48 (NZ_CP032631.1) using Bowtie2 (version 2.3.4.3).
Binding peaks (q < 0.01) were identified using MACS2 software (version 2.1.0).
The enriched loci for each TF were annotated using the R package ChIPpeakAnno (version 3.18.2).
Assembly: P. syringae 1448A genome (NC_005773.3), DC3000 (NC_004578.1), B728a (NC_007005.1) and C48 (NZ_CP032631.1)
Supplementary files format and content: bigWig. narrow.Peak (except for input sample)

molecule: genomic DNA

organism: Pseudomonas syringae pv. actinidiae str. Shaanxi_M228

source_name: bacterial cell

growth_protocol: King' B media, with rifampicin at 50 μg/ml and spectinomycin at 50 μg/ml. Bateria were culture at 28℃ at 220 rpm.

extract_protocol:
Bacterial cultures were cross-linked with 1% formaldehyde for 10 min at 28°C and then the reaction was stopped by the addition of 125 mM glycine for 5 min. The centrifugated bacteria were washed twice with Tris Buffer (20 mM Tris-HCl [pH 7.5] and 150 mM NaCl) and washed again with IP Buffer (50 mM HEPES–KOH [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and mini-protease inhibitor cocktail).
The 150-250-bp DNA fragments were selected  for library construction. The libraries were sequenced using the HiSeq 2000 system (Illumina). Two biological replications have been performed for all ChIP-seq experiments.

treatment_protocol: Cutured to OD=0.6.

value: bacterial cell

value: WT

tag: chip antibody

value: HA


title: A549_BatchC_ethanol extract of Atractylodis Rhizoma (High dose)_rep1

description:
sample 9-1-4
RCM_tonifying_A549.txt

value: Atractylodis Rhizoma ethanol extract 500 μg/mL


title: A549_BatchC_ethanol extract of Poria Cocos (High dose)_rep1

description:
sample 9-1-1
RCM_tonifying_A549.txt


title: PsaOmpR-1


title: P5_INF_M

value: Nasal Epithelial Cells at Air-Liquid-Interface

value: MOCK


title: A549_BatchC_ethanol extract of Poria Cocos (Medium dose)_rep2

description:
sample 9-2-2
RCM_tonifying_A549.txt

value: Poria Cocos ethanol extract 100 μg/mL


title: A549_BatchC_water extract of Sibjeondaebo-tang (Low dose)_rep3

description:
sample 8-3-6
RCM_tonifying_A549.txt

value: Sibjeondaebo-tang water extract 20 μg/mL


title: P4_INF_S


title: A549_BatchC_water extract of Sibjeondaebo-tang (Medium dose)_rep3

description:
sample 8-3-5
RCM_tonifying_A549.txt

value: Sibjeondaebo-tang water extract 100 μg/mL


title: Psa-EV-6

description: no processed data file


title: A549_BatchC_water extract of Sibjeondaebo-tang (High dose)_rep3

description:
sample 8-3-4
RCM_tonifying_A549.txt

value: Sibjeondaebo-tang water extract 500 μg/mL


title: P4_INF_M


title: Psa-EV-5

description: no processed data file


title: A549_BatchC_water extract of Palmul-tang (Low dose)_rep3

description:
sample 8-3-3
RCM_tonifying_A549.txt

value: Palmul-tang water extract 20 μg/mL


title: A549_BatchC_ethanol extract of Poria Cocos (Medium dose)_rep1

description:
sample 9-1-2
RCM_tonifying_A549.txt


title: A549_BatchC_water extract of Palmul-tang (Medium dose)_rep3

description:
sample 8-3-2
RCM_tonifying_A549.txt

value: Palmul-tang water extract 100 μg/mL


title: A549_BatchC_water extract of Sibjeondaebo-tang (Low dose)_rep2

description:
sample 8-2-6
RCM_tonifying_A549.txt


title: P3_INF_S

value: Primary nasal cells


title: A549_BatchC_water extract of Palmul-tang (High dose)_rep3

description:
sample 8-3-1
RCM_tonifying_A549.txt

value: Palmul-tang water extract 500 μg/mL


title: P2_INF_S

value: Epithelial cells

value: INFLUENZA A (H3N2)


title: Psa-3122-2


title: A549_BatchC_water extract of Palmul-tang (Medium dose)_rep2

description:
sample 8-2-2
RCM_tonifying_A549.txt


title: P2_INF_M


title: A549_BatchC_water extract of Palmul-tang (Low dose)_rep2

description:
sample 8-2-3
RCM_tonifying_A549.txt


title: Psa-3122-1


title: A549_BatchC_water extract of Sibjeondaebo-tang (High dose)_rep2

description:
sample 8-2-4
RCM_tonifying_A549.txt


title: A549_BatchC_water extract of Sibjeondaebo-tang (Medium dose)_rep2

description:
sample 8-2-5
RCM_tonifying_A549.txt


title: P3_INF_M


title: A549_BatchC_water extract of Palmul-tang (High dose)_rep2

description:
sample 8-2-1
RCM_tonifying_A549.txt


title: Psa-4127-1


title: Psa-4127-2


title: A549_BatchC_water extract of Sibjeondaebo-tang (Low dose)_rep1

description:
sample 8-1-6
RCM_tonifying_A549.txt


title: P1_INF_S


title: Psa-0222-2


title: A549_BatchC_water extract of Sibjeondaebo-tang (Medium dose)_rep1

description:
sample 8-1-5
RCM_tonifying_A549.txt


title: P1_INF_M


title: A549_BatchC_water extract of Sibjeondaebo-tang (High dose)_rep1

description:
sample 8-1-4
RCM_tonifying_A549.txt


title: A549_BatchC_Vehicle(DMSO)_rep3

description:
sample C1-3-1
RCM_tonifying_A549.txt

value: 0.1% DMSO


title: Psa-0222-1

value: bacterial cell


title: A549_BatchC_Vehicle(DMSO)_rep2

description:
sample C1-2-1
RCM_tonifying_A549.txt


title: T5_INF_S

value: WT


title: Psa-2193-2

value: HA


title: T5_INF_M


title: A549_BatchB_water extract of Palmul-tang (Low dose)_rep1

description:
sample 8-1-3
RCM_tonifying_A549.txt


title: A549_BatchC_Vehicle(DMSO)_rep1

description:
sample C1-1-1
RCM_tonifying_A549.txt


title: Psa-2193-1


title: T4_INF_S


title: A549_BatchB_water extract of Samul-tang (Low dose)_rep3

description:
sample 7-3-6
RCM_tonifying_A549.txt

value: Samul-tang water extract 20 μg/mL


title: A549_BatchB_water extract of Palmul-tang (High dose)_rep1

description:
sample 8-1-1
RCM_tonifying_A549.txt


title: Psa-EV-3

description: no processed data file


title: Psa-EV-4

description: no processed data file


title: T4_INF_M

value: Nasal Epithelial Cells at Air-Liquid-Interface


title: A549_BatchB_water extract of Sagunja-tang (Low dose)_rep3

description:
sample 7-3-3
RCM_tonifying_A549.txt

value: Sagunja-tang water extract 20 μg/mL


title: A549_BatchB_water extract of Samul-tang (Medium dose)_rep3

description:
sample 7-3-5
RCM_tonifying_A549.txt

value: Samul-tang water extract 100 μg/mL


title: A549_BatchB_water extract of Sagunja-tang (Medium dose)_rep3

description:
sample 7-3-2
RCM_tonifying_A549.txt

value: Sagunja-tang water extract 100 μg/mL


title: A549_BatchB_water extract of Samul-tang (Low dose)_rep2

description:
sample 7-2-6
RCM_tonifying_A549.txt


title: T2_INF_S


title: T3_INF_M

value: MOCK


title: Psa-EV-1

description: no processed data file


title: A549_BatchB_water extract of Sagunja-tang (High dose)_rep3

description:
sample 7-3-1
RCM_tonifying_A549.txt

value: Sagunja-tang water extract 500 μg/mL


title: Psa-EV-2

description: no processed data file


title: A549_BatchB_water extract of Sagunja-tang (Low dose)_rep2

description:
sample 7-2-3
RCM_tonifying_A549.txt


title: A549_BatchB_water extract of Samul-tang (Medium dose)_rep2

description:
sample 7-2-5
RCM_tonifying_A549.txt


title: B728a-3122-2

organism: Pseudomonas syringae pv. syringae B728a


title: T2_INF_M


title: A549_BatchB_water extract of Samul-tang (High dose)_rep2

description:
sample 7-2-4
RCM_tonifying_A549.txt

value: Samul-tang water extract 500 μg/mL


title: A549_BatchB_water extract of Palmul-tang (Medium dose)_rep1

description:
sample 8-1-2
RCM_tonifying_A549.txt

value: Palmul-tang water extract 100 μg/mL


title: T1_INF_S

value: Primary nasal cells


title: A549_BatchB_water extract of Sagunja-tang (Medium dose)_rep2

description:
sample 7-2-2
RCM_tonifying_A549.txt


title: A549_BatchB_water extract of Samul-tang (High dose)_rep3

description:
sample 7-3-4
RCM_tonifying_A549.txt


title: T1_INF_M


title: A549_BatchB_water extract of Sagunja-tang (High dose)_rep2

description:
sample 7-2-1
RCM_tonifying_A549.txt


title: B728a-4127-2


title: A549_BatchB_water extract of Samul-tang (Low dose)_rep1

description:
sample 7-1-6
RCM_tonifying_A549.txt


title: A549_BatchB_water extract of Samul-tang (Medium dose)_rep1

description:
sample 7-1-5
RCM_tonifying_A549.txt


title: A5_INF_S


title: A549_BatchB_water extract of Samul-tang (High dose)_rep1

description:
sample 7-1-4
RCM_tonifying_A549.txt


title: A549_BatchB_water extract of Sagunja-tang (Medium dose)_rep1

description:
sample 7-1-2
RCM_tonifying_A549.txt


title: A549_BatchB_water extract of Sagunja-tang (Low dose)_rep1

description:
sample 7-1-3
RCM_tonifying_A549.txt


title: A5_INF_M


title: A4_INF_S


title: B728a-0222-2


title: B728a-4127-1


title: A549_BatchB_water extract of Sagunja-tang (High dose)_rep1

description:
sample 7-1-1
RCM_tonifying_A549.txt


title: A549_BatchB_water extract of Astragali Radix (Low dose)_rep3

description:
sample 6-3-6
RCM_tonifying_A549.txt

value: Astragali Radix water extract 20 μg/mL


title: A549_BatchB_water extract of Astragali Radix (High dose)_rep3

description:
sample 6-3-4
RCM_tonifying_A549.txt

value: Astragali Radix water extract 500 μg/mL


title: A549_BatchB_water extract of Astragali Radix (Medium dose)_rep3

description:
sample 6-3-5
RCM_tonifying_A549.txt

value: Astragali Radix water extract 100 μg/mL


title: B728a-0222-1


title: A4_INF_M

value: Epithelial cells


title: B728a-3122-1

value: bacterial cell


title: A549_BatchB_water extract of Cinnamomi Cortex (Medium dose)_rep3

description:
sample 6-3-2
RCM_tonifying_A549.txt

value: Cinnamomi Cortex water extract 100 μg/mL


title: B728a-2193-1

value: WT

value: HA


title: A549_BatchB_water extract of Cinnamomi Cortex (Low dose)_rep3

description:
sample 6-3-3
RCM_tonifying_A549.txt

value: Cinnamomi Cortex water extract 20 μg/mL


title: A3_INF_M

value: Nasal Epithelial Cells at Air-Liquid-Interface


title: A3_INF_S

value: INFLUENZA A (H3N2)


title: A549_BatchB_water extract of Cinnamomi Cortex (High dose)_rep3

description:
sample 6-3-1
RCM_tonifying_A549.txt

value: Cinnamomi Cortex water extract 500 μg/mL


title: B728a-OmpR-2


title: A549_BatchB_water extract of Astragali Radix (Low dose)_rep2

description:
sample 6-2-6
RCM_tonifying_A549.txt


title: A2_INF_S


title: A549_BatchB_water extract of Astragali Radix (Medium dose)_rep2

description:
sample 6-2-5
RCM_tonifying_A549.txt


title: A2_INF_M

value: MOCK


title: B728a-OmpR-1


title: 1370824

city: Rende

first: Rosamaria

last: Lappano

state: Cs

address: via P. Bucci

country: Italy

institute: University of Calabria

data_processing:
Reads preprocessing was performed by using fastp v0.20.0 applying specific parameters to remove residual adapter sequences and to keep only high-quality data (qualified_quality_phred=20, unqualified_percent_limit=30, average_qual=25, low_complexity_filter=True, complexity_threshold=30). The percentage of uniquely mapped reads resulted high with the mean value of 89% (mean value for sample: unmapped reads 6%, quality base >q30 90%). Then, passing filter reads were mapped to the genome reference (Homo sapiens) using STAR v2.7.0 with standard parameters, except for sjdbOverhang option set on read length. Genome and transcript annotations provided as input were downloaded from v105 of the Ensembl repository. Alignments were then elaborated by RSEM v1.3.3, to estimate transcript and gene abundances. Subsequently, the sample-specific gene-level abundances were merged into a single raw expression matrix by applying a dedicated RSEM command (rsem-generate-data-matrix). Genes with at least 10 counts in N samples were then selected, where N corresponds to the sample number in the smallest experimental group.
Assembly: Homo sapiens
Supplementary files format and content: tab-delimited includes raw counts for each sample

source_name: Prostate cancer-associated fibroblast

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen).
RNA integrity for library preparation was determined by analysis of extracted total RNA using a 2100 Bioanalyzer (Agilent Technologies) with RNA 6000 NanoChip. RNA concentrations were measured using Qubit RNA Assay Kit. Libraries were prepared from total RNA according to manufacturer instructions with Illumina Stranded mRNA Prep kit. Libraries quality was evaluated by size analysis on 2100 Bioanlyzer (Chip DNA HS) and concentrations were determined using Qubit DNA HS assay kit (Thermo Fisher Scientific).

value: Prostate cancer-associated fibroblast


title: 1370823


title: B728a-EV-4

description: no processed data file


title: 1370822


title: B728a-2193-2


title: A549_BatchB_water extract of Astragali Radix (High dose)_rep2

description:
sample 6-2-4
RCM_tonifying_A549.txt


title: B728a-EV-3

description: no processed data file


title: A549_BatchB_water extract of Cinnamomi Cortex (Medium dose)_rep2

description:
sample 6-2-2
RCM_tonifying_A549.txt


title: 1370819

source_name: Breast cancer-associated fibroblast

value: Breast cancer-associated fibroblast


title: A549_BatchB_water extract of Cinnamomi Cortex (High dose)_rep2

description:
sample 6-2-1
RCM_tonifying_A549.txt


title: B728a-EV-1

description: no processed data file


title: B728a-EV-2

description: no processed data file


title: 1370820


title: CD8+, CD45RA-, high salt 3

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

institute: Leibniz Institute for Natural Product Research and Infection Biology

data_processing:
Read mapping to reference genome with STAR (v2.6.1a).
Transcripts were quantified with salmon (v0.11.3) in the alignment-based mode.
Assembly: hg38 (GRCh38)
Supplementary files format and content: counts.csv: Comma-delimited text file including count values for each sample.
Supplementary files format and content: counts_rlog.csv: Comma-delimited text file including rlog normalized count values for each sample.

source_name: CD8+ CD45RA- T cells

growth_protocol: CD8+ memory T cells were isolated ex vivo and stimulated for 48 h with anti-CD3 and anti-CD28 mAbs.

extract_protocol:
Total RNA was extracted from cells lysed in TRI reagent (Sigma-Aldrich) according to the manufacturer’s protocol.
Library preparation for RNA-seq was performed using the TruSeq® Stranded Total RNA Sample Preparation Guide (Illumina).

treatment_protocol: Total culture time of 5 days in the presence of low and high NaCl concentrations.

value: CD8+ CD45RA- T cells

value: high salt

tag: treatment duration

value: 5 days


title: CD8+, CD45RA-, low salt 3

value: low salt


title: DC3000-OmpR-6

organism: Pseudomonas syringae pv. tomato str. DC3000


title: CD8+, CD45RA-, high salt 2


title: A549_BatchB_water extract of Astragali Radix (Low dose)_rep1

description:
sample 6-1-6
RCM_tonifying_A549.txt

value: Astragali Radix water extract 20 μg/mL


title: Fish 2, Ctrl

city: Valdeolmos

first: Pablo

last: Jiménez-Barrios

state: Madrid

address: Carretera de Algete a El Casar, Km 8

department: Animal Health Research Centre

country: Spain

institute: CISA-INIA (CSIC)

description: Chromium Single Cell 5’ Gene Expression

data_processing:
Assembly and count using cellranger-3.0.2. cellranter count --chemistry=fiveprime --r1-lenght=100 --r2-length=100 --expected-cells=1000
Genome_build: Customized reference transcriptome based in Oncorhynchus mykiss genome v1.0 (GCF_002163495.1)
Assembly: Omyk_1.0
Supplementary files format and content: Tab-separated value files and features, barcodes, and matrix

organism: Oncorhynchus mykiss

source_name: PBLs

extract_protocol:
Chromium Single Cell 5′ Gel Beads Kit (10x Genomics, CA, USA)
Chromium Single Cell 5’ Library Construction Kit (10x Genomics, CA, USA)

value: PBLs

value: untreated


title: DC3000-OmpR-5

value: bacterial cell


title: CD8+, CD45RA-, low salt 2


title: 1370821


title: Fish 1, IPNV

description: Chromium Single Cell 5’ Gene Expression

value: IPNV infected


title: A549_BatchB_water extract of Cinnamomi Cortex (Low dose)_rep2

first: Musun

address: 1672 Yuseong-daero, Yuseong-gu

institute: Korean Institute of Oriental Medicine

description:
sample 6-2-3
RCM_tonifying_A549.txt

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.


title: A549_BatchB_water extract of Astragali Radix (Medium dose)_rep1

description:
sample 6-1-5
RCM_tonifying_A549.txt

value: Astragali Radix water extract 100 μg/mL


title: A1_INF_S

value: Primary nasal cells

value: Epithelial cells

value: WT


title: DC3000-OmpR-4

value: HA


title: CD8+, CD45RA-, high salt 1


title: A1_INF_M

value: Nasal Epithelial Cells at Air-Liquid-Interface

value: MOCK


title: Fish 1, Ctrl

description: Chromium Single Cell 5’ Gene Expression


title: DC3000-OmpR-3


title: A549_BatchB_water extract of Cinnamomi Cortex (Low dose)_rep1

description:
sample 6-1-3
RCM_tonifying_A549.txt

value: Cinnamomi Cortex water extract 20 μg/mL


title: sehB-2

description: sehB replicate 2

data_processing:
The sequencing adapter removal and quality-based trimming for the raw data were performed using Trimmomatic v. 0.36.
Cleaned reads were mapped to the reference genome using bowtie2 with a default parameter.
For counting the reads mapped to each CDS (coding sequence), featureCounts was used.
Finally, the count from each CDS was normalized using DeSeq2 package.
Assembly: GCF_000022165.1
Supplementary files format and content: tab-limited file includes DeSeq2 normalized result between wild type and sehB mutant

extract_protocol:
Total RNA was isolated using RNeasy Kit (Qiagen), according to the manufacturer’s instructions.
For ribosomal RNA depletion, 5 μg of the total RNA was processed by Ribo-Zero rRNA Removal Kit (Bacteria). Sequencing libraries for RNA-Seq were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760S), following the manufacturer’s instructions.

value: sehB mutant


title: CD8+, CD45RA-, low salt 1

value: CD8+ CD45RA- T cells


title: Fish 2, IPNV

description: Chromium Single Cell 5’ Gene Expression


title: A549_BatchB_water extract of Cinnamomi Cortex (Medium dose)_rep1

description:
sample 6-1-2
RCM_tonifying_A549.txt

value: Cinnamomi Cortex water extract 100 μg/mL


title: DC3000-EV-6

description: no processed data file


title: sehB-1

description: sehB replicate 1


title: CD8Tm+NaCl 5' Gene expression

description: 10x Genomics

value: 3days TCR activation+3hr PMA/Iono+NaCl

value: female


title: CD8Tm 5' Gene expression

description: 10x Genomics

value: 3days TCR activation+3hr PMA/Iono


title: wild type-2

description: wild type replcate 2

value: wild type


title: DC3000-EV-5

description: no processed data file

value: bacterial cell


title: DC3000-3122-2


title: wild type-1

description: wild type replcate 1


title: DC3000-3122-1


title: A549_BatchB_water extract of  Rehmanniae Radix Preparata (Low dose)_rep3

description:
sample 5-3-6
RCM_tonifying_A549.txt

value: Rehmanniae Radix Preparata water extract 20 μg/mL


title: A549_BatchB_water extract of  Rehmanniae Radix Preparata (Medium dose)_rep3

description:
sample 5-3-5
RCM_tonifying_A549.txt

value: Rehmanniae Radix Preparata water extract 100 μg/mL


title: A549_BatchB_water extract of Astragali Radix (High dose)_rep1

description:
sample 6-1-4
RCM_tonifying_A549.txt

value: Astragali Radix water extract 500 μg/mL