title: thrb:tdTomato+ cells from 5-dpf larval eyes, samd7-/-, rep2

status: Public on Jun 21 2024

city: Saint Louis

first: Joseph

last: Corbo

state: MO

address: 660 S. Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

data_processing:
Sequencing adapters were trimmed using trimgalore 0.6.1 (https://github.com/FelixKrueger/TrimGalore)61. RNA-seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next, Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression, DESeq2 1.34.0 was used in R 4.1.3, using a log2 fold-change threshold of 0 and an FDR (p-adj) of 0.164. Volcano plots were then labeled to identify genes with p-adj < 0.05. To identify genes as photoreceptor subtype-specific, manual curation was performed using publicly available RNA-seq data from adult zebrafish photoreceptor subtypes4,5. To identify rod-specific-gene dysregulated in the samd7-/- adult retina (Table S3), we manually cross-referenced the top 40 most enriched rod-specific genes and mafba from Ogawa et al5.
Assembly: danRer10
Supplementary files format and content: csv file of DESeq2-normalized counts and averages from three samd7-/- and WT replicates, derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p-adj.

organism: Danio rerio

source_name: eye

extract_protocol:
To perform RNA-seq on 5-dpf thrb:tdTomato+ cells, the following crosses were performed: WT × WT;thrb:tdTomato+/- or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/-. A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40-50 eyes from 20-25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10,000-25,000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit (Qiagen); RNA was then extracted using the Rneasy Micro Kit (Qiagen), and on-column DNAse treatment performed using the Rnase-Free Dnase Set (Qiagen). RNA concentrations ranged from 40-190 pg/µl (0.3-1.8 ng total), with RNA integrity (RIN) scores ranging from 7.4-8.4.
Library preparation was performed with 10 ng of total RNA for 5-dpf whole eye and adult retina samples and with 300 pg of total RNA for 5-dpf thrb:tdTomato+ cells. Double-stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol using 12 amplification cycles for 5-dpf whole eye and adult retina samples, and 14 amplification cycles for 5-dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt-ended using a combination of T4 DNA Polymerase, Klenow Fragment DNA Polymerase, and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow (3'-5' exo-), and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase (Qiagen-Enzymatics). Ligated fragments were then amplified for 12 cycles for 5-dpf whole eye samples, and 15 cycles for adult retina and 5-dpf thrb:tdTomato+ cell samples using primers incorporating unique dual-index tags, using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq-6000 using 150 bp paired-end reads.

value: thrb:tdTomato+ cells

value: eye

tag: developmental stage

value: 5-dpf larvae


title: thrb:tdTomato+ cells from 5-dpf larval eyes, samd7-/-, rep1

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: cell type

tag: tissue

tag: genotype


title: thrb:tdTomato+ cells from 5-dpf larval eyes, samd7-/-, rep3


title: thrb:tdTomato+ cells from 5-dpf larval eyes, WT, rep3

value: WT


title: thrb:tdTomato+ cells from 5-dpf larval eyes, WT, rep2


title: Hypoxia replicate 3

status: Public on Jun 22 2024

city: Chicago

first: Dongbo

last: Yang

state: IL

address: 929 E 57th St

institute: University of Chicago

data_processing:
Sequencing: The libraries were sequenced by a NovaSeq 6000 sequencer to generate paired-end 100bp reads.
Quality and adapter trimming were performed on the raw sequencing reads using Trim Galore! 0.6.3.
RNA-seq: reads were mapped to the human genome (UCSC hg19 with GENCODE annotation) using RNA STAR 2.7.5b. ChIP-seq: IP and input reads for each sample were mapped to the human genome (UCSC hg19 with GENCODE annotation) using BWA-MEM 0.7.17.1 and the mapped reads were converted to SAM files using samtools 1.2.
RNA-seq: mapped reads from each sample were counted by featureCounts 1.6.4 for per-gene read counts. ChIP-seq: peak calling was performed by Homer 4.11.1 using the IP and input SAM files for each sample (settings for peak calling were included in the submitted peak files).
Assembly: Human (hg19)
Supplementary files format and content: RNA-seq: a tab delimited text file containing a matrix table with raw gene counts for every gene and every sample. ChIP-seq: a peak text files for each sample.

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in 10% FBS DMEM media and 1% penicillin/streptomycin in 5% CO2.

extract_protocol:
Total RNA was extracted from cell culture samples using the RNeasy Plus Mini Kit (Qiagen).
RNA-seq and ChIP-seq libraries were prepared for sequencing by the University of Chicago Genomics Facility following standard protocols.

tag: treatment

value: Vehicle, 1percent oxygen


title: thrb:tdTomato+ cells from 5-dpf larval eyes, WT, rep1


title: Adult retina, WT, rep3

data_processing:
Sequencing adapters were trimmed using trimgalore 0.6.1 (https://github.com/FelixKrueger/TrimGalore)61. RNA-seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next, Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression, DESeq2 1.34.0 was used in R 4.1.3, using a log2 fold-change threshold of 0 and an FDR (p-adj) of 0.164. Volcano plots were then labeled to identify genes with p-adj < 0.05. To identify genes as photoreceptor subtype-specific, manual curation was performed using publicly available RNA-seq data from adult zebrafish photoreceptor subtypes4,5. To identify rod-specific-gene dysregulated in the samd7-/- adult retina (Table S3), we manually cross-referenced the top 40 most enriched rod-specific genes and mafba from Ogawa et al5.
Assembly: danRer10
Supplementary files format and content: csv file of DESeq2-normalized counts and averages from three samd7-/- and WT replicates, derived from adult retina. Genes are ranked by p-adj.

source_name: retina

extract_protocol:
To perform RNA-seq on 3 month-old adult retinas, samd7stl888/+ heterozygotes were intercrossed to produce mixed genotype offspring and grown to adulthood. After adults were genotyped, pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate, and RNA was extracted using the RNEasy Mini Kit (Qiagen) with on-column DNAse treatment using the Rnase-Free Dnase Set (Qiagen). RNA concentrations ranged from 20-37 ng/µl (600-1100 ng total), with RIN scores ranging from 9-9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.
Library preparation was performed with 10 ng of total RNA for 5-dpf whole eye and adult retina samples and with 300 pg of total RNA for 5-dpf thrb:tdTomato+ cells. Double-stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol using 12 amplification cycles for 5-dpf whole eye and adult retina samples, and 14 amplification cycles for 5-dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt-ended using a combination of T4 DNA Polymerase, Klenow Fragment DNA Polymerase, and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow (3'-5' exo-), and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase (Qiagen-Enzymatics). Ligated fragments were then amplified for 12 cycles for 5-dpf whole eye samples, and 15 cycles for adult retina and 5-dpf thrb:tdTomato+ cell samples using primers incorporating unique dual-index tags, using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq-6000 using 150 bp paired-end reads.

value: retina

value: adult


title: Adult retina, WT, rep2


title: Adult retina, samd7-/-, rep1


title: Adult retina, samd7-/-, rep2


title: Adult retina, WT, rep1


title: 5-dpf larval eyes, samd7-/-, rep3

data_processing:
Sequencing adapters were trimmed using trimgalore 0.6.1 (https://github.com/FelixKrueger/TrimGalore)61. RNA-seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next, Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression, DESeq2 1.34.0 was used in R 4.1.3, using a log2 fold-change threshold of 0 and an FDR (p-adj) of 0.164. Volcano plots were then labeled to identify genes with p-adj < 0.05. To identify genes as photoreceptor subtype-specific, manual curation was performed using publicly available RNA-seq data from adult zebrafish photoreceptor subtypes4,5. To identify rod-specific-gene dysregulated in the samd7-/- adult retina (Table S3), we manually cross-referenced the top 40 most enriched rod-specific genes and mafba from Ogawa et al5.
Assembly: danRer10
Supplementary files format and content: csv file of DESeq2-normalized counts and averages from three samd7-/- and WT replicates, derived from 5dpf larval eyes. Genes are ranked by p-adj.

extract_protocol:
To perform RNA-seq on 5-dpf larvae, samd7stl888/+ heterozygotes were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine, anterior halves of the body were collected in RNAlater (Invitrogen) and stored at 4°C, and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed, eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA-extracted using the RNeasy Micro Kit (Qiagen), then DNAse-treated and repurified using the Rneasy MinElute Cleanup Kit (Qiagen). RNA concentrations ranged from 1.5-2.2 ng/µl (~20 ng RNA total), with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.
Library preparation was performed with 10 ng of total RNA for 5-dpf whole eye and adult retina samples and with 300 pg of total RNA for 5-dpf thrb:tdTomato+ cells. Double-stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol using 12 amplification cycles for 5-dpf whole eye and adult retina samples, and 14 amplification cycles for 5-dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt-ended using a combination of T4 DNA Polymerase, Klenow Fragment DNA Polymerase, and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow (3'-5' exo-), and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase (Qiagen-Enzymatics). Ligated fragments were then amplified for 12 cycles for 5-dpf whole eye samples, and 15 cycles for adult retina and 5-dpf thrb:tdTomato+ cell samples using primers incorporating unique dual-index tags, using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq-6000 using 150 bp paired-end reads.


title: 5-dpf larval eyes, samd7-/-, rep2


title: 5-dpf larval eyes, samd7-/-, rep1


title: 5-dpf larval eyes, WT, rep2


title: 5-dpf larval eyes, WT, rep3


title: 5-dpf larval eyes, WT, rep1


title: SIC_264_1047_1_heart

city: Charlestown

first: Neal

middle: Patrick

last: Smith

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was pre-processed with CellRanger (v3.0.2, 10x Genomics) to demultiplex FASTQ reads, align reads to the human reference genome (GRCh38, v3.0.0 from 10x Genomics), and count unique molecular identifiers (UMI) to produce a cell x gene count matrix
Assembly: GRCh38
Supplementary files format and content: combined_tissue_data.h5ad includes the counts for all cells that passed QC in .h5 format
Supplementary files format and content: combined_pbmc_data.h5ad includes the counts for all demultiplexed cells that passed QC in .h5 format
Supplementary files format and content: raw_feature_bc_matrix.h5 files includes the UMI counts for all droplets for each sample in .h5 format
Supplementary files format and content: all_contig_annotations_tcr.csv files include the TCR data for the associated samples
Supplementary files format and content: fbc.csv files contains data for featured barcodes for applicable samples (all PBMC samples)
Supplementary files format and content: hashing_info.csv includes information about which samples correspond to which fbc hashtags in the PBMC samples
Supplementary files format and content: cite_info.csv includes information about the antibodies included in the FBC pool

molecule: polyA RNA

source_name: Heart tissue

extract_protocol:
Tissue samples obtained by biopsy or autopsy were immediately placed in ice-cold HypoThermosol solution (BioLife Solutions, Bothell, WA) and kept on ice during transfer to the research facility. Tissue was then washed twice with cold phosphate buffered saline. Tissue was then dissociated using the human tumor dissociation kit according to the manufacturer’s instructions (Miltenyi Biotic, Bergisch Gladbach, Germany) with modification such that calcium chloride was added to the enzymatic cocktail to a final concentration of 1.25 mM. Tubes containing tissue fragments in the enzymatic cocktail were placed in a heated shaker at 37° C with shaking at 750 RPM for 25 minutes with the machine placed on its side to prevent tissue fragments from settling. Following incubation, the reaction was quenched through the addition of 100 µl human serum. The mixture was further dissociated through manual trituration followed by filtration through 70 µm mesh. Following centrifugation at 350 x g for 12 minutes, the supernatant was removed and RBC lysis was performed (ACK lysing buffer, Lonza, Basel, Switzerland). Following a wash step, cells were resuspended in phenol-free RPMI with 2% (v/v) human AB serum.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart tissue

tag: age

tag: Sex

value: male

tag: group

value: irMyocarditis


title: Sarcoma708

city: New York

first: Karan

last: Luthria

state: New York

address: 650 W 168th Street

department: Medicine

institute: Columbia University Vagelos College of Physicians and Surgeons

description: Single-nuclei RNA sequencing

data_processing:
Raw snRNA-seq data were analyzed using Cell Ranger (v6.1.2). Transcripts were aligned to the human GRCh38 reference genome.
Ambient RNA was removed using CellBender (v0.2.0). Gene expression matrices were processed individually in R (v4.1.2) using Seurat (v4.1.1).
Filters were applied to keep cells with 300-7,500 genes, 600 - 40,000  UMIs, and <10% of mitochondrial reads in each individual sample.
Scrublet v0.2.1 (Wolock et al., 2019) was applied to identify and remove doublets with an expected doublet rate ranging from 11% based on the loading rate.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix

source_name: Sarcoma

extract_protocol:
Single-nuclei suspension from frozen sarcoma metastases were generated using methods published in Slyper et al. (Nature Medicine, 2020) with modifications. The tissue was first cut in 20 µm sections using a cryostat and stored on dry ice until the next step. Then the tissue was put on wet ice and washed once with 5 ml PBS to remove OCT. After this step nuclei were extracted by vigorous pipetting in salt-tris buffer with Tween-20 (TST) followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 15,000 nuclei were separated for droplet-based RNA capture and reverse transcription using 10x Genomics 5' v1.1 or 5' V2.0  reagents and a Chromium controller.
Single-nuclei RNAseq (snRNA-seq) libraries were generated using Chromium 5' (V1.1 and V2) reagents according to the manufacturer protocol with one additional cycle during library amplification to account for lower material input from nuclei compared to whole cells.
Other: single nuclei RNAseq

tag: metastatic site

value: Undifferentiated Polymorphic Sarcoma (UPS)

tag: patient id

tag: stk11 mutation

value: Pre IO

tag: kras mutation status

tag: sequencing technique

value: snRNA-seq

tag: tcr-seq

value: yes


title: SarcomaS408

description: Single-nuclei RNA sequencing

value: Post tx

value: no


title: SarcomaS410

description: Single-nuclei RNA sequencing

value: Intimal Sarcomas (INS) of the Pulmonary Artery

value: X

value: Post IO

value: Intimal Sarcomas (INS)


title: SarcomaS914

description: Single-nuclei RNA sequencing

value: Y


title: Sarcoma167

description: Single-nuclei RNA sequencing


title: Sarcoma322

description: Single-nuclei RNA sequencing


title: SarcomaS914_S120_L002

description: Single-nuclei RNA sequencing

data_processing:
Fastq files were analyzed using vdj in Cell Ranger (v6.1.2, 10x Genomics). Transcripts were aligned to the human GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger vdj output files (csv)
Library strategy: single-cell RNAseq (TCR-seq)

extract_protocol:
Single-nuclei suspension from frozen sarcoma metastases were generated using methods published in Slyper et al. (Nature Medicine, 2020) with modifications. The tissue was first cut in 20 µm sections using a cryostat and stored on dry ice until the next step. Then the tissue was put on wet ice and washed once with 5 ml PBS to remove OCT. After this step nuclei were extracted by vigorous pipetting in salt-tris buffer with Tween-20 (TST) followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 15,000 nuclei were separated for droplet-based RNA capture and reverse transcription using 10x Genomics 5' v1.1 or 5' v2.0 reagents and a Chromium controller.
Chromium Single Cell V(D)J Enrichment Kit for human T cells Reagent Kit, v 1.1 or Single Cell Human TCR Amplification Kit were utilized for snTCR library generation (10X genomics) depending on whether 5' V1 or 5' V2 kits were utilized for cDNA library generation, respectively. Final sequencing libraries were prepared using Single Index Kit T Set A or Library construction kit (catalog no. 1000190) and Dual Index Kit TT set A (catalog no. 1000215).

tag: stk11 mutation status


title: lp-WGS SarcomaS914_S120_L002

description: low pass whole genome sequencing

library_source: genomic

data_processing:
fastq to sam conversion using bowtie2 v2.4.5
sam to bam conversion using samtools v1.16.1
bam to wig conversion using readCounter (hmmcopy_utils)
wig to seg file conversion using ichorCNA v0.2.0
Assembly: hg38
Supplementary files format and content: segementation file for CNA

molecule: genomic DNA

extract_protocol:
Nuclei from snRNA-seq sample preparations were collected by centrifugation (500g, 5 min), snap frozen after removing excess ST buffer, and stored at -20C until further processing. If insufficient nuclei (<100,000) were present, additional tissue curls were cut and processed in the same manner as for single-nuclei extraction. Genomic DNA was extracted from nuclei using DNeasy Blood and Tissue kit (Qiagen, catalog no.69504) according to manufacturer's instructions. DNA was quantified using a Nanodrop.
20-50 ng of genomic DNA was utilized for input for library prepation with Lotus DNA Library Prep Kit (Integrated DNA Technologies- IDT, Corlville, IA) using xGEN Stubby Adapter and UDI Primer pairs according to manufacturer's instructions with the folllowing specifications. During the enzymatic preparation program, sampless were held at 32C for 9 minutees. Adapters were not diluted, and the optional PCR (5 cycles) and cleanup were performed. After library cleanup with AMPure beads (Beckman Coulter, Brea, CA), libraries were quantified with Tapestation D5000 HS tapes (Agilent) and stored at -20C until sequencing
low pass whole genome sequencing

tag: pre/post io

tag: tumor pathology

value: lp-WGS


title: lp-WGS SarcomaS956_S119_L002

description: low pass whole genome sequencing


title: Sarcoma322_S133_L001

description: Single-nuclei RNA sequencing


title: lp-WGS SarcomaS410_S123_L002

description: low pass whole genome sequencing


title: Adult retina, samd7-/-, rep3

value: retina

tag: developmental stage


title: Sarcoma167_S130_L001

description: Single-nuclei RNA sequencing


title: Sarcoma708_S131_L001

description: Single-nuclei RNA sequencing


title: lp-WGS SarcomaS408_S121_L002

description: low pass whole genome sequencing


title: lp-WGS Sarcoma708_S131_L001

description: low pass whole genome sequencing


title: lp-WGS Sarcoma167_S130_L001

description: low pass whole genome sequencing


title: SarcomaS956

description: Single-nuclei RNA sequencing


title: Control_3

city: Xi'an

first: Li juan

last: Sun

address: 229 Taibai North Road, Xi'an

country: China

institute: Northwest University

data_processing:
cutadapt-1.9 (cutadapt.readthedocs.io/en/stable/)was used to remove the reads that contained adapter contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC v0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used hisat2-2.0.4 (ccb.jhu.edu/software/hisat2/)to map reads to the genome, Ensembl v96 (command line: hisat2 -1 R1.fastq.gz -2 R2.fastq.gz -S mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: ensembl.org/pub/release-101/fasta/mus_musculus/dna/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: control

growth_protocol: All the mice were housed in a temperature (22℃)-controlled environment.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were divided into control group that were subjected once daily at 9 am to gastric instillation with 1ml water of room temperature (20-25℃)and cold water group that were subjected once daily at 8 am to gastric instillation with 1ml water of low temperature (0-4℃), for 14 consecutive days.

tag: cell type

value: Proximal jejunum tissue

value: control


title: lp-WGS Sarcoma322_S133_L001

description: low pass whole genome sequencing


title: Control_2


title: Control_1


title: cold_water_3

source_name: intestinal function disorder model induced by cold water in mice

value: cold water


title: Sarcoma559

description: Single-nuclei RNA sequencing


title: cold_water_2


title: cold_water_1


title: Quadriceps muscle, MKO03

city: Shanghai

first: Xuelian

last: Xiong

address: NO. 180, Fenglin Road

department: Zhongshan Hospital, Fudan University

institute: Department of Endocrinology and Metabolism

description: Total RNAs were extracted from powdered quadriceps muscles using Eastep Super Total RNA Extraction Kit (Promega, LS1040) following the manufacturer’s instructions.RNA libraries were prepared for sequencing using standard Illumina protocols.

data_processing:
Quality controlled was done by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA
Fold change and p-value were calculated based on FPKM
Genome_build: MM10
Supplementary_files_format_and_content: Excel file includes read counts for each sample

source_name: quadriceps muscle

extract_protocol:
Total RNAs were extracted from powdered quadriceps muscles using Eastep Super Total RNA Extraction Kit (Promega, LS1040) following the manufacturer’s instructions.Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

treatment_protocol: Mouse quadriceps muscles were harvested and immediately frozen into liquid nitrogen

value: MCK-Cre+/-, Fbxw7 flox/flox

tag: tissue

value: quadriceps muscle


title: Quadriceps muscle, MKO02

tag: genotype


title: Quadriceps muscle, COM03

value: Fbxw7 flox/flox


title: Quadriceps muscle, MKO01


title: Quadriceps muscle, COM01


title: Sarcoma559_S132_L001

description: Single-nuclei RNA sequencing

value: Pre IO

value: snRNA-seq


title: Quadriceps muscle, COM02


title: LPL9_Post_TCR

city: Duarte

first: Szymon

last: Szymura

state: CA

address: 1500 E Duarte Rd

department: Toni Stephenson Lymphoma Center

institute: City of Hope

data_processing:
The alignments, demultiplexing, barcode processing and gene counting was performed using CellRanger software version 3.1.0
Processing of sequencing data from V(D)J libraries was performed using CellRanger 3.1.0 vdj pipeline
Supplementary files format and content: Based on 10x Genomics support page provided fasta files contain assembled contig sequences from barcodes that passed their algorithm's filtering steps  https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-5p-outputs-fastq-vdj. CellRanger vdj pipeline provides amino acid and nucleotide sequences for framework and complementarity determining regions (CDRs). CSV files provide high-level annotations with one contig, consensus, or clonotype per row. https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-5p-outputs-annotations-vdj
Assembly: hg19

source_name: bone marrow

extract_protocol:
Snap frozen bone marrow samples were thawed in culture media, washed with wash buffer and loaded onto 10x Genomics Chromium Chip
Library preparation for gene expression was performed using 5' 10x Genomics Kit according to manufacturer's protocol

value: bone marrow

tag: cell line

value: primary cells

value: bone marrow cells

tag: individual

tag: treatment

value: Post


title: LPL5_Pre_TCR

value: Pre


title: LPL4_Pre_TCR


title: LPL8_PrePost_TCR

value: PrePost


title: LPL7_Post_TCR


title: LPL6_Post_TCR


title: LPL5_Post_TCR


title: LPL9_Pre_TCR


title: LPL3_Pre_TCR


title: lp-WGS Sarcoma559_S132_L001

description: low pass whole genome sequencing

value: Intimal Sarcomas (INS) of the Pulmonary Artery

value: Intimal Sarcomas (INS)

value: yes


title: LPL3_Post_TCR


title: LPL2_Pre_TCR


title: LPL2_Post_TCR


title: LPL1_Pre_TCR


title: LPL9_Pre_BCR


title: LPL1_Post_TCR


title: LPL9_Post_BCR


title: LPL8_PrePost_BCR


title: LPL7_Pre_BCR


title: LPL6_Post_BCR


title: LPL7_Post_BCR


title: LPL5_Post_BCR


title: LPL5_Pre_BCR


title: LPL3_Pre_BCR


title: LPL4_Pre_BCR


title: LPL4_Post_BCR


title: LPL7_Pre_TCR


title: LPL3_Post_BCR


title: LPL4_Post_TCR


title: LPL1_Pre_BCR


title: MDA-MB-436-20RB cells, LLY283_2

city: Hangzhou

first: Sheyu

last: Zhang

address: Dongfang Road 150

institute: Hangzhou Institute of Medicine Chinese Academy of Sciences

description:
counts_cell _line.csv
Q9-_MDAMB436-20B-1uM_LLY283-Rep1_S9

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.

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: TNBC


title: LPL2_Post_BCR


title: MDA-MB-436-20RB cells, DMSO_2

description:
counts_cell _line.csv
Q7-_MDAMB436-20B-DMSO-Rep1_S7

value: DMSO


title: MDA-MB-436-20RA cells, LLY283_2

description:
counts_cell _line.csv
Q6-_MDAMB436-20A-1uM_LLY283-Rep1_S6


title: MDA-MB-436-20RA cells, DMSO_2

description:
counts_cell _line.csv
Q4-_MDAMB436-20A-DMSO-Rep1_S29


title: Hs 579T-20RA cells, LLY283_1

description:
counts_cell _line.csv
Q30-_Hs578T-20A-1uM_LLY283-Rep1_S30

source_name: Hs 579T

value: Hs 579T


title: MDA-MB-436-20RC cells,GSK591_2

description:
counts_cell _line.csv
Q23-_MDAMB436-20C-1uM_GSK591-Rep2_S23


title: MDA-MB-436 cells, LLY283_2

description:
counts_cell _line.csv
Q3-_MDAMB436-Par-1uM_LLY283-Rep1_S3


title: MDA-MB-436-20RC cells, DMSO_2

description:
counts_cell _line.csv
Q22-_MDAMB436-20C-DMSO-Rep2_S22


title: MDA-MB-436-20RC cells, LLY283_2

description:
counts_cell _line.csv
Q24-_MDAMB436-20C-1uM_LLY283-Rep2_S24


title: Hs 578T-20RA cells, DMSO_1

description:
counts_cell _line.csv
Q28-_Hs578T-20A-DMSO-Rep1_S28

source_name: Hs 578T

value: Hs 578T


title: MDA-MB-436-20RB cells, LLY283_1

description:
counts_cell _line.csv
Q21-_MDAMB436-20B-1uM_LLY283-Rep2_S21


title: MDA-MB-436-20RA cells,GSK591_1

description:
counts_cell _line.csv
Q17-_MDAMB436-20A-1uM_GSK591-Rep2_S17


title: MDA-MB-436-20RA cells, LLY283_1

description:
counts_cell _line.csv
Q18-_MDAMB436-20A-1uM_LLY283-Rep2_S18


title: MDA-MB-436-20RB cells, DMSO_1

description:
counts_cell _line.csv
Q19-_MDAMB436-20B-DMSO-Rep2_S19


title: MDA-MB-436 cells, GSK591_2

description:
counts_cell _line.csv
Q2-_MDAMB436-Par-1uM_GSK591-Rep1_S2


title: LPL2_Pre_BCR


title: MDA-MB-436 cells, LLY283_1

description:
counts_cell _line.csv
Q15-_MDAMB436-Par-1uM_LLY283-Rep2_S15


title: MDA-MB-436-20RA cells, DMSO_1

description:
counts_cell _line.csv
Q16-_MDAMB436-20A-DMSO-Rep2_S16


title: MDA-MB-436 cells, DMSO_2

description:
counts_cell _line.csv
Q13-_MDAMB436-Par-DMSO-Rep2_S13


title: LPL1_Post_BCR


title: MDA-MB-436-20RB cells,GSK591_2

description:
counts_cell _line.csv
Q8-_MDAMB436-20B-1uM_GSK591-Rep1_S8


title: MDA-MB-436-20RC cells, DMSO_1

description:
counts_cell _line.csv
Q10-_MDAMB436-20C-DMSO-Rep1_S10


title: MDA-MB-436 cells, DMSO_1

description:
counts_cell _line.csv
Q1-_MDAMB436-Par-DMSO-Rep1_S1


title: MDA-MB-436-20RA cells,GSK591_2

description:
counts_cell _line.csv
Q5-_MDAMB436-20A-1uM_GSK591-Rep1_S5


title: MDA-MB-436-20RC cells,GSK591_1

description:
counts_cell _line.csv
Q11-_MDAMB436-20C-1uM_GSK591-Rep1_S30


title: plasmid library B, replicate 2

city: Houston

first: Jielin

last: Liu

state: TX

address: 7455 Fannin St

department: Genitourinary Medical Oncology

institute: MD Anderson Cancer Center

description:
pDB2
plasmid_and_cell_pool_counts.csv

library_source: other

data_processing:
Fastq files were aligned to custom index to generate count files using the makeCounts function in the casTLE software.
Counts from the plasmid library were bind column-wise.
Counts from tumor samples were first normalized to sequencing depth, mean counts for each condition were then calculated and reported.
Assembly: A custom bowtie index was generated for each sub library using the makeIndices function in the casTLE software.
Supplementary files format and content: raw counts
Supplementary files format and content: mean counts
Library strategy: Amplicon-seq

molecule: other

organism: synthetic construct

source_name: plasmid

extract_protocol:
plasmid DNA was extracted using Midiprep kit (QIAGEN); DNA from cell pools and tumors were extracted using Quick-DNA Midiprep Plus kit (ZYMO Research).
Library was generated by two rounds of PCR to amplify DNA fragments containing sgRNA sequences.

value: plasmid


title: plasmid library B, replicate 1

description:
pDB1
plasmid_and_cell_pool_counts.csv


title: plasmid library A, replicate 2

description:
pDA2
plasmid_and_cell_pool_counts.csv


title: plasmid library A, replicate 1

description:
pDA1
plasmid_and_cell_pool_counts.csv


title: MDA-MB-436-20RB cells,GSK591_1

description:
counts_cell _line.csv
Q20-_MDAMB436-20B-1uM_GSK591-Rep2_S20


title: syn_OA

city: Fort Collins

first: Dylan

middle: T

last: Ammons

state: CO

address: 200 W Lake St

department: Clinical Sciences

institute: Colorado State University

description:
10x Genomics
syn_oa_1

data_processing:
The demultiplexing, barcode processing, and gene counting was completed using Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: Equus_caballus.EquCab3.0.107
Supplementary files format and content: Tab-separated values files and matrix files

organism: Equus caballus

source_name: Synovial tissue

extract_protocol:
Synovial fluid (5 to 10 mL) was sampled from the affected middle carpal joint (osteoarthritic sample) and tibiotarsal joint (normal sample). Synoviocenteses to obtain synovial fluid were performed implementing aseptic technique using sterile gloves, needles (20 gauge, 1.5 inches), and syringes (23). Synovial fluid samples were washed with PBS, filtered through a 40 µM cell strainer, then red blood cells were removed using Ammonium-Chloride-Potassium (ACK) lysis buffer. Red blood cell depleted suspensions were subsequently resuspended in PBS with 0.04% molecular grade BSA (Sigma-Aldrich; St. Louis, MO).  Synovium was obtained immediately following euthanasia.  Briefly, the horse was euthanized with pentobarbital (1 mL / 5 kg body weight) administered via indwelling catheter, then the middle carpal and tibiotarsal joints were dissected aseptically and synovium was sampled from four quadrants of each joint (dorsomedial, dorsolateral, palmar- or plantaromedial, palmar- or plantarolateral) and pooled for analysis. Synovial tissue samples were then disaggregated into single cell suspensions. Briefly, synovial tissue fragments were separated mechanically and enzymatically into digestion buffer (Liberase TL (Sigma-Aldrich) 100 µg/mL and DNAase I (New England Biolabs) 100 µg/mL in RPMI) in a 37°C water bath for 30 minutes. Digested suspensions were washed with PBS then resuspended in PBS with 0.04% non-acetylated BSA (Sigma-Aldrich). To remove small debris and platelets, a final wash at 100 rcf for 15 minutes was completed. The samples were then prepared to be run on a Chomium iX instument by resusspending in 0.04% molecular grade BSA. The instrument was loaded to target 5,000 cells per sample.
Library construction was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ Kit v3.1 protocol, 10x Genomics). Briefly, a Chromium iX instrument was used to pass cells and oligonucleotide coated gel beads at a limiting dilution to obtain a coupling of cells and beads in a 1:1 ratio. The cell-bead pair was then passed from an aqueous phase to an oil phase to form an emulsion. Within the emulsions, cells were lysed, and the oligonucleotide sequences on the gel beads pull down message RNA and other RNA molecules that have long adenosine stretches with an oligo-d(T) pull down. After hybridization, reverse transcription is completed to generate a cDNA library with each transcript now associated with a unique cell barcode and an Illumina R1 primer sequence.  Once cells were barcoded and unique molecular identifiers (UMIs) added, a standard Illumina library preparation kit was completed with SPRIselect used for fragment size selection. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Synovial tissue

tag: tissue source

value: OA affected joint

tag: animal id

value: horse 2

value: Wt


title: sf_OA3

description:
10x Genomics
sf_oa_3

source_name: Synovial fluid

value: Synovial fluid

value: horse 3


title: sf_N3

description:
10x Genomics
sf_normal_3

value: unaffected normal joint

value: horse 4


title: sf_OA1

description:
10x Genomics
sf_oa_1

value: horse 1


title: sf_OA2

description:
10x Genomics
sf_oa_2


title: sf_N2

description:
10x Genomics
sf_normal_2


title: MDA-MB-436-20RC cells, LLY283_1

description:
counts_cell _line.csv
Q12-_MDAMB436-20C-1uM_LLY283-Rep1_S31


title: recombinant CDV-infected ferret organ homogenate (passage 1)

city: Rochester

first: Christian

middle: Karl

last: Pfaller

state: MN

address: 200 First Street SW

department: Molecular Medicine

institute: Mayo Clinic

data_processing:
Assembly: GCA_000215625.1
Adapter sequences were removed from raw fastq files using SeqPurge v0.1-1000-gb4d1b1c. Quality trimming was disabled (-qcut 0 -ncut 0) and adapter recognition sequences (read 1: GATCG GAAGA GCACA CGTCT GAACT CCAGT CACNN NNNNA TCTCG TATGC CGTCT TCTGC TTG; read2: AGATC GGAAG AGCGT CGTGT AGGGA AAGAG TGTAG ATCTC GGTGG TCGCC GTATC ATT) were provided.
Quality trimming and filtering was performed using Atropos version 1.1.17 with minimum base quality cutoffs of 30 at both sides of the read (-q 30,30) and discarding reads with Ns and a length below 30 bp after trimming (-max-n 0 -m 30).
Mapping was performed with BWA mem v 0.7.12-r1039 using default parameters unless stated otherwise. Host sequences in ferret- and cell culture-derived samples were removed by mapping quality-controlled reads against either the ferret (Mustela putorius furo) or the African green monkey genome (Chlorocebus sabeus), respectively, specifying the minimum seed length (-k 31). Unmapped reads were extracted using samtools v1.7, and bamToFastq v2.17.0, and subsequently mapped to the CDV reference genome.
Host-free alignments were deduplicated using picard-tools MarkDuplicates (http://broadinstitute.github.io/picard) and left aligned using GATK LeftAlignIndels v4.0.
Assembly: CDV5804_NGS_ref.fasta
Supplementary files format and content: base count tables (wig format) of bam alignments to CDV5804_NGS_ref.fasta reference sequence

organism:
Mustela putorius furo
canine distemper virus

source_name: lymph node / spleen / lung homogenate

growth_protocol: ferrets were intranasally infected with recombinant P0 CDV and euthanized 7 days post infection. Organ homogenates were generated from lymph nodes, spleen, and lung. RNA was extracted from mixed homogenates.

extract_protocol:
RNA was isolated from cell-associated infectious virus released from infected cells by freeze-thawing. 100 µl virus stock aliquots were processed with Trizol reagent using the Zymo Direct-zol RNA kit (Zymo Research Europe GmbH, Freiburg, Germany). To extract RNA from tissues, 100 mg pieces were homogenized in 350 µl RLT buffer and processed according to the instructions of the RNeasy Mini kit manual (Qiagen, Hilden, Germany).
500 µg of purified RNA were processed with the Illumina TrueSeq StrandedTotal RNA kit (Illumina, San Diego, USA), including depletion of ribosomal RNA via Ribo-Zero Gold rRNA Removal kit (Illumina, San Diego, USA) following the manufacturer’s protocols. Libraries generated with single indexed adapters were then validated and sequenced as 2x150 base pairs paired-end reads.

value: lymph node / spleen / lung homogenate

value: recombinant CDV r5804

value: passage 1


title: MDA-MB-436 cells, GSK591_1

description:
counts_cell _line.csv
Q14-_MDAMB436-Par-1uM_GSK591-Rep2_S14

value: TNBC


title: recombinant CDV-infected ferret organ homogenate (passage 2)

growth_protocol: ferrets were intranasally infected with recombinant P1 CDV and euthanized 7 days post infection. Organ homogenates were generated from lymph nodes, spleen, and lung. RNA was extracted from mixed homogenates.

value: passage 2


title: CDV-infected ferret organ homogenate (passage 2)

growth_protocol: ferrets were intranasally infected with P1 CDV and euthanized 7 days post infection. Organ homogenates were generated from lymph nodes, spleen, and lung. RNA was extracted from mixed homogenates.

value: tissue culture-adapted CDV isolate 5804


title: PSPPH-2872-1

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

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)

organism: Pseudomonas savastanoi pv. phaseolicola 1448A

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: PSPPH-1136-1


title: PSPPH-2859-2


title: PSPPH-1136-2


title: PSPPH-2859-1


title: PSPPH-2872-2


title: PSPPH-2219-2


title: PSPPH-2219-1


title: PSPPH-4056-1


title: PSPPH-4844-2


title: PSPPH-3900-2


title: PSPPH-4056-2


title: recombinant CDV-infected ferret organ homogenate (passage 3)

growth_protocol: ferrets were intranasally infected with recombinant P2 CDV and euthanized 7 days post infection. Organ homogenates were generated from lymph nodes, spleen, and lung. RNA was extracted from mixed homogenates.

value: passage 3


title: PSPPH-1222-1


title: sf_N1

description:
10x Genomics
sf_normal_1


title: PSPPH-1222-2


title: CDV-infected ferret organ homogenate (passage 3)

growth_protocol: ferrets were intranasally infected with P2 CDV and euthanized 7 days post infection. Organ homogenates were generated from lymph nodes, spleen, and lung. RNA was extracted from mixed homogenates.


title: syn_N

description:
10x Genomics
syn_normal_1

value: Synovial tissue

value: horse 2


title: PSPPH-1734-1


title: PSPPH-3900-1


title: recombinant CDV-infected ferret organ homogenate (passage 6)

growth_protocol: ferrets were intranasally infected with recombinant P5 CDV and euthanized 7 days post infection. Organ homogenates were generated from lymph nodes, spleen, and lung. RNA was extracted from mixed homogenates.

value: passage 6


title: PSPPH-2832-2


title: PSPPH-1734-2


title: CDV-infected ferret organ homogenate (passage 1)

growth_protocol: ferrets were intranasally infected with P0 CDV and euthanized 7 days post infection. Organ homogenates were generated from lymph nodes, spleen, and lung. RNA was extracted from mixed homogenates.


title: PSPPH-2665-1


title: PSPPH-2665-2


title: PSPPH-2630-2


title: PSPPH-2832-1


title: PSPPH-3099-1


title: PSPPH-4644-2


title: PSPPH-2133-1


title: PSPPH-3555-2


title: PSPPH-2133-2


title: PSPPH-4644-1


title: PSPPH-4844-1


title: PSPPH-1380-2


title: PSPPH-1380-1


title: PSPPH-1519-1


title: PSPPH-3555-1


title: PSPPH-2905-1


title: PSPPH-4377-2


title: PSPPH-3099-2


title: PSPPH-1519-2


title: PSPPH-4377-1


title: PSPPH-2905-2


title: PSPPH-5042-2


title: PSPPH-5042-1


title: PSPPH-0239-2


title: PSPPH-0239-1


title: PSPPH-1762-2


title: PSPPH-1762-1


title: PSPPH-2194-1


title: PSPPH-4694-1


title: PSPPH-4694-2


title: PSPPH-2194-2


title: PSPPH-2792-1


title: PSPPH-2792-2


title: PSPPH-2630-1


title: PSPPH-4324-2


title: PSPPH-2337-2


title: PSPPH-2151-1


title: PSPPH-2151-2


title: PSPPH-2337-1


title: PSPPH-2984-2


title: PSPPH-2994-2


title: PSPPH-2984-1


title: PSPPH-2994-1


title: PSPPH-0286-2


title: PSPPH-2421-2


title: PSPPH-0286-1


title: PSPPH-2214-1


title: PSPPH-2214-2


title: EV-2

description: no processed data file


title: EV-1

description: no processed data file


title: PSPPH-4324-1


title: PSPPH-1700-2


title: PSPPH-0863-1


title: PSPPH-0061-2


title: PSPPH-4320-1


title: PSPPH-1700-1


title: PSPPH-3983-2


title: PSPPH-4320-2


title: PSPPH-0863-2


title: PSPPH-3504-2


title: PSPPH-4920-2


title: PSPPH-3504-1


title: PSPPH-0061-1


title: PSPPH-2421-1


title: PSPPH-0101-1


title: PSPPH-3182-2


title: PSPPH-3182-1


title: PSPPH-1456-1


title: PSPPH-4920-1


title: PSPPH-3203-2


title: PSPPH-4700-2


title: PSPPH-3983-1


title: PSPPH-3203-1


title: PSPPH-0101-2


title: PSPPH-1456-2


title: PSPPH-4700-1


title: PSPPH-4356-2


title: PSPPH-2149-2


title: PSPPH-1818-2


title: PSPPH-4673-2


title: PSPPH-4673-1


title: PSPPH-3168-2


title: PSPPH-3168-1


title: PSPPH-2149-1


title: PSPPH-4356-1


title: PSPPH-4255-1


title: PSPPH-4255-2


title: PSPPH-2229-2


title: PSPPH-1818-1


title: PSPPH-1169-2


title: PSPPH-2229-1


title: PSPPH-2893-1


title: PSPPH-1776-2


title: PSPPH-1169-1


title: PSPPH-3522-1


title: PSPPH-3522-2


title: PSPPH-2983-2


title: PSPPH-0218-2


title: PSPPH-1969-1


title: PSPPH-0218-1


title: PSPPH-3486-2


title: PSPPH-3486-1


title: PSPPH-2893-2


title: PSPPH-3872-1


title: PSPPH-1595-2


title: PSPPH-3202-2


title: PSPPH-1595-1


title: PSPPH-3202-1


title: PSPPH-1776-1


title: PSPPH-2305-2


title: PSPPH-0755-2


title: PSPPH-2106-1


title: PSPPH-2204-2


title: PSPPH-2106-2


title: PSPPH-2204-1


title: PSPPH-2983-1


title: PSPPH-1969-2


title: PSPPH-0031-2


title: PSPPH-2423-2


title: pspph-3468-2


title: PSPPH-4788-2


title: pspph-3468-1


title: pspph-0411-2


title: PSPPH-2305-1


title: PSPPH-3872-2


title: PSPPH-0031-1


title: pspph-5132-1


title: PSPPH-3643-2


title: pspph-2553-2


title: PSPPH-2423-1


title: pspph-2300-1


title: PSPPH-4788-1


title: PSPPH-3643-1


title: pspph-2580-1


title: pspph-1951-1


title: pspph-1758-1


title: pspph-2300-2


title: pspph-0411-1


title: pspph-5132-2


title: pspph-5144-2


title: pspph-5144-1


title: PSPPH-0755-1


title: pspph-2553-1


title: pspph-2580-2


title: pspph-2454-2


title: pspph-2454-1


title: pspph-2193-1


title: pspph-0700-2


title: pspph-0700-1


title: pspph-1758-2


title: pspph-4638-1


title: pspph-3411-2


title: pspph-1951-2


title: pspph-3798-2


title: pspph-4998-2


title: pspph-3411-1


title: pspph-4998-1


title: pspph-1493-2


title: pspph-2048-2


title: pspph-2048-1


title: pspph-2638-2


title: pspph-2193-2


title: pspph-4670-2


title: pspph-1435-2


title: pspph-4670-1


title: pspph-1435-1


title: pspph-4638-2


title: hack-2

description: no processed data file


title: pspph-2444-1


title: pspph-3798-1


title: PSPPH-4646-2


title: PSPPH-4646-1


title: PSPPH-0861-2


title: pspph-1493-1


title: pspph-2638-1


title: PSPPH-5194-2


title: pspph-0711-1


title: pspph-0711-2


title: hack-1

description: no processed data file


title: PSPPH-0406-1


title: pspph-2444-2


title: PSPPH-4822-1


title: PSPPH-3351-1


title: PSPPH-0102-1


title: PSPPH-4637-1


title: PSPPH-2188-2


title: PSPPH-2188-1


title: PSPPH-3923-2


title: PSPPH-3247-1


title: PSPPH-3923-1


title: PSPPH-0406-2


title: PSPPH-4822-2


title: PSPPH-5054-2


title: PSPPH-5054-1


title: PSPPH-3351-2


title: PSPPH-0102-2


title: PSPPH-0861-1


title: PSPPH-0226-1


title: PSPPH-4238-2


title: PSPPH-3530-1


title: PSPPH-2478-2


title: PSPPH-5194-1


title: PSPPH-3195-2


title: PSPPH-3195-1


title: PSPPH-1393-1


title: PSPPH-4637-2


title: PSPPH-3439-2


title: PSPPH-2995-2


title: PSPPH-2995-1


title: PSPPH-3439-1


title: PSPPH-3247-2


title: PSPPH-3453-1


title: PSPPH-3530-2


title: PSPPH-3040-2


title: PSPPH-0082-1


title: PSPPH-0846-1


title: PSPPH-3040-1


title: PSPPH-0222-2


title: PSPPH-0222-1


title: PSPPH-4238-1


title: PSPPH-2478-1


title: PSPPH-0226-2


title: PSPPH-0653-2


title: PSPPH-0846-2


title: PSPPH-0653-1


title: PSPPH-3431-2


title: PSPPH-1393-2


title: PSPPH-2917-1


title: PSPPH-3431-1


title: PSPPH-2917-2


title: PSPPH-4127-1


title: PSPPH-2774-2


title: PSPPH-0082-2


title: PSPPH-2774-1


title: PSPPH-1962-2


title: PSPPH-1670-2


title: PSPPH-4744-1


title: PSPPH-1670-1


title: PSPPH-4744-2


title: PSPPH-1962-1


title: PSPPH-3122-2


title: PSPPH-3453-2


title: PSPPH-3122-1


title: PSPPH-2862-2


title: PSPPH-3005-1


title: PSPPH-0486-1


title: PSPPH-2862-1


title: PSPPH-0486-2


title: PSPPH-4127-2


title: PSPPH-1097-1


title: PSPPH-2357-1


title: PSPPH-2357-2


title: PSPPH-1097-2


title: PSPPH-4692-1


title: PSPPH-4253-2


title: PSPPH-0349-1


title: PSPPH-0349-2


title: PSPPH-3936-2


title: PSPPH-2937-2


title: PSPPH-4253-1


title: PSPPH-2937-1


title: PSPPH-3005-2


title: PSPPH-3936-1


title: PSPPH-4692-2


title: PSPPH-4768-2


title: PSPPH-3268-2


title: PSPPH-4768-1


title: PSPPH-5138-2


title: PSPPH-5138-1


title: PSPPH-3268-1


title: PSPPH-4899-2


title: PSPPH-0735-2


title: PSPPH-4899-1


title: PSPPH-4012-1


title: PSPPH-3487-2


title: PSPPH-1728-1


title: PSPPH-1730-1


title: PSPPH-4495-1


title: PSPPH-0376-2


title: PSPPH-4495-2


title: PSPPH-1728-2


title: PSPPH-0735-1


title: PSPPH-2407-2


title: PSPPH-4622-1


title: PSPPH-1730-2


title: PSPPH-2407-1


title: PSPPH-2236-2


title: PSPPH-1579-1


title: PSPPH-2476-2


title: PSPPH-4012-2


title: PSPPH-4622-2


title: PSPPH-2476-1


title: PSPPH-3487-1


title: PSPPH-1049-1


title: PSPPH-1579-2


title: PSPPH-0376-1


title: PSPPH-2631-2


title: PSPPH-0077-1


title: PSPPH-2236-1


title: PSPPH-3014-2


title: PSPPH-3014-1


title: PSPPH-4620-2


title: PSPPH-1049-2


title: PSPPH-2439-1


title: PSPPH-4620-1


title: PSPPH-2555-1


title: PSPPH-2309-1


title: PSPPH-2439-2


title: PSPPH-2309-2


title: PSPPH-2555-2


title: PSPPH-1100-2


title: PSPPH-2967-1


title: PSPPH-2967-2


title: PSPPH-0141-2


title: PSPPH-0141-1


title: PSPPH-0077-2


title: PSPPH-1100-1


title: PSPPH-3464-1


title: PSPPH-2301-2


title: PSPPH-2301-1


title: PSPPH-2631-1


title: PSPPH-3817-1


title: PSPPH-3155-1


title: CK-2

description: no processed data file


title: CK-1

description: no processed data file


title: PSPPH-3817-2


title: BatchF_ethanol extract of Sibjeondaebo-tang (Medium 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 15-3-5

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

growth_protocol: Human astrocytoma cell line, SW1783 (HTB-13) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). SW1783 cells were maintained in Leibovitz's L-15 medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 0% 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: Leibovitz's L-15, 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 100 microg/mL

tag: time


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

description: sample 15-3-3

value: Palmul-tang ethanol extract 20 microg/mL


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

description: sample 15-3-6

value: Sibjeondaebo-tang ethanol extract 20 microg/mL


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

description: sample 15-3-1

value: Palmul-tang ethanol extract 500 microg/mL


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

description: sample 15-3-2

value: Palmul-tang ethanol extract 100 microg/mL


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

description: sample 15-2-5


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

description: sample 15-2-4

value: Sibjeondaebo-tang ethanol extract 500 microg/mL


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

description: sample 15-2-2


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

description: sample 15-2-3


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

description: sample 15-2-1


title: PSPPH-3464-2


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

description: sample 15-1-6


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

description: sample 15-1-4


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

description: sample 15-1-3


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

description: sample 15-1-5


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

description: sample 15-1-2


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

description: sample 14-3-6

value: Samul-tang ethanol extract 20 microg/mL


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

description: sample 15-1-1


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

description: sample 14-3-5

value: Samul-tang ethanol extract 100 microg/mL


title: PSPPH-3155-2


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

description: sample 14-3-3

value: Sagunja-tang ethanol extract 20 microg/mL


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

description: sample 14-3-2

value: Sagunja-tang ethanol extract 100 microg/mL


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

description: sample 15-3-4


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

description: sample 14-3-1

value: Sagunja-tang ethanol extract 500 microg/mL


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

description: sample 14-2-6


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

description: sample 14-2-4

value: Samul-tang ethanol extract 500 microg/mL


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

description: sample 14-2-3


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

description: sample 14-2-2


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

description: sample 15-2-6


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

description: sample 14-2-5


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

description: sample 14-1-6


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

description: sample 14-1-3


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

description: sample 14-1-4


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

description: sample 13-3-5

value: Cinnamomi Cortex ethanol extract 100 microg/mL


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

description: sample 14-1-1


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

description: sample 14-1-5


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

description: sample 14-1-2


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

description: sample 13-3-6

value: Cinnamomi Cortex ethanol extract 20 microg/mL


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

description: sample 14-3-4


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

description: sample 13-2-2

value: Astragali Radix ethanol extract 44 microg/mL


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

description: sample 13-2-4

value: Cinnamomi Cortex ethanol extract 500 microg/mL


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

description: sample 13-2-5


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

description: sample 13-1-6


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

description: sample 13-1-5


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

description: sample 14-2-1


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

description: sample 13-3-4


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

description: sample 13-1-1

value: Astragali Radix ethanol extract 220 microg/mL


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

description: sample 12-3-4

value: Rehmanniae Radix Preparata ethanol extract 500 microg/mL


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

description: sample 13-3-2


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

description: sample 13-3-1


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

description: sample 13-2-6


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

description: sample 13-2-3

value: Astragali Radix ethanol extract 8.8 microg/mL


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

description: sample 12-3-2

value: Cnidii Rhizoma ethanol extract 100 microg/mL


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

description: sample 12-3-3

value: Cnidii Rhizoma ethanol extract 20 microg/mL


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

description: sample 13-1-4


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

description: sample 13-2-1


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

description: sample 12-2-5

value: Rehmanniae Radix Preparata ethanol extract 100 microg/mL


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

description: sample 13-1-2


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

description: sample 12-3-6

value: Rehmanniae Radix Preparata ethanol extract 20 microg/mL


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

description: sample 12-3-5


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

description: sample 13-1-3


title: BatchF_Vehicle(DMSO)_rep3

description: sample F1-3-1

value: 0.1% DMSO


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

description: sample 12-2-1

value: Cnidii Rhizoma ethanol extract 500 microg/mL


title: BatchF_Vehicle(DMSO)_rep2

description: sample F1-2-1


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

description: sample 13-3-3


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

description: sample 12-1-4


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

description: sample 12-1-2


title: BatchF_Vehicle(DMSO)_rep1

description: sample F1-1-1


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

description: sample 12-2-4


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

description: sample 12-2-6


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

description: sample 12-3-1


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

description: sample 11-3-2

value: Angelicae Gigantis Radix ethanol extract 100 microg/mL


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

description: sample 11-3-4

value: Paeoniae Radix ethanol extract 500 microg/mL


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

description: sample 11-3-3

value: Angelicae Gigantis Radix ethanol extract 20 microg/mL


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

description: sample 11-3-5

value: Paeoniae Radix ethanol extract 100 microg/mL


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

description: sample 12-2-3


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

description: sample 11-2-4


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

description: sample 11-2-6

value: Paeoniae Radix ethanol extract 20 microg/mL


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

description: sample 11-2-5


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

description: sample 12-1-3


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

description: sample 12-1-6


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

description: sample 11-2-3


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

description: sample 12-1-5


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

description: sample 12-2-2


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

description: sample 11-3-6


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

description: sample 12-1-1


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

description: sample 11-2-2


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

description: sample 11-2-1

value: Angelicae Gigantis Radix ethanol extract 500 microg/mL


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

description: sample 11-3-1


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

description: sample 11-1-5


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

description: sample 11-1-2


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

description: sample 11-1-4


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

description: sample 11-1-6


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

description: sample 11-1-1


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

description: sample 10-3-5

value: Panax Ginseng ethanol extract 100 microg/mL


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

description: sample 10-3-6

value: Panax Ginseng ethanol extract 20 microg/mL


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

description: sample 10-3-4

value: Panax Ginseng ethanol extract 500 microg/mL


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

description: sample 10-3-3

value: Glycyrrhizae Radix ethanol extract 12 microg/mL


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

description: sample 11-1-3


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

description: sample 10-3-1

value: Glycyrrhizae Radix ethanol extract 300 microg/mL


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

description: sample 10-3-2

value: Glycyrrhizae Radix ethanol extract 60 microg/mL


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

description: sample 10-2-4


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

description: sample 10-2-5


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

description: sample 10-2-3


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

description: sample 10-2-6


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

description: sample 10-1-6


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

description: sample 10-2-2


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

description: sample 10-1-5


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

description: sample 10-1-2


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

description: sample 10-1-1


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

description: sample 10-2-1


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

description: sample 9-3-3

value: Poria Cocos ethanol extract 20 microg/mL


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

description: sample 9-3-5

value: Atractylodis Rhizoma ethanol extract 100 microg/mL


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

description: sample 9-3-6

value: Atractylodis Rhizoma ethanol extract 20 microg/mL


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

description: sample 10-1-3


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

description: sample 10-1-4


title: BatchE_Vehicle(DMSO)_rep3

description: sample E1-3-1

value: 0.1% DMSO


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

description: sample 9-3-4

value: Atractylodis Rhizoma ethanol extract 500 microg/mL


title: BatchE_Vehicle(DMSO)_rep1

description: sample E1-1-1


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

description: sample 9-3-1

value: Poria Cocos ethanol extract 500 microg/mL


title: BatchE_Vehicle(DMSO)_rep2

description: sample E1-2-1


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

description: sample 9-2-6

value: Atractylodis Rhizoma ethanol extract 20 μg/mL


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

description: sample 9-3-2

value: Poria Cocos ethanol extract 100 microg/mL


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

description: sample 9-2-5

value: Atractylodis Rhizoma ethanol extract 100 μg/mL


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

description: sample 9-2-4

value: Atractylodis Rhizoma ethanol extract 500 μg/mL


title: BatchD_Vehicle(DMSO)_rep3

description: sample D1-3-1


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

description: sample 9-2-3

value: Poria Cocos ethanol extract 20 μg/mL


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

description: sample 9-2-2

value: Poria Cocos ethanol extract 100 μg/mL


title: BatchD_Vehicle(DMSO)_rep2

description: sample D1-2-1


title: BatchD_Vehicle(DMSO)_rep1

description: sample D1-1-1


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

description: sample 9-1-6


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

description: sample 9-1-4


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

description: sample 9-1-2


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

description: sample 9-1-3


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

description: sample 9-1-1


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

description: sample 8-3-4

value: Sibjeondaebo-tang water extract 500 microg/mL


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

description: sample 8-3-6

value: Sibjeondaebo-tang water extract 20 microg/mL


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

description: sample 8-3-3

value: Palmul-tang water extract 20 microg/mL


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

description: sample 8-3-1

value: Palmul-tang water extract 500 microg/mL


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

description: sample 8-3-2

value: Palmul-tang water extract 100 microg/mL


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

description: sample 8-2-6


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

description: sample 8-2-3


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

description: sample 8-2-5

value: Sibjeondaebo-tang water extract 100 microg/mL


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

description: sample 8-2-2


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

description: sample 9-2-1

value: Poria Cocos ethanol extract 500 μg/mL


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

description: sample 8-2-4


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

description: sample 8-1-3


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

description: sample 8-2-1


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

description: sample 8-1-6


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

description: sample 7-3-5

value: Samul-tang water extract 100 microg/mL


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

description: sample 8-1-5


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

description: sample 7-3-4

value: Samul-tang water extract 500 microg/mL


title: BatchC_Vehicle(DMSO)_rep1

description: sample C1-1-1

value: 0.1% DMSO


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

description: sample 8-1-2


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

description: sample 8-1-4


title: BatchC_Vehicle(DMSO)_rep2

description: sample C1-2-1


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

description: sample 8-1-1


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

description: sample 9-1-5

value: Atractylodis Rhizoma ethanol extract 100 microg/mL


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

description: sample 7-3-1

treatment_protocol: Leibovitz's L-15, 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: Sagunja-tang water extract 500 microg/mL


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

description: sample 7-2-6

value: Samul-tang water extract 20 microg/mL


title: BatchC_Vehicle(DMSO)_rep3

description: sample C1-3-1


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

description: sample 7-2-3

value: Sagunja-tang water extract 20 microg/mL


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

description: sample 7-2-1


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

description: sample 7-3-3


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

description: sample 8-3-5


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

description: sample 7-3-2

value: Sagunja-tang water extract 100 microg/mL


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

description: sample 7-1-6


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

description: sample 7-2-5


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

description: sample 7-2-4


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

description: sample 6-3-6

value: Astragali Radix water extract 20 microg/mL


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

description: sample 7-3-6


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

description: sample 6-3-5

value: Astragali Radix water extract 100 microg/mL


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

description: sample 7-1-5


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

description: sample 7-2-2


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

description: sample 7-1-1


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

description: sample 7-1-4


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

description: sample 6-3-2

value: Cinnamomi Cortex water extract 100 microg/mL


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

description: sample 6-2-6


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

description: sample 6-3-4

value: Astragali Radix water extract 500 microg/mL


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

description: sample 6-2-3

value: Cinnamomi Cortex water extract 20 microg/mL


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

description: sample 7-1-2


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

description: sample 6-2-2


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

description: sample 6-1-6


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

description: sample 6-3-3


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

description: sample 6-2-5


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

description: sample 6-2-1

value: Cinnamomi Cortex water extract 500 microg/mL


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

description: sample 6-1-1


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

description: sample 6-1-5


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

description: sample 6-1-3


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

description: sample 7-1-3


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

description: sample 6-2-4


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

description: sample 6-1-2


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

description: sample 5-2-3

value: Cnidii Rhizoma water extract 20 microg/mL


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

description: sample 6-1-4


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

description: sample 5-3-6

value: Rehmanniae Radix Preparata water extract 20 microg/mL


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

description: sample 5-3-5

value: Rehmanniae Radix Preparata water extract 100 microg/mL


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

description: sample 5-3-2

value: Cnidii Rhizoma water extract 100 microg/mL


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

description: sample 5-1-5


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

description: sample 5-1-2


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

description: sample 5-3-1

value: Cnidii Rhizoma water extract 500 microg/mL


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

description: sample 6-3-1


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

description: sample 5-3-4

value: Rehmanniae Radix Preparata water extract 500 microg/mL


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

description: sample 5-2-6


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

description: sample 5-1-1


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

description: sample 4-3-4

value: Paeoniae Radix water extract 500 microg/mL


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

description: sample 5-2-1


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

description: sample 5-2-2


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

description: sample 5-1-6


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

description: sample 5-2-5


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

description: sample 5-2-4


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

description: sample 4-3-3

value: Angelicae Gigantis Radix water extract 20 microg/mL


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

description: sample 4-3-6

value: Paeoniae Radix water extract 20 microg/mL


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

description: sample 4-3-2

value: Angelicae Gigantis Radix water extract 100 microg/mL


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

description: sample 5-1-4


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

description: sample 4-3-5

value: Paeoniae Radix water extract 100 microg/mL


title: BatchB_Vehicle(DMSO)_rep1

description: sample B1-1-1

value: 0.1% DMSO


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

description: sample 5-3-3


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

description: sample 5-1-3


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

description: sample 4-2-5


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

description: sample 4-2-4


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

description: sample 4-3-1

value: Angelicae Gigantis Radix water extract 500 microg/mL


title: BatchB_Vehicle(DMSO)_rep3

description: sample B1-3-1


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

description: sample 4-2-2


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

description: sample 4-1-5


title: BatchB_Vehicle(DMSO)_rep2

description: sample B1-2-1


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

description: sample 4-1-4


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

description: sample 4-1-3


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

description: sample 4-2-6


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

description: sample 3-3-3

value: Glycyrrhizae Radix water extract 20 microg/mL


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

description: sample 3-2-6

value: Panax Ginseng water extract 20 microg/mL


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

description: sample 4-2-3


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

description: sample 4-2-1


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

description: sample 3-2-3


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

description: sample 4-1-6


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

description: sample 4-1-2


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

description: sample 4-1-1


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

description: sample 3-2-1

value: Glycyrrhizae Radix water extract 500 microg/mL


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

description: sample 3-3-6


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

description: sample 3-3-5

value: Panax Ginseng water extract 100 microg/mL


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

description: sample 3-1-3


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

description: sample 3-1-2

value: Glycyrrhizae Radix water extract 100 microg/mL


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

description: sample 3-3-2


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

description: sample 3-3-4

value: Panax Ginseng water extract 500 microg/mL


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

description: sample 3-2-5


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

description: sample 2-3-6

value: Atractylodis Rhizoma water extract 20 microg/mL


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

description: sample 2-3-4

value: Atractylodis Rhizoma water extract 500 microg/mL


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

description: sample 2-3-2

value: Poria Cocos water extract 100 microg/mL


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

description: sample 2-3-3

value: Poria Cocos water extract 20 microg/mL


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

description: sample 3-2-4


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

description: sample 3-1-4


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

description: sample 3-1-6


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

description: sample 3-1-1


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

description: sample 3-3-1


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

description: sample 3-1-5


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

description: sample 2-2-6


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

description: sample 2-3-1

value: Poria Cocos water extract 500 microg/mL


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

description: sample 2-3-5

value: Atractylodis Rhizoma water extract 100 microg/mL


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

description: sample 2-2-3


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

description: sample 3-2-2


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

description: sample 2-2-2


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

description: sample 2-2-5


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

description: sample 2-2-1


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

description: sample 2-2-4


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

description: sample 2-1-5


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

description: sample 2-1-6


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

description: sample 2-1-4


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

description: sample 2-1-3


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

description: sample 2-1-1


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

description: sample 2-1-2


title: BatchA_Thioridazine_rep2

description: sample 1-2-6

value: Thioridazine 10 uM


title: BatchA_LY294002_rep1

description: sample 1-1-5


title: BatchA_LY294002_rep2

description: sample 1-2-5


title: BatchA_Thioridazine_rep1

description: sample 1-1-6


title: BatchA_Wortmannin_rep3

description: sample 1-3-4

value: wortmannin 10 uM


title: BatchA_Wortmannin_rep1

description: sample 1-1-4


title: BatchA_Thioridazine_rep3

description: sample 1-3-6


title: HepG2_BatchE_ethanol extract of Sibjeondaebo-tang (Low dose)_rep3

description:
sample 15-3-6
RCM_tonifying_HepG2.txt

growth_protocol: Human hepatocellular carcinoma cell line, HepG2 (HB-8065) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). HepG2 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.

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.

value: Sibjeondaebo-tang ethanol extract 20 μg/mL


title: BatchA_Vehicle(DMSO)_rep3

description: sample A1-3-1

value: 0.1% DMSO


title: BatchA_Vehicle(DMSO)_rep2

description: sample A1-2-1


title: BatchA_Vehicle(DMSO)_rep1

description: sample A1-1-1


title: HepG2_BatchE_ethanol extract of Sibjeondaebo-tang (High dose)_rep3

description:
sample 15-3-4
RCM_tonifying_HepG2.txt

value: Sibjeondaebo-tang ethanol extract 500 μg/mL


title: HepG2_BatchE_ethanol extract of Palmul-tang (Medium dose)_rep3

description:
sample 15-3-2
RCM_tonifying_HepG2.txt

value: Palmul-tang ethanol extract 100 μg/mL


title: HepG2_BatchE_ethanol extract of Sibjeondaebo-tang (Medium dose)_rep3

description:
sample 15-3-5
RCM_tonifying_HepG2.txt

value: Sibjeondaebo-tang ethanol extract 100 μg/mL


title: HepG2_BatchE_ethanol extract of Sibjeondaebo-tang (Medium dose)_rep2

description:
sample 15-2-5
RCM_tonifying_HepG2.txt


title: BatchA_LY294002_rep3

description: sample 1-3-5


title: HepG2_BatchE_ethanol extract of Sibjeondaebo-tang (High dose)_rep2

description:
sample 15-2-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_ethanol extract of Sibjeondaebo-tang (Low dose)_rep2

description:
sample 15-2-6
RCM_tonifying_HepG2.txt


title: BatchA_Wortmannin_rep2

description: sample 1-2-4


title: HepG2_BatchE_ethanol extract of Palmul-tang (Low dose)_rep2

description:
sample 15-2-3
RCM_tonifying_HepG2.txt

value: Palmul-tang ethanol extract 20 μg/mL


title: HepG2_BatchE_ethanol extract of Palmul-tang (High dose)_rep2

description:
sample 15-2-1
RCM_tonifying_HepG2.txt

value: Palmul-tang ethanol extract 500 μg/mL


title: HepG2_BatchE_ethanol extract of Sibjeondaebo-tang (High dose)_rep1

description:
sample 15-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_ethanol extract of Palmul-tang (Medium dose)_rep1

description:
sample 15-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_ethanol extract of Palmul-tang (Low dose)_rep3

description:
sample 15-3-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_ethanol extract of Samul-tang (Medium dose)_rep2

description:
sample 14-2-5
RCM_tonifying_HepG2.txt

value: Samul-tang ethanol extract 100 μg/mL


title: HepG2_BatchE_ethanol extract of Palmul-tang (High dose)_rep1

description:
sample 15-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_ethanol extract of Samul-tang (Low dose)_rep2

description:
sample 14-2-6
RCM_tonifying_HepG2.txt

value: Samul-tang ethanol extract 20 μg/mL


title: HepG2_BatchE_ethanol extract of Sagunja-tang (Low dose)_rep3

description:
sample 14-3-3
RCM_tonifying_HepG2.txt

value: Sagunja-tang ethanol extract 20 μg/mL


title: HepG2_BatchE_ethanol extract of Sagunja-tang (Medium dose)_rep3

description:
sample 14-3-2
RCM_tonifying_HepG2.txt

value: Sagunja-tang ethanol extract 100 μg/mL


title: HepG2_BatchE_Vehicle(DMSO)_rep3

description:
sample E1-3-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_ethanol extract of Samul-tang (High dose)_rep3

description:
sample 14-3-4
RCM_tonifying_HepG2.txt

value: Samul-tang ethanol extract 500 μg/mL


title: HepG2_BatchE_ethanol extract of Sagunja-tang (High dose)_rep3

description:
sample 14-3-1
RCM_tonifying_HepG2.txt

value: Sagunja-tang ethanol extract 500 μg/mL


title: HepG2_BatchE_ethanol extract of Palmul-tang (High dose)_rep3

description:
sample 15-3-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_ethanol extract of Samul-tang (Low dose)_rep3

description:
sample 14-3-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_Vehicle(DMSO)_rep2

description:
sample E1-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_ethanol extract of Samul-tang (Medium dose)_rep3

description:
sample 14-3-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Sagunja-tang (Medium dose)_rep2

description:
sample 14-2-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_Vehicle(DMSO)_rep1

description:
sample E1-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Sagunja-tang (High dose)_rep2

description:
sample 14-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Sagunja-tang (Low dose)_rep2

description:
sample 14-2-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Samul-tang (Medium dose)_rep1

description:
sample 14-1-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Samul-tang (High dose)_rep1

description:
sample 14-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Sagunja-tang (Medium dose)_rep1

description:
sample 14-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Cinnamomi Cortex (Low dose)_rep3

description:
sample 13-3-6
RCM_tonifying_HepG2.txt

value: Cinnamomi Cortex ethanol extract 20 μg/mL


title: HepG2_BatchD_ethanol extract of Samul-tang (Low dose)_rep1

description:
sample 14-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Sagunja-tang (Low dose)_rep1

description:
sample 14-1-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Sagunja-tang (High dose)_rep1

description:
sample 14-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_ethanol extract of Sibjeondaebo-tang (Low dose)_rep1

description:
sample 15-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_ethanol extract of Sibjeondaebo-tang (Medium dose)_rep1

description:
sample 15-1-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchE_ethanol extract of Palmul-tang (Medium dose)_rep2

description:
sample 15-2-2
RCM_tonifying_HepG2.txt