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

description:
sample 13-3-4
RCM_tonifying_HepG2.txt

value: Cinnamomi Cortex ethanol extract 500 μg/mL


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

status: Public on Jun 21 2024

type: SRA

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description:
sample 13-3-5
RCM_tonifying_HepG2.txt

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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.

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

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

tag: cell line

tag: treatment

value: Cinnamomi Cortex ethanol extract 100 μg/mL

tag: time


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

description:
sample 15-1-3
RCM_tonifying_HepG2.txt

value: Palmul-tang ethanol extract 20 μg/mL


title: HepG2_BatchD_ethanol extract of Astragali Radix (Low dose)_rep3

description:
sample 13-3-3
RCM_tonifying_HepG2.txt

value: Astragali Radix ethanol extract 20 μg/mL


title: HepG2_BatchD_ethanol extract of Cinnamomi Cortex (Medium dose)_rep2

description:
sample 13-2-5
RCM_tonifying_HepG2.txt


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

description:
sample 14-2-4
RCM_tonifying_HepG2.txt

value: Samul-tang ethanol extract 500 μg/mL


title: HepG2_BatchD_ethanol extract of Astragali Radix (Medium dose)_rep2

description:
sample 13-2-2
RCM_tonifying_HepG2.txt

value: Astragali Radix ethanol extract 100 μg/mL


title: HepG2_BatchD_ethanol extract of Cinnamomi Cortex (High dose)_rep2

description:
sample 13-2-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Cinnamomi Cortex (Low dose)_rep2

description:
sample 13-2-6
RCM_tonifying_HepG2.txt

value: Cinnamomi Cortex ethanol extract 20 μg/mL


title: HepG2_BatchD_ethanol extract of Cinnamomi Cortex (Medium dose)_rep1

description:
sample 13-1-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Astragali Radix (High dose)_rep2

description:
sample 13-2-1
RCM_tonifying_HepG2.txt

value: Astragali Radix ethanol extract 500 μg/mL


title: HepG2_BatchD_ethanol extract of Cinnamomi Cortex (Low dose)_rep1

description:
sample 13-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Astragali Radix (Low dose)_rep2

description:
sample 13-2-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Astragali Radix (Low dose)_rep1

description:
sample 13-1-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Astragali Radix (Medium dose)_rep1

description:
sample 13-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Rehmanniae Radix Preparata (High dose)_rep3

description:
sample 12-3-4
RCM_tonifying_HepG2.txt

value: Rehmanniae Radix Preparata ethanol extract 500 μg/mL


title: HepG2_BatchD_ethanol extract of Astragali Radix (High dose)_rep1

description:
sample 13-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Cnidii Rhizoma (Low dose)_rep3

description:
sample 12-3-3
RCM_tonifying_HepG2.txt

value: Cnidii Rhizoma ethanol extract 20 μg/mL


title: HepG2_BatchD_ethanol extract of Cnidii Rhizoma (Medium dose)_rep3

description:
sample 12-3-2
RCM_tonifying_HepG2.txt

value: Cnidii Rhizoma ethanol extract 100 μg/mL


title: HepG2_BatchD_ethanol extract of Cnidii Rhizoma (High dose)_rep3

description:
sample 12-3-1
RCM_tonifying_HepG2.txt

value: Cnidii Rhizoma ethanol extract 500 μg/mL


title: HepG2_BatchD_ethanol extract of Astragali Radix (Medium dose)_rep3

description:
sample 13-3-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Rehmanniae Radix Preparata (Low dose)_rep3

description:
sample 12-3-6
RCM_tonifying_HepG2.txt

value: Rehmanniae Radix Preparata ethanol extract 20 μg/mL


title: HepG2_BatchD_ethanol extract of Astragali Radix (High dose)_rep3

description:
sample 13-3-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Cinnamomi Cortex (High dose)_rep1

description:
sample 13-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Rehmanniae Radix Preparata (Low dose)_rep2

description:
sample 12-2-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Rehmanniae Radix Preparata (Medium dose)_rep2

description:
sample 12-2-5
RCM_tonifying_HepG2.txt

value: Rehmanniae Radix Preparata ethanol extract 100 μg/mL


title: HepG2_BatchD_ethanol extract of Rehmanniae Radix Preparata (High dose)_rep2

description:
sample 12-2-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Cnidii Rhizoma (Low dose)_rep2

description:
sample 12-2-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Cnidii Rhizoma (Medium dose)_rep2

description:
sample 12-2-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Rehmanniae Radix Preparata (Low dose)_rep1

description:
sample 12-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Cnidii Rhizoma (High dose)_rep2

description:
sample 12-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Rehmanniae Radix Preparata (Medium dose)_rep1

description:
sample 12-1-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Cnidii Rhizoma (Medium dose)_rep1

description:
sample 12-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Cnidii Rhizoma (Low dose)_rep1

description:
sample 12-1-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Paeoniae Radix (Low dose)_rep3

description:
sample 11-3-6
RCM_tonifying_HepG2.txt

value: Paeoniae Radix ethanol extract 20 μg/mL


title: HepG2_BatchD_ethanol extract of Rehmanniae Radix Preparata (Medium dose)_rep3

description:
sample 12-3-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Paeoniae Radix (High dose)_rep2

description:
sample 11-2-4
RCM_tonifying_HepG2.txt

value: Paeoniae Radix ethanol extract 500 μg/mL


title: HepG2_BatchD_ethanol extract of Angelicae Gigantis Radix (High dose)_rep3

description:
sample 11-3-1
RCM_tonifying_HepG2.txt

value: Angelicae Gigantis Radix ethanol extract 500 μg/mL


title: HepG2_BatchD_ethanol extract of Angelicae Gigantis Radix (Low dose)_rep2

description:
sample 11-2-3
RCM_tonifying_HepG2.txt

value: Angelicae Gigantis Radix ethanol extract 20 μg/mL


title: HepG2_BatchD_ethanol extract of Cnidii Rhizoma (High dose)_rep1

description:
sample 12-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Paeoniae Radix (Medium dose)_rep3

description:
sample 11-3-5
RCM_tonifying_HepG2.txt

value: Paeoniae Radix ethanol extract 100 μg/mL


title: HepG2_BatchD_ethanol extract of Paeoniae Radix (High dose)_rep3

description:
sample 11-3-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Angelicae Gigantis Radix (Low dose)_rep3

description:
sample 11-3-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_Vehicle(DMSO)_rep1

description:
sample D1-1-1
RCM_tonifying_HepG2.txt

value: 0.1% DMSO


title: HepG2_BatchD_Vehicle(DMSO)_rep2

description:
sample D1-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Paeoniae Radix (Low dose)_rep2

description:
sample 11-2-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_Vehicle(DMSO)_rep3

description:
sample D1-3-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Angelicae Gigantis Radix (Medium dose)_rep3

description:
sample 11-3-2
RCM_tonifying_HepG2.txt

value: Angelicae Gigantis Radix ethanol extract 100 μg/mL


title: HepG2_BatchC_ethanol extract of Paeoniae Radix (Medium dose)_rep1

description:
sample 11-1-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Paeoniae Radix (Medium dose)_rep2

description:
sample 11-2-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Paeoniae Radix (High dose)_rep1

description:
sample 11-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Rehmanniae Radix Preparata (High dose)_rep1

description:
sample 12-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Paeoniae Radix (Low dose)_rep1

description:
sample 11-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchD_ethanol extract of Angelicae Gigantis Radix (High dose)_rep2

description:
sample 11-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Glycyrrhizae Radix (Low dose)_rep3

description:
sample 10-3-3
RCM_tonifying_HepG2.txt

value: Glycyrrhizae Radix ethanol extract 20 μg/mL


title: HepG2_BatchC_ethanol extract of Angelicae Gigantis Radix (High dose)_rep1

description:
sample 11-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Panax Ginseng (Low dose)_rep3

description:
sample 10-3-6
RCM_tonifying_HepG2.txt

value: Panax Ginseng ethanol extract 20 μg/mL


title: HepG2_BatchC_ethanol extract of Glycyrrhizae Radix (High dose)_rep3

description:
sample 10-3-1
RCM_tonifying_HepG2.txt

value: Glycyrrhizae Radix ethanol extract 500 μg/mL


title: HepG2_BatchC_ethanol extract of Angelicae Gigantis Radix (Medium dose)_rep1

description:
sample 11-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Glycyrrhizae Radix (Medium dose)_rep3

description:
sample 10-3-2
RCM_tonifying_HepG2.txt

value: Glycyrrhizae Radix ethanol extract 100 μg/mL


title: HepG2_BatchD_ethanol extract of Angelicae Gigantis Radix (Medium dose)_rep2

description:
sample 11-2-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Panax Ginseng (High dose)_rep3

description:
sample 10-3-4
RCM_tonifying_HepG2.txt

value: Panax Ginseng ethanol extract 500 μg/mL


title: HepG2_BatchC_ethanol extract of Panax Ginseng (Medium dose)_rep2

description:
sample 10-2-5
RCM_tonifying_HepG2.txt

value: Panax Ginseng ethanol extract 100 μg/mL


title: HepG2_BatchC_ethanol extract of Panax Ginseng (High dose)_rep2

description:
sample 10-2-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Glycyrrhizae Radix (Medium dose)_rep2

description:
sample 10-2-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Panax Ginseng (Low dose)_rep2

description:
sample 10-2-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Glycyrrhizae Radix (Low dose)_rep2

description:
sample 10-2-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Angelicae Gigantis Radix (Low dose)_rep1

description:
sample 11-1-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Panax Ginseng (Medium dose)_rep1

description:
sample 10-1-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Panax Ginseng (High dose)_rep1

description:
sample 10-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Glycyrrhizae Radix (Medium dose)_rep1

description:
sample 10-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Glycyrrhizae Radix (High dose)_rep2

description:
sample 10-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Glycyrrhizae Radix (Low dose)_rep1

description:
sample 10-1-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Atractylodis Rhizoma (Low dose)_rep3

description:
sample 9-3-6
RCM_tonifying_HepG2.txt

value: Atractylodis Rhizoma ethanol extract 20 μg/mL


title: HepG2_BatchC_ethanol extract of Panax Ginseng (Low dose)_rep1

description:
sample 10-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Atractylodis Rhizoma (High dose)_rep3

description:
sample 9-3-4
RCM_tonifying_HepG2.txt

value: Atractylodis Rhizoma ethanol extract 500 μg/mL


title: HepG2_BatchC_ethanol extract of Panax Ginseng (Medium dose)_rep3

description:
sample 10-3-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Poria Cocos (Low dose)_rep3

description:
sample 9-3-3
RCM_tonifying_HepG2.txt

value: Poria Cocos ethanol extract 20 μg/mL


title: HepG2_BatchC_ethanol extract of Glycyrrhizae Radix (High dose)_rep1

description:
sample 10-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Poria Cocos (High dose)_rep3

description:
sample 9-3-1
RCM_tonifying_HepG2.txt

value: Poria Cocos ethanol extract 500 μg/mL


title: HepG2_BatchC_ethanol extract of Poria Cocos (Medium dose)_rep3

description:
sample 9-3-2
RCM_tonifying_HepG2.txt

value: Poria Cocos ethanol extract 100 μg/mL


title: HepG2_BatchC_ethanol extract of Atractylodis Rhizoma (Low dose)_rep2

description:
sample 9-2-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Atractylodis Rhizoma (High dose)_rep2

description:
sample 9-2-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Poria Cocos (Low dose)_rep2

description:
sample 9-2-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Atractylodis Rhizoma (Medium dose)_rep2

description:
sample 9-2-5
RCM_tonifying_HepG2.txt

value: Atractylodis Rhizoma ethanol extract 100 μg/mL


title: HepG2_BatchC_ethanol extract of Poria Cocos (Medium dose)_rep2

description:
sample 9-2-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Atractylodis Rhizoma (Medium dose)_rep1

description:
sample 9-1-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Poria Cocos (Low dose)_rep1

description:
sample 9-1-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Atractylodis Rhizoma (High dose)_rep1

description:
sample 9-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Atractylodis Rhizoma (Low dose)_rep1

description:
sample 9-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_water extract of Sibjeondaebo-tang (Low dose)_rep3

description:
sample 8-3-6
RCM_tonifying_HepG2.txt

value: Sibjeondaebo-tang water extract 20 μg/mL


title: HepG2_BatchC_ethanol extract of Poria Cocos (Medium dose)_rep1

description:
sample 9-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Poria Cocos (High dose)_rep1

description:
sample 9-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Poria Cocos (High dose)_rep2

description:
sample 9-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_ethanol extract of Atractylodis Rhizoma (Medium dose)_rep3

description:
sample 9-3-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_water extract of Sibjeondaebo-tang (Medium dose)_rep3

description:
sample 8-3-5
RCM_tonifying_HepG2.txt

value: Sibjeondaebo-tang water extract 100 μg/mL


title: HepG2_BatchC_water extract of Palmul-tang (Medium dose)_rep3

description:
sample 8-3-2
RCM_tonifying_HepG2.txt

value: Palmul-tang water extract 100 μg/mL


title: HepG2_BatchC_water extract of Palmul-tang (High dose)_rep3

description:
sample 8-3-1
RCM_tonifying_HepG2.txt

value: Palmul-tang water extract 500 μg/mL


title: HepG2_BatchC_water extract of Sibjeondaebo-tang (Low dose)_rep2

description:
sample 8-2-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_water extract of Sibjeondaebo-tang (Medium dose)_rep2

description:
sample 8-2-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_water extract of Sibjeondaebo-tang (High dose)_rep2

description:
sample 8-2-4
RCM_tonifying_HepG2.txt

value: Sibjeondaebo-tang water extract 500 μg/mL


title: HepG2_BatchC_water extract of Sibjeondaebo-tang (High dose)_rep3

description:
sample 8-3-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_water extract of Palmul-tang (Medium dose)_rep2

description:
sample 8-2-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_water extract of Palmul-tang (Low dose)_rep3

description:
sample 8-3-3
RCM_tonifying_HepG2.txt

value: Palmul-tang water extract 20 μg/mL


title: HepG2_BatchC_water extract of Palmul-tang (Low dose)_rep2

description:
sample 8-2-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_water extract of Sibjeondaebo-tang (Medium dose)_rep1

description:
sample 8-1-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_water extract of Sibjeondaebo-tang (Low dose)_rep1

description:
sample 8-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_Vehicle(DMSO)_rep3

description:
sample C1-3-1
RCM_tonifying_HepG2.txt

value: 0.1% DMSO


title: HepG2_BatchC_Vehicle(DMSO)_rep1

description:
sample C1-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_water extract of Sibjeondaebo-tang (High dose)_rep1

description:
sample 8-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Palmul-tang (Low dose)_rep1

description:
sample 8-1-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_Vehicle(DMSO)_rep2

description:
sample C1-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchC_water extract of Palmul-tang (High dose)_rep2

description:
sample 8-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Palmul-tang (High dose)_rep1

description:
sample 8-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Samul-tang (High dose)_rep3

description:
sample 7-3-4
RCM_tonifying_HepG2.txt

value: Samul-tang water extract 500 μg/mL


title: HepG2_BatchB_water extract of Samul-tang (Low dose)_rep3

description:
sample 7-3-6
RCM_tonifying_HepG2.txt

value: Samul-tang water extract 20 μg/mL


title: HepG2_BatchB_water extract of Sagunja-tang (Low dose)_rep3

description:
sample 7-3-3
RCM_tonifying_HepG2.txt

value: Sagunja-tang water extract 20 μg/mL


title: HepG2_BatchB_water extract of Sagunja-tang (Medium dose)_rep3

description:
sample 7-3-2
RCM_tonifying_HepG2.txt

value: Sagunja-tang water extract 100 μg/mL


title: HepG2_BatchB_water extract of Samul-tang (Medium dose)_rep3

description:
sample 7-3-5
RCM_tonifying_HepG2.txt

value: Samul-tang water extract 100 μg/mL


title: HepG2_BatchB_water extract of Sagunja-tang (High dose)_rep3

description:
sample 7-3-1
RCM_tonifying_HepG2.txt

value: Sagunja-tang water extract 500 μg/mL


title: HepG2_BatchB_water extract of Samul-tang (Medium dose)_rep2

description:
sample 7-2-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Samul-tang (Low dose)_rep2

description:
sample 7-2-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Palmul-tang (Medium dose)_rep1

description:
sample 8-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Sagunja-tang (Low dose)_rep2

description:
sample 7-2-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Sagunja-tang (High dose)_rep2

description:
sample 7-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Sagunja-tang (Medium dose)_rep2

description:
sample 7-2-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Samul-tang (High dose)_rep1

description:
sample 7-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Sagunja-tang (High dose)_rep1

description:
sample 7-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Sagunja-tang (Low dose)_rep1

description:
sample 7-1-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Samul-tang (Low dose)_rep1

description:
sample 7-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Astragali Radix (Low dose)_rep3

description:
sample 6-3-6
RCM_tonifying_HepG2.txt

value: Astragali Radix water extract 20 μg/mL


title: HepG2_BatchB_water extract of Astragali Radix (Medium dose)_rep3

description:
sample 6-3-5
RCM_tonifying_HepG2.txt

value: Astragali Radix water extract 100 μg/mL


title: HepG2_BatchB_water extract of Sagunja-tang (Medium dose)_rep1

description:
sample 7-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Astragali Radix (High dose)_rep3

description:
sample 6-3-4
RCM_tonifying_HepG2.txt

value: Astragali Radix water extract 500 μg/mL


title: HepG2_BatchB_water extract of Cinnamomi Cortex (Medium dose)_rep3

description:
sample 6-3-2
RCM_tonifying_HepG2.txt

value: Cinnamomi Cortex water extract 100 μg/mL


title: HepG2_BatchB_water extract of Cinnamomi Cortex (Low dose)_rep3

description:
sample 6-3-3
RCM_tonifying_HepG2.txt

value: Cinnamomi Cortex water extract 20 μg/mL


title: HepG2_BatchB_water extract of Cinnamomi Cortex (High dose)_rep3

description:
sample 6-3-1
RCM_tonifying_HepG2.txt

value: Cinnamomi Cortex water extract 500 μg/mL


title: HepG2_BatchB_water extract of Astragali Radix (Low dose)_rep2

description:
sample 6-2-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Astragali Radix (High dose)_rep2

description:
sample 6-2-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Astragali Radix (Medium dose)_rep1

description:
sample 6-1-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cinnamomi Cortex (Medium dose)_rep1

description:
sample 6-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cinnamomi Cortex (Low dose)_rep2

description:
sample 6-2-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Samul-tang (High dose)_rep2

description:
sample 7-2-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Astragali Radix (High dose)_rep1

description:
sample 6-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of  Rehmanniae Radix Preparata (Medium dose)_rep3

description:
sample 5-3-5
RCM_tonifying_HepG2.txt

value: Rehmanniae Radix Preparata water extract 100 μg/mL


title: HepG2_BatchB_water extract of Cinnamomi Cortex (High dose)_rep2

description:
sample 6-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Astragali Radix (Medium dose)_rep2

description:
sample 6-2-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Astragali Radix (Low dose)_rep1

description:
sample 6-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of  Rehmanniae Radix Preparata (High dose)_rep3

description:
sample 5-3-4
RCM_tonifying_HepG2.txt

value: Rehmanniae Radix Preparata water extract 500 μg/mL


title: HepG2_BatchB_water extract of  Rehmanniae Radix Preparata (Low dose)_rep3

description:
sample 5-3-6
RCM_tonifying_HepG2.txt

value: Rehmanniae Radix Preparata water extract 20 μg/mL


title: HepG2_BatchB_water extract of Cinnamomi Cortex (Medium dose)_rep2

description:
sample 6-2-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cinnamomi Cortex (Low dose)_rep1

description:
sample 6-1-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cnidii Rhizoma (Low dose)_rep3

description:
sample 5-3-3
RCM_tonifying_HepG2.txt

value: Cnidii Rhizoma water extract 20 μg/mL


title: HepG2_BatchB_water extract of  Rehmanniae Radix Preparata (Low dose)_rep2

description:
sample 5-2-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cnidii Rhizoma (Medium dose)_rep3

description:
sample 5-3-2
RCM_tonifying_HepG2.txt

value: Cnidii Rhizoma water extract 100 μg/mL


title: HepG2_BatchB_water extract of Samul-tang (Medium dose)_rep1

description:
sample 7-1-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cnidii Rhizoma (High dose)_rep3

description:
sample 5-3-1
RCM_tonifying_HepG2.txt

value: Cnidii Rhizoma water extract 500 μg/mL


title: HepG2_BatchB_water extract of  Rehmanniae Radix Preparata (Medium dose)_rep2

description:
sample 5-2-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cnidii Rhizoma (Low dose)_rep2

description:
sample 5-2-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of  Rehmanniae Radix Preparata (High dose)_rep2

description:
sample 5-2-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cnidii Rhizoma (Medium dose)_rep2

description:
sample 5-2-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of  Rehmanniae Radix Preparata (Low dose)_rep1

description:
sample 5-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of  Rehmanniae Radix Preparata (Medium dose)_rep1

description:
sample 5-1-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of  Rehmanniae Radix Preparata (High dose)_rep1

description:
sample 5-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cnidii Rhizoma (Low dose)_rep1

description:
sample 5-1-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cinnamomi Cortex (High dose)_rep1

description:
sample 6-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cnidii Rhizoma (High dose)_rep1

description:
sample 5-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_Vehicle(DMSO)_rep3

description:
sample B1-3-1
RCM_tonifying_HepG2.txt

value: 0.1% DMSO


title: HepG2_BatchB_Vehicle(DMSO)_rep2

description:
sample B1-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cnidii Rhizoma (Medium dose)_rep1

description:
sample 5-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_Vehicle(DMSO)_rep1

description:
sample B1-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Paeoniae Radix (Medium dose)_rep3

description:
sample 4-3-5
RCM_tonifying_HepG2.txt

value: Paeoniae Radix water extract 100 μg/mL


title: HepG2_BatchA_water extract of Paeoniae Radix (Low dose)_rep3

description:
sample 4-3-6
RCM_tonifying_HepG2.txt

value: Paeoniae Radix water extract 20 μg/mL


title: HepG2_BatchA_water extract of Angelicae Gigantis Radix (Low dose)_rep3

description:
sample 4-3-3
RCM_tonifying_HepG2.txt

value: Angelicae Gigantis Radix water extract 20 μg/mL


title: HepG2_BatchA_water extract of Angelicae Gigantis Radix (High dose)_rep3

description:
sample 4-3-1
RCM_tonifying_HepG2.txt

value: Angelicae Gigantis Radix water extract 500 μg/mL


title: HepG2_BatchA_water extract of Paeoniae Radix (High dose)_rep3

description:
sample 4-3-4
RCM_tonifying_HepG2.txt

value: Paeoniae Radix water extract 500 μg/mL


title: HepG2_BatchA_water extract of Paeoniae Radix (Medium dose)_rep2

description:
sample 4-2-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Angelicae Gigantis Radix (Medium dose)_rep3

description:
sample 4-3-2
RCM_tonifying_HepG2.txt

value: Angelicae Gigantis Radix water extract 100 μg/mL


title: HepG2_BatchA_water extract of Paeoniae Radix (Low dose)_rep2

description:
sample 4-2-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Angelicae Gigantis Radix (Low dose)_rep2

description:
sample 4-2-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Angelicae Gigantis Radix (Low dose)_rep1

description:
sample 4-1-3
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Angelicae Gigantis Radix (High dose)_rep2

description:
sample 4-2-1
RCM_tonifying_HepG2.txt


title: WT_clone_2h_r1, CHiC

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

country: USA

institute: University of California Los Angeles

library_source: genomic

data_processing:
Capture Hi-C sequence reads underwent processing using HiCUP with default settings for mapping, pairing, filtering, and deduplication.
The unique and valid read pairs were further analyzed through CHiCAGO. A chinput file was generated, presenting raw counts for each interaction, and loops were identified with parameters tailored for four-cutter restriction enzyme digestion, as suggested at https://bitbucket.org/chicagoTeam/chicago/src/master. A CHiCAGO score greater than 5 served as the cutoff for designating loops as significant.
For the visualization of PCHi-C data in a 4C-like style (virtual 4C), data exclusively associated with an individual promoter were extracted from the chinput file. A bedgraph file was then generated using a custom script that incorporated the coordinates of each nonbait anchor fragment and the normalized PCHi-C counts.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include raw read counts

molecule: genomic DNA

organism: Mus musculus

source_name: macrophage

growth_protocol: WT macrophage cells were grown in BMDM media (20% FBS, 10% CMG condition medium [containing M-CSF], 1x Pen-Strep [GIBCO, #15140-122], 1x L-Glutamine [GIBCO, #25030-081], 0.5 mM sodium pyruvate [GIBCO, #11360-070] in Dubecco’s Modified Eagle Medium) for 6 days to obtain mature BMDMs prior to stimulation.

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 10 min at room temperature and quenched with 2M Tris-HCl pH 8.0 (final 0.125M) for 10 min at room temperature. Cells then were lysed in 300μL of cold lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% Igepal supplemented with protease inhibitor). The nuclei were digested in 1x NEBuffer 2 containing 100 units of MboI and incubated for 6 hr at 37 oC following by heat inactivation (65oC for 10 min). DNA polymerase I, Large (Klenow) fragment, and biotin-14-dATP were used to fill in restriction fragment overhangs and biotinylate DNA ends. 4000 units of T4 DNA ligase then added for proximate ligation and incubated at 16oC overnight. After reverse crosslinking, DNA was extracted with phenol/chloroform and ethanol precipitation. Sonication was then performed to make the biotinylated DNA size suitable for high-throughput sequencing (300-500 bp). DNA was dissolved in 130μL 10mM Tris-HCl pH 8.0 and transferred to microTUBE (Covaris, 520045) for sonication (Peak Incidence Power 50W, Duty Factor 10%, 200 Cycle per Burst, 60 sec). Sonicated DNA was size selected for fragments in the range of 300-500 bp by AMPure XP purification beads. The fragments marked with biotin were pulled down with Dynabeads™ MyOne™ Streptavidin T1 beads. End repair, A-tailing, and paired-end Agilent adaptor ligation (SureSelect XT Library Prep Kit ILM) were performed and followed by on-bead PCR amplification before hybridizing to the customized probe library (Custom 6-11.9 Mb library for 16 samples). The samples were prepared and hybridized to the capture library according to the protocol provided by Agilent (https://www.agilent.com/cs/library/usermanuals/Public/G7530-90000.pdf).
The final PCR amplification was carried out for 9 cycles and purified by using AMPure XP beads. The library was paired-end sequenced for 150 bp on the Illumina Novaseq platform.
Promoter captured HiC

treatment_protocol: Macrophage cells were stimulated with lipid-A for 0 and 2 hours.

tag: strain

tag: cell type

value: macrophage

tag: genotype

value: wildtype

value: lipid-A stimulated


title: HepG2_BatchA_water extract of Paeoniae Radix (Low dose)_rep1

description:
sample 4-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Paeoniae Radix (Medium dose)_rep1

description:
sample 4-1-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Glycyrrhizae Radix (Low dose)_rep3

description:
sample 3-3-3
RCM_tonifying_HepG2.txt

value: Glycyrrhizae Radix water extract 20 μg/mL


title: HepG2_BatchA_water extract of Panax Ginseng (Medium dose)_rep3

description:
sample 3-3-5
RCM_tonifying_HepG2.txt

value: Panax Ginseng water extract 100 μg/mL


title: SI QKO scRNA-seq

city: Tianjin

first: Yun Huan

last: Gao

address: 94 Weijin Road, Nankai District, Tianjin

country: China

institute: Nankai University

library_source: transcriptomic single cell

data_processing:
For bioinformatics analysis, results from Illumina sequencing were converted to FASTQ format using bcl2fastq software (version 5.0.1). The scRNA-seq sequencing data were compared to reference genome using CellRanger software, and cellular and individual cellular 3' end transcripts were identified and counted in thesequenced samples (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is cell-ranger , version 7.0.0).
Assembly: mm10
Supplementary files format and content: Taq-separated value files and matrix files

source_name: small intestinal epithelium

extract_protocol:
Fresh tissues from Adipfl/fl mice and Adipfl/flpVilli-CreT mice were transferred to a Petri dish pre-spiked with 1×PBS (without RNase and Ca, Mg ions) and washed with 1× PBS to remove blood stains, grease and other adherents from the tissue surface.The tissue was then cut into 0.5 mm2 pieces and washed again with 1×PBS. The washed pieces were added with dissociation solvent(0.35% collagenase IV5, 2 mg/ml papain, 120 Units/ml DNase I) and reacted for 20 min.The cell was filtered and collected.Add 100μl of Dead Cell Removal MicroBeads (MACS,130-090-101), mix well and incubate for 15min at room temperature. At the end of incubation, binding buffer was added, after MS Columns (130-042-201) to remove reagents, and dead cells.
For chromium 10´ Genomics library and sequencing, single-cell suspension was added to the 10´ Chromium chip according to the instructions for the 10´ Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 8,000 cells. cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced by LC-Bio Technology (Hangzhou, China) on an Illumina NovaSeq 6000 sequencing system (double-end sequencing, 150 bp) at a minimum depth of 20,000 reads per cell.

tag: tissue

value: small intestinal epithelium

value: Adipfl/flpVilli-CreT


title: SI QNC scRNA-seq

value: Adipfl/fl


title: HepG2_BatchA_water extract of Angelicae Gigantis Radix (Medium dose)_rep1

description:
sample 4-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Angelicae Gigantis Radix (High dose)_rep1

description:
sample 4-1-1
RCM_tonifying_HepG2.txt


title: WT_clone_0h_r1, CHiC

value: Unstimulated


title: HepG2_BatchA_water extract of Panax Ginseng (Low dose)_rep3

description:
sample 3-3-6
RCM_tonifying_HepG2.txt

value: Panax Ginseng water extract 20 μg/mL


title: WT_clone_0h_r2, CHiC


title: WT_clone_2h_r2, CHiC


title: HepG2_BatchA_water extract of Paeoniae Radix (High dose)_rep1

description:
sample 4-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchB_water extract of Cnidii Rhizoma (High dose)_rep2

description:
sample 5-2-1
RCM_tonifying_HepG2.txt

value: Cnidii Rhizoma water extract 500 μg/mL


title: KD3

city: Hangzhou

first: Shiqun

last: Wang

state: Zhejiang Province

address: No. 150, Fucheng Road, Hangzhou Economic and Technological Development Zone

institute: Institute of Cancer and Basic Medicine, Chinese Academy of Sciences (CAS)

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Mus_musculus (GRCm39)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: KPC

extract_protocol:
Total RNA was isolated and purified using TRIzol (ThermoFisher, 15596018) following the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: For bulk RNA-seq, 1 x 106 KPC-shScramble and KPC-shUBE2D3-1 cells were inoculated in 6-well plates. After 24 h, cells were harvested.

value: KPC

value: cancer cell

value: KPC shUBE2D3_1_3


title: HepG2_BatchA_water extract of Panax Ginseng (High dose)_rep3

description:
sample 3-3-4
RCM_tonifying_HepG2.txt

value: Panax Ginseng water extract 500 μg/mL


title: KD2

value: KPC shUBE2D3_1_2


title: HepG2_BatchA_water extract of Panax Ginseng (High dose)_rep2

description:
sample 3-2-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Paeoniae Radix (High dose)_rep2

description:
sample 4-2-4
RCM_tonifying_HepG2.txt

value: Paeoniae Radix water extract 500 μg/mL


title: Scr1

value: KPC shScr_1


title: HepG2_BatchA_water extract of Panax Ginseng (Medium dose)_rep2

description:
sample 3-2-5
RCM_tonifying_HepG2.txt


title: KD1

value: KPC shUBE2D3_1_1


title: HepG2_BatchA_water extract of Glycyrrhizae Radix (Medium dose)_rep3

description:
sample 3-3-2
RCM_tonifying_HepG2.txt

value: Glycyrrhizae Radix water extract 100 μg/mL


title: Scr3

value: KPC shScr_3


title: HepG2_BatchA_water extract of Glycyrrhizae Radix (High dose)_rep3

description:
sample 3-3-1
RCM_tonifying_HepG2.txt

value: Glycyrrhizae Radix water extract 500 μg/mL


title: Scr2

value: KPC shScr_2


title: HepG2_BatchA_water extract of Glycyrrhizae Radix (High dose)_rep2

description:
sample 3-2-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Panax Ginseng (Low dose)_rep2

description:
sample 3-2-6
RCM_tonifying_HepG2.txt


title: M046- 001-AirX31

city: Groningen

first: Jelmer

last: Vlasma

state: Groningen

department: Pathology and Medical Biology

country: Netherlands

institute: UMCG

data_processing:
FASTQC
Cutadapt v2.10
STAR v2.5.4
Assembly: GRCm38+H3N2
Supplementary files format and content: CSV, contains raw counts generated by STAR alignment

source_name: Lung

extract_protocol:
Maxwell 16 LEV SimplyRNA extraction kit (Promega)
Illumina short read sequencing

value: Lung

value: BALB/c


title: M047- 001-AirX31


title: M045- 001-AirX31


title: M011- 002CSSalDmso


title: HepG2_BatchA_water extract of Glycyrrhizae Radix (Medium dose)_rep2

description:
sample 3-2-2
RCM_tonifying_HepG2.txt


title: M024- 002AirX31Dmso


title: M081- 001AirSal


title: M044- 001-AirX31


title: HepG2_BatchA_water extract of Panax Ginseng (Medium dose)_rep1

description:
sample 3-1-5
RCM_tonifying_HepG2.txt

value: Panax Ginseng water extract 100 μg/mL


title: M095- 002AirSalDmso


title: HepG2_BatchA_water extract of Panax Ginseng (High dose)_rep1

description:
sample 3-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Glycyrrhizae Radix (High dose)_rep1

description:
sample 3-1-1
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Glycyrrhizae Radix (Low dose)_rep1

description:
sample 3-1-3
RCM_tonifying_HepG2.txt

value: Glycyrrhizae Radix water extract 20 μg/mL


title: M053- 001CSSal


title: HepG2_BatchA_water extract of Glycyrrhizae Radix (Low dose)_rep2

description:
sample 3-2-3
RCM_tonifying_HepG2.txt


title: M023- 002AirX31Dmso


title: M094- 002AirSalDmso


title: HepG2_BatchA_water extract of Atractylodis Rhizoma (Low dose)_rep3

description:
sample 2-3-6
RCM_tonifying_HepG2.txt

value: Atractylodis Rhizoma water extract 20 μg/mL


title: M106- 002CSX31Dmso


title: M072- 001CSX31


title: HepG2_BatchA_water extract of Atractylodis Rhizoma (Medium dose)_rep3

description:
sample 2-3-5
RCM_tonifying_HepG2.txt

value: Atractylodis Rhizoma water extract 100 μg/mL


title: HepG2_BatchA_water extract of Panax Ginseng (Low dose)_rep1

description:
sample 3-1-6
RCM_tonifying_HepG2.txt

value: Panax Ginseng water extract 20 μg/mL


title: HepG2_BatchA_water extract of Atractylodis Rhizoma (High dose)_rep3

description:
sample 2-3-4
RCM_tonifying_HepG2.txt

value: Atractylodis Rhizoma water extract 500 μg/mL


title: M052- 001CSSal


title: HepG2_BatchA_water extract of Poria Cocos (Low dose)_rep3

description:
sample 2-3-3
RCM_tonifying_HepG2.txt

value: Poria Cocos water extract 20 μg/mL


title: HepG2_BatchA_water extract of Poria Cocos (Medium dose)_rep3

description:
sample 2-3-2
RCM_tonifying_HepG2.txt

value: Poria Cocos water extract 100 μg/mL


title: M022- 002AirX31Dmso


title: HepG2_BatchA_water extract of Atractylodis Rhizoma (Medium dose)_rep2

description:
sample 2-2-5
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Poria Cocos (High dose)_rep3

description:
sample 2-3-1
RCM_tonifying_HepG2.txt

value: Poria Cocos water extract 500 μg/mL


title: HepG2_BatchA_water extract of Atractylodis Rhizoma (Low dose)_rep2

description:
sample 2-2-6
RCM_tonifying_HepG2.txt


title: M105- 002CSX31Dmso


title: M009- 002CSSalDmso


title: M071- 001CSX31


title: HepG2_BatchA_water extract of Atractylodis Rhizoma (High dose)_rep2

description:
sample 2-2-4
RCM_tonifying_HepG2.txt


title: M093- 002AirSalDmso


title: HepG2_BatchA_water extract of Glycyrrhizae Radix (Medium dose)_rep1

description:
sample 3-1-2
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Poria Cocos (Low dose)_rep2

description:
sample 2-2-3
RCM_tonifying_HepG2.txt


title: M010- 002CSSalDmso


title: M051- 001CSSal


title: HepG2_BatchA_water extract of Poria Cocos (Medium dose)_rep2

description:
sample 2-2-2
RCM_tonifying_HepG2.txt


title: M021- 002AirX31Dmso


title: HepG2_BatchA_water extract of Poria Cocos (High dose)_rep2

description:
sample 2-2-1
RCM_tonifying_HepG2.txt


title: M008- 002AirSalDmso


title: HepG2_BatchA_water extract of Atractylodis Rhizoma (Low dose)_rep1

description:
sample 2-1-6
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Atractylodis Rhizoma (Medium dose)_rep1

description:
sample 2-1-5
RCM_tonifying_HepG2.txt


title: M091- 002AirSalDmso


title: HepG2_BatchA_water extract of Atractylodis Rhizoma (High dose)_rep1

description:
sample 2-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_water extract of Poria Cocos (Low dose)_rep1

description:
sample 2-1-3
RCM_tonifying_HepG2.txt


title: M070- 001CSX31


title: HepG2_BatchA_water extract of Angelicae Gigantis Radix (Medium dose)_rep2

description:
sample 4-2-2
RCM_tonifying_HepG2.txt

value: Angelicae Gigantis Radix water extract 100 μg/mL


title: M019- 002AirX31Dmso


title: HepG2_BatchA_water extract of Poria Cocos (Medium dose)_rep1

description:
sample 2-1-2
RCM_tonifying_HepG2.txt


title: M103- 002CSSalDmso


title: HepG2_BatchA_water extract of Poria Cocos (High dose)_rep1

description:
sample 2-1-1
RCM_tonifying_HepG2.txt


title: M090- 002AirSalDmso


title: HepG2_BatchA_Wortmannin_rep3

description:
sample 1-3-4
RCM_tonifying_HepG2.txt

value: wortmannin 10 uM


title: M069- 001CSX31


title: M032- 002CSX31Dmso


title: HepG2_BatchA_Wortmannin_rep1

description:
sample 1-1-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_Vehicle(DMSO)_rep3

description:
sample A1-3-1
RCM_tonifying_HepG2.txt

value: 0.1% DMSO


title: M006- 002AirSalDmso


title: HepG2_BatchA_Vehicle(DMSO)_rep1

description:
sample A1-1-1
RCM_tonifying_HepG2.txt


title: M048- 001AirX31


title: M018- 002AirX31Dmso


title: M102- 002CSSalDmso


title: M104- 002CSSalDmso


title: M089- 002AirSalDmso


title: M068- 001CSX31


title: HT29_BatchE_ethanol extract of Sibjeondaebo-tang (Medium dose)_rep3

description:
sample 15-3-5
RCM_tonifying_HT29.txt

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

value: Sibjeondaebo-tang ethanol extract 100 μg/mL


title: HT29_BatchE_ethanol extract of Sibjeondaebo-tang (Low dose)_rep3

description:
sample 15-3-6
RCM_tonifying_HT29.txt

value: Sibjeondaebo-tang ethanol extract 20 μg/mL


title: HT29_BatchE_ethanol extract of Sibjeondaebo-tang (High dose)_rep3

description:
sample 15-3-4
RCM_tonifying_HT29.txt

value: Sibjeondaebo-tang ethanol extract 500 μg/mL


title: M017- 002AirX31Dmso

value: Lung


title: HT29_BatchE_ethanol extract of Palmul-tang (Low dose)_rep3

description:
sample 15-3-3
RCM_tonifying_HT29.txt

value: Palmul-tang ethanol extract 20 μg/mL


title: HT29_BatchE_ethanol extract of Palmul-tang (Medium dose)_rep3

description:
sample 15-3-2
RCM_tonifying_HT29.txt

value: Palmul-tang ethanol extract 100 μg/mL


title: M031- 002CSX31Dmso

value: BALB/c


title: HT29_BatchE_ethanol extract of Palmul-tang (High dose)_rep3

description:
sample 15-3-1
RCM_tonifying_HT29.txt

value: Palmul-tang ethanol extract 500 μg/mL


title: M005- 002AirSalDmso


title: M101- 002CSSalDmso


title: HT29_BatchE_ethanol extract of Sibjeondaebo-tang (Low dose)_rep2

description:
sample 15-2-6
RCM_tonifying_HT29.txt


title: HT29_BatchE_ethanol extract of Sibjeondaebo-tang (Medium dose)_rep2

description:
sample 15-2-5
RCM_tonifying_HT29.txt


title: M067- 001CSX31


title: HepG2_BatchA_Wortmannin_rep2

description:
sample 1-2-4
RCM_tonifying_HepG2.txt


title: HepG2_BatchA_Vehicle(DMSO)_rep2

description:
sample A1-2-1
RCM_tonifying_HepG2.txt


title: M030- 002CSX31Dmso


title: HT29_BatchE_ethanol extract of Sibjeondaebo-tang (High dose)_rep2

description:
sample 15-2-4
RCM_tonifying_HT29.txt


title: HT29_BatchE_ethanol extract of Palmul-tang (High dose)_rep2

description:
sample 15-2-1
RCM_tonifying_HT29.txt


title: HT29_BatchE_ethanol extract of Palmul-tang (Medium dose)_rep2

description:
sample 15-2-2
RCM_tonifying_HT29.txt


title: M112- 002CSX31Dmso


title: HT29_BatchE_ethanol extract of Sibjeondaebo-tang (Low dose)_rep1

description:
sample 15-1-6
RCM_tonifying_HT29.txt


title: HT29_BatchE_ethanol extract of Sibjeondaebo-tang (Medium dose)_rep1

description:
sample 15-1-5
RCM_tonifying_HT29.txt


title: M004- 002AirSalDmso


title: M100- 002CSSalDmso


title: HT29_BatchE_ethanol extract of Sibjeondaebo-tang (High dose)_rep1

description:
sample 15-1-4
RCM_tonifying_HT29.txt


title: HT29_BatchE_ethanol extract of Palmul-tang (Low dose)_rep1

description:
sample 15-1-3
RCM_tonifying_HT29.txt


title: M087- 001AirSal


title: M066- 001CSX31


title: HT29_BatchE_ethanol extract of Palmul-tang (Medium dose)_rep1

description:
sample 15-1-2
RCM_tonifying_HT29.txt


title: M029- 002CSX31Dmso


title: M015- 002CSSalDmso


title: HT29_BatchE_ethanol extract of Palmul-tang (High dose)_rep1

description:
sample 15-1-1
RCM_tonifying_HT29.txt


title: M088- 001AirSal


title: M003- 002AirSalDmso


title: HT29_BatchE_ethanol extract of Samul-tang (High dose)_rep3

description:
sample 14-3-4
RCM_tonifying_HT29.txt

value: Samul-tang ethanol extract 500 μg/mL


title: M099- 002CSSalDmso


title: HT29_BatchE_ethanol extract of Samul-tang (Low dose)_rep3

description:
sample 14-3-6
RCM_tonifying_HT29.txt

value: Samul-tang ethanol extract 20 μg/mL


title: M086- 001AirSal


title: HT29_BatchE_ethanol extract of Palmul-tang (Low dose)_rep2

description:
sample 15-2-3
RCM_tonifying_HT29.txt


title: M065- 001CSX31


title: HT29_BatchE_ethanol extract of Sagunja-tang (Medium dose)_rep3

description:
sample 14-3-2
RCM_tonifying_HT29.txt

value: Sagunja-tang ethanol extract 100 μg/mL


title: M016- 002CSSalDmso


title: BMDM_peak68866_2h

data_processing:
The fastq file containing all reads was concerted into a format compatible with downstream processing, accomplished through the "–fastq2raw" function within the pipeline. De-multiplexing was conducted based on barcodes and reading primer sequences specific to each library. The "–map" function was utilized to map reads to a fragmented mm9 genome, virtually digested by the restriction enzyme. Normalization and graphing were executed using the "–nearcis" function, with default settings employed throughout, except for adjusting the ylim of the trend line to enhance the visualization of promoter-enhancer or promoter-boundary interactions.
When using R.4C-Ker, a reduced genome was constructed via Bowtie2, containing only sequences flanking the primary restriction enzyme sites (51 bp on both sides). Reads were then de-multiplexed, and barcode and primer sequences were trimmed using a custom script. The trimmed reads were mapped to the reduced genome by Bowtie2 with the specified option –p 12 –N 0. To eliminate self-ligated and undigested fragments, the fragments preceding and following the bait fragment were excluded. Near-cis interactions were scrutinized using the "nearBaitAnalysis" function in 4C-Ker, with default settings applied.
To visualize the interactions, R package ggplot2 was used to generate the line graphs showing normalized counts across the selected genomic regions.
Assembly: mm9
Supplementary files format and content: bed
Library strategy: 4C

source_name: Bone marrow

growth_protocol: Bone marrow precursors were grown in BMDM media (20% FBS, 10% CMG condition medium [containing M-CSF], 1x Pen-Strep [GIBCO, #15140-122], 1x L-Glutamine [GIBCO, #25030-081], 0.5 mM sodium pyruvate [GIBCO, #11360-070] in Dubecco’s Modified Eagle Medium) for 6 days to obtain mature BMDMs prior to stimulation.

extract_protocol:
We crosslinked the lipid-A treated BMDMs with 1% formaldehyde for 10 min and quenched them with 2M Tris (0.125M final concentration) for 10 min at room temperature. Cells were lysed for 30 min in 1mL cold lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, and 0.2% NP-40 supplemented with protease inhibitor). Nuclei were pelleted and resuspended in 500μL of the first restriction enzyme buffer with 0.1% SDS and incubated for 1 hr at 37oC at 1200 rpm. Triton-X 100 (final concentration 0.8%) was then added, following incubation for 1 hr. 400 units of the first restriction enzyme (DpnII) was then added to the samples, incubated at 37oC for 6 hr, following by addition of another 400 units of enzyme for overnight digestion. The first restriction enzyme was inactivated by incubating at 65oC for 10 min and samples were placed on ice immediately. Ligation buffer (66mM Tris-HCl pH 7.5, 5mM MgCl2, 5mM DTT, 1mM ATP) was added to dilute samples to a total volume of 7mL. 2,000 units of T4 DNA ligase was added to each sample and incubated at 16oC overnight to achieve proximal ligation. Reverse crosslinking and RNA digestion were performed and followed by phenol/chloroform DNA extraction. Ligation efficiency was confirmed by running the samples before and after ligation on a 1% agarose gel. The ligated DNA was digested overnight in a volume of 500μL with 200 units of the second restriction enzyme (CviQI). The digested samples were diluted in the ligation buffer into a total volume of 7mL. Proximal ligation was performed by adding 4000 units of T4 DNA ligase, followed by overnight incubation at 16oC. The 4C template DNA was extracted by phenol/chloroform and ethanol precipitation. The extracted DNA was further purified using the QIAquick PCR Purificatioin kit.
To generate the library for subsequent sequencing, reading and non-reading primers were designed for each viewpoint. Choice-Taq™ DNA Polymerase was used to PCR amplify 4C DNA templates containing the viewpoints in four of 25μL reactions. The PCR products were purified with the illustra™ GFX PCR DNA and Gel Band Purification Kit to remove primer dimers. Libraries were sequenced for 50-bp single-end reads on the Illumina Hiseq2000 platform.

treatment_protocol: BMDMs from C57/B16 mice were stimulated with lipid-A for 0 and 2 hours.

value: Bone marrow

value: primary culture

value: bone marrow-derived macrophages

value: wildtype

value: lipid-A stimulated


title: HT29_BatchE_ethanol extract of Samul-tang (Low dose)_rep2

description:
sample 14-2-6
RCM_tonifying_HT29.txt


title: M014- 002CSSalDmso


title: HT29_BatchE_ethanol extract of Samul-tang (Medium dose)_rep2

description:
sample 14-2-5
RCM_tonifying_HT29.txt

value: Samul-tang ethanol extract 100 μg/mL


title: BMDM_peak68866_0h

value: Unstimulated


title: HT29_BatchE_ethanol extract of Samul-tang (High dose)_rep2

description:
sample 14-2-4
RCM_tonifying_HT29.txt


title: M002- 002AirSalDmso


title: HT29_BatchE_ethanol extract of Sagunja-tang (Low dose)_rep2

description:
sample 14-2-3
RCM_tonifying_HT29.txt

value: Sagunja-tang ethanol extract 20 μg/mL


title: HT29_BatchE_ethanol extract of Sagunja-tang (Medium dose)_rep2

description:
sample 14-2-2
RCM_tonifying_HT29.txt


title: M110- 002CSX31Dmso


title: B_1000_p2

city: Greensboro

first: Ramji

middle: Kumar

last: Bhandari

state: NC

address: 321 McIver St

department: Biology

institute: University of North Carolina Greensboro

data_processing:
Sequencing reads from each sample were mapped to medaka reference transcripts (Ensembl version 95) using HISAT2 software with default parameters. Only uniquely mapped reads were used for subsequent analysis. Cufflinks software (http://cole-trapnell-lab.github.io/cufflinks/, University of Washington) was used to conduct differentially expressed gene (DEG) analysis on the raw count data.
Genome_build: ASM223467v1.95
Supplementary_files_format_and_content: FPKM

organism: Oryzias latipes

source_name: Primordial germ cells

growth_protocol: The olvas-GFP medaka fish was used in the present study. Fish were raised in 38-liter tanks with constant aeration and water flow of about 76 liters/day. The water temperature was maintained at 25 ± 1 °C under a light: dark cycle of 14 h: 10 h.

extract_protocol:
Primordial germ cells (PGCs) were isolated according to the method developed by Wang and Bhandari (2020). Genomic DNA and total RNA were extracted using ZR-Duet™ DNA/RNA MiniPrep kit (Zymo Research, Irvine, U.S.A.).
RNA sequencing libraries were prepared with NEBNext® UltraTM II RNA Library Prep Kit for Illumina accordingly to the manufacturer’s instructional manual. For each sample, 500ng total RNA was used.
RNAseq libraries were sequenced on the Illumina platform using the 150 bp pair-end sequencing strategy.

treatment_protocol: The (KCIO4) solutions were prepared (0, 10, 100 and 1000 μg/L) and stored at 4 °C in dark. Fertilized eggs were incubated in a 10 ml exposure solution, which was replaced daily with working solution. Upon hatching, Fry was transferred to Petri dishes containing 30ml of exposure solution, which was replaced daily. Exposure lasted until the 15-dpf (days post fertilization).

value: PGC

tag: replicate


title: HT29_BatchE_ethanol extract of Samul-tang (Medium dose)_rep3

description:
sample 14-3-5
RCM_tonifying_HT29.txt


title: M098- 002CSSalDmso

value: Lung


title: HT29_BatchE_ethanol extract of Sagunja-tang (High dose)_rep2

description:
sample 14-2-1
RCM_tonifying_HT29.txt

value: Sagunja-tang ethanol extract 500 μg/mL


title: HT29_BatchE_Vehicle(DMSO)_rep2

description:
sample E1-2-1
RCM_tonifying_HT29.txt

value: 0.1% DMSO


title: HT29_BatchD_ethanol extract of Samul-tang (Low dose)_rep1

description:
sample 14-1-6
RCM_tonifying_HT29.txt


title: M111- 002CSX31Dmso

value: BALB/c


title: HT29_BatchE_Vehicle(DMSO)_rep1

description:
sample E1-1-1
RCM_tonifying_HT29.txt


title: M085- 001AirSal


title: B_1000_p1


title: M027- 002CSX31Dmso


title: HT29_BatchE_ethanol extract of Sagunja-tang (High dose)_rep3

description:
sample 14-3-1
RCM_tonifying_HT29.txt


title: HT29_BatchE_ethanol extract of Sagunja-tang (Low dose)_rep3

description:
sample 14-3-3
RCM_tonifying_HT29.txt


title: M056- 001CSSal


title: B_100_p2


title: HT29_BatchD_ethanol extract of Samul-tang (High dose)_rep1

description:
sample 14-1-4
RCM_tonifying_HT29.txt


title: HT29_BatchD_ethanol extract of Sagunja-tang (Low dose)_rep1

description:
sample 14-1-3
RCM_tonifying_HT29.txt


title: M043- 001AirX31


title: HT29_BatchD_ethanol extract of Sagunja-tang (High dose)_rep1

description:
sample 14-1-1
RCM_tonifying_HT29.txt


title: B_1000_p3


title: HT29_BatchD_ethanol extract of Cinnamomi Cortex (Low dose)_rep3

description:
sample 13-3-6
RCM_tonifying_HT29.txt

value: Cinnamomi Cortex ethanol extract 20 μg/mL


title: B_10_p3

value: 10 μg/L


title: HT29_BatchD_ethanol extract of Cinnamomi Cortex (Medium dose)_rep3

description:
sample 13-3-5
RCM_tonifying_HT29.txt

value: Cinnamomi Cortex ethanol extract 100 μg/mL


title: M013- 002CSSalDmso


title: HT29_BatchD_ethanol extract of Astragali Radix (Low dose)_rep3

description:
sample 13-3-3
RCM_tonifying_HT29.txt

value: Astragali Radix ethanol extract 20 μg/mL


title: B_10_p2


title: M001- 002AirSalDmso


title: HT29_BatchD_ethanol extract of Cinnamomi Cortex (High dose)_rep3

description:
sample 13-3-4
RCM_tonifying_HT29.txt

value: Cinnamomi Cortex ethanol extract 500 μg/mL


title: HT29_BatchD_ethanol extract of Astragali Radix (High dose)_rep3

description:
sample 13-3-1
RCM_tonifying_HT29.txt

value: Astragali Radix ethanol extract 500 μg/mL


title: B_10_p1


title: M109- 002CSX31Dmso


title: B_0_p3

value: Control


title: HT29_BatchD_ethanol extract of Cinnamomi Cortex (Medium dose)_rep2

description:
sample 13-2-5
RCM_tonifying_HT29.txt


title: HT29_BatchD_ethanol extract of Cinnamomi Cortex (Low dose)_rep2

description:
sample 13-2-6
RCM_tonifying_HT29.txt


title: B_0_p2


title: B_100_p3


title: HT29_BatchD_ethanol extract of Astragali Radix (Medium dose)_rep3

description:
sample 13-3-2
RCM_tonifying_HT29.txt

value: Astragali Radix ethanol extract 100 μg/mL


title: HT29_BatchD_ethanol extract of Cinnamomi Cortex (High dose)_rep2

description:
sample 13-2-4
RCM_tonifying_HT29.txt


title: M055- 001CSSal


title: HT29_BatchD_ethanol extract of Astragali Radix (Low dose)_rep2

description:
sample 13-2-3
RCM_tonifying_HT29.txt


title: HT29_BatchD_ethanol extract of Astragali Radix (Medium dose)_rep2

description:
sample 13-2-2
RCM_tonifying_HT29.txt


title: B_100_p1


title: M097- 002CSSalDmso


title: HT29_BatchD_ethanol extract of Sagunja-tang (Medium dose)_rep1

description:
sample 14-1-2
RCM_tonifying_HT29.txt

value: Sagunja-tang ethanol extract 100 μg/mL


title: HT29_BatchD_ethanol extract of Astragali Radix (High dose)_rep2

description:
sample 13-2-1
RCM_tonifying_HT29.txt


title: M026- 002CSX31Dmso


title: HT29_BatchD_ethanol extract of Cinnamomi Cortex (Low dose)_rep1

description:
sample 13-1-6
RCM_tonifying_HT29.txt


title: M042- 001AirX31


title: M025- 002CSX31Dmso


title: HT29_BatchD_ethanol extract of Cinnamomi Cortex (High dose)_rep1

description:
sample 13-1-4
RCM_tonifying_HT29.txt


title: HT29_BatchD_ethanol extract of Cinnamomi Cortex (Medium dose)_rep1

description:
sample 13-1-5
RCM_tonifying_HT29.txt


title: HT29_BatchD_ethanol extract of Astragali Radix (Low dose)_rep1

description:
sample 13-1-3
RCM_tonifying_HT29.txt


title: M012- 002CSSalDmso


title: SLE_DMSO

first: Henan

last: XU

address: No.94 Weijin Road

department: immunology

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio base  quality less than or equal to 5) is more than 20%
Removing reads whose unknown  base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: hg38
Supplementary files format and content: Excel table with TPM value for diffirential expressing genes in corresponding signaling pathways in all samples.

source_name: blood

extract_protocol:
Total RNA was extracted from the PBMC using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. PBMC were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After   deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA)
Limited RNA（more than 200pg, high-quality）was amplified with oligo-dT and dNTPs, incubated at 72℃ and immediately put back on ice, then reverse transcribed to cDNA based on polyA tail. The template was switched to the 5' end of the RNA and the fulllength cDNA was generated by PCR. Agilent 2100 bioanalyzer instrument (Thermo Fisher Scientific, MA, USA) was used to determine the average molecule length of PCR product. Purified cDNA from previous steps was fragmented into small pieces with fragment buffer by PCR, and the product was purified and selected by the Agencourt AMPure XP-Medium kit (Thermo Fisher Scientific, USA). cDNA was quantified by Agilent Technologies 2100 bioanalyzer. The double stranded PCR product undergo QC step was heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library.  The final library was quantitated in two ways in order to ensure the high quality of the sequencing data: Determined the average molecule length used the Agilent 2100 bioanalyzer instrument, quantified library used real-time quantitative PCR (qPCR).The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular , DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on DNBSEQ G400 platform(BGI-Shenzhen, China) .

value: blood

value: PBMC

value: Peripheral blood mononuclear cell

value: DMSO


title: HC


title: HT29_BatchD_ethanol extract of Astragali Radix (Medium dose)_rep1

description:
sample 13-1-2
RCM_tonifying_HT29.txt


title: HT29_BatchD_ethanol extract of Astragali Radix (High dose)_rep1

description:
sample 13-1-1
RCM_tonifying_HT29.txt


title: HT29_BatchD_ethanol extract of Rehmanniae Radix Preparata (Low dose)_rep3

description:
sample 12-3-6
RCM_tonifying_HT29.txt

value: Rehmanniae Radix Preparata ethanol extract 20 μg/mL


title: biol rep 3: SLE_S_low_3

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio base  quality less than or equal to 5) is more than 20%
Removing reads whose unknown  base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: hg38
Supplementary files format and content: Table with average TPM value for samples with high or low spermine content

tag: condition

value: SLE

tag: phenotype

value: Low spermine content

value: interferon alpha


title: biol rep 2: SLE_S_low_2


title: HT29_BatchD_ethanol extract of Rehmanniae Radix Preparata (High dose)_rep3

description:
sample 12-3-4
RCM_tonifying_HT29.txt

value: Rehmanniae Radix Preparata ethanol extract 500 μg/mL


title: M096- 002AirSalDmso

value: Lung

value: BALB/c


title: B_0_p1

value: PGC


title: HT29_BatchD_ethanol extract of Cnidii Rhizoma (Medium dose)_rep3

description:
sample 12-3-2
RCM_tonifying_HT29.txt

value: Cnidii Rhizoma ethanol extract 100 μg/mL


title: HT29_BatchD_ethanol extract of Cnidii Rhizoma (Low dose)_rep3

description:
sample 12-3-3
RCM_tonifying_HT29.txt

value: Cnidii Rhizoma ethanol extract 20 μg/mL


title: biol rep 1: SLE_S_low_1


title: HT29_BatchD_ethanol extract of Cnidii Rhizoma (High dose)_rep3

description:
sample 12-3-1
RCM_tonifying_HT29.txt

value: Cnidii Rhizoma ethanol extract 500 μg/mL


title: HT29_BatchD_ethanol extract of Rehmanniae Radix Preparata (Medium dose)_rep3

description:
sample 12-3-5
RCM_tonifying_HT29.txt

value: Rehmanniae Radix Preparata ethanol extract 100 μg/mL


title: M054- 001CSSal


title: HT29_BatchD_ethanol extract of Rehmanniae Radix Preparata (Low dose)_rep2

description:
sample 12-2-6
RCM_tonifying_HT29.txt


title: biol rep 3: SLE_S_high_3

value: High spermine content


title: SLE_SPM

value: blood

value: spermine


title: HT29_BatchD_ethanol extract of Rehmanniae Radix Preparata (Medium dose)_rep2

description:
sample 12-2-5
RCM_tonifying_HT29.txt


title: M041- 001AirX31


title: M083- 001AirSal


title: HT29_BatchD_ethanol extract of Rehmanniae Radix Preparata (High dose)_rep2

description:
sample 12-2-4
RCM_tonifying_HT29.txt


title: HT29_BatchD_ethanol extract of Cnidii Rhizoma (Low dose)_rep2

description:
sample 12-2-3
RCM_tonifying_HT29.txt


title: biol rep 2: SLE_S_high_2

value: PBMC

value: Peripheral blood mononuclear cell


title: HT29_BatchD_ethanol extract of Cnidii Rhizoma (Medium dose)_rep2

description:
sample 12-2-2
RCM_tonifying_HT29.txt


title: biol rep 1: SLE_S_high_1


title: M108- 002CSX31Dmso


title: HT29_BatchD_ethanol extract of Cnidii Rhizoma (High dose)_rep2

description:
sample 12-2-1
RCM_tonifying_HT29.txt


title: MC38 cells, shdusp18_2

city: Zhengzhou

first: Xiaojun

last: Zhou

state: Henan

address: 100 Lianhua Street

department: College of Bioengineering

institute: Henan University of Technology

description: gene.count.matrix.xlsx

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

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

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

value: CRC cells

value: Dusp 18 knockdown


title: MC38 cells, shdusp18_3

description: gene.count.matrix.xlsx


title: HT29_BatchD_ethanol extract of Rehmanniae Radix Preparata (Low dose)_rep1

description:
sample 12-1-6
RCM_tonifying_HT29.txt

value: Rehmanniae Radix Preparata ethanol extract 20 μg/mL


title: biol rep 3: HC_3

value: control

value: Healthy control

value: interferon alpha


title: HT29_BatchD_ethanol extract of Rehmanniae Radix Preparata (Medium dose)_rep1

description:
sample 12-1-5
RCM_tonifying_HT29.txt


title: MC38 cells, shdusp18_1

description: gene.count.matrix.xlsx


title: HT29_BatchD_ethanol extract of Rehmanniae Radix Preparata (High dose)_rep1

description:
sample 12-1-4
RCM_tonifying_HT29.txt

value: Rehmanniae Radix Preparata ethanol extract 500 μg/mL


title: HT29_BatchD_ethanol extract of Cnidii Rhizoma (Low dose)_rep1

description:
sample 12-1-3
RCM_tonifying_HT29.txt


title: biol rep 2: HC_2


title: biol rep 1: HC_1


title: MC38 cells, shCt_3

description: gene.count.matrix.xlsx

value: WT


title: HT29_BatchD_ethanol extract of Cnidii Rhizoma (Medium dose)_rep1

description:
sample 12-1-2
RCM_tonifying_HT29.txt

value: Cnidii Rhizoma ethanol extract 100 μg/mL


title: MC38 cells, shCt_2

description: gene.count.matrix.xlsx


title: MC38 cells, shCt_1

description: gene.count.matrix.xlsx


title: HT29_BatchD_ethanol extract of Paeoniae Radix (Medium dose)_rep3

description:
sample 11-3-5
RCM_tonifying_HT29.txt

value: Paeoniae Radix ethanol extract 100 μg/mL


title: HT29_BatchD_ethanol extract of Paeoniae Radix (High dose)_rep3

description:
sample 11-3-4
RCM_tonifying_HT29.txt

value: Paeoniae Radix ethanol extract 500 μg/mL


title: HT29_BatchD_ethanol extract of Paeoniae Radix (Low dose)_rep3

description:
sample 11-3-6
RCM_tonifying_HT29.txt

value: Paeoniae Radix ethanol extract 20 μg/mL


title: HT29_BatchD_ethanol extract of Angelicae Gigantis Radix (Low dose)_rep3

description:
sample 11-3-3
RCM_tonifying_HT29.txt

value: Angelicae Gigantis Radix ethanol extract 12.8 μg/mL


title: HT29_BatchD_ethanol extract of Angelicae Gigantis Radix (High dose)_rep3

description:
sample 11-3-1
RCM_tonifying_HT29.txt

value: Angelicae Gigantis Radix ethanol extract 320 μg/mL


title: HC3, IL2

city: Paris

first: Quentin

last: Riller

address: 24 Boulevard du Montparnasse

country: France

institute: INSERM UMRS 1163, Imagine Institute

data_processing:
FASTQ files were mapped to the HG38reference using HISAT2 and counted by featureCounts from the Subread R package.
Assembly: Ensembl genome GRCh38.91
Supplementary files format and content: Raw data count

source_name: Activated T cells

growth_protocol: The expanded T cells were starved of IL-2 for 24h, plated at cell concentration of 1.10^6 cells/ ml in Panserin medium

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen) and quality was assessed using Fragment Analyzer (Agilent Technologies) with RNA Integrity Number >8 and 28S/18S ratio around 2.
Messenger RNA was finally converted to complementary DNA by capture of poly-A+ RNA, amplified and sequenced to a depth of at least 50 million reads using the Illumina technology (Novaseq 6000 sequencer) at the Genomic Plateform of Imagine Institut. R v3.6.1 was used for analysis, FASTQ files were mapped to the HG38reference using HISAT2 and counted by featureCounts from the Subread R package.
Read count normalizations and groups comparisons were performed by three independent and complementary statistical methods: DESeq2 (v1.24.0), edgeR (v3.26.8), Limma Voom (v3.40.6). Flags were computed from counts normalized to the mean coverage. All normalized counts <20 were considered as background (flag 0) and >=20 as signal (flag=1). The results of the three methods were filtered at pvalue<=0.05 and lists of genes statistically overexpressed with fold change of 1.2 comparing patient and control groups are used for pathway enrichments.

treatment_protocol: Cells were left unstimulated or stimulated with IFN-a (104U/ml, Millipore, #IF007) or IL-2 (104U/ml) during 3h at 37°C.

value: Activated T cells


title: 201T2pulmon

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

data_processing:
Reads were aligned to GRCm39 mouse genome with “Rbowtie2”
counts extracted with featureCounts function from “Rsubread” and gencode annotation release 27 (gencode.vM27.annotation.gtf)
DESeq2 was used to identify genes that were differentially expressed in the 46LCNEC_allo and 57SCLC_allo tumors versus non-tumor lung (Lung). Gene set enrichment analyses were conducted with GSEA (version 4.1.0) software 74, using the DESeq2 normalized count values.
Assembly: GRCm39
Supplementary files format and content: normalized counts

source_name: tumor

extract_protocol:
Tissues and cells were embedded in RNALater (Ambion Inc., Austin, TX, USA) and RNA was isolated and purified using miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s instructions. RNA yield and quality were determined using Agilent 2100 Bioanalyzer.
RNA sequencing was performed after poly-A selection using Illumina NovaSeq 2x150 bp sequencing.

value: tumor


title: HT29_BatchD_ethanol extract of Angelicae Gigantis Radix (Medium dose)_rep3

description:
sample 11-3-2
RCM_tonifying_HT29.txt

value: Angelicae Gigantis Radix ethanol extract 64 μg/mL


title: HT29_BatchD_ethanol extract of Paeoniae Radix (Low dose)_rep2

description:
sample 11-2-6
RCM_tonifying_HT29.txt


title: HC3, NS

value: NS


title: 201TTraquea


title: 201T1pulmon


title: HT29_BatchD_ethanol extract of Paeoniae Radix (Medium dose)_rep2

description:
sample 11-2-5
RCM_tonifying_HT29.txt


title: HT29_BatchD_ethanol extract of Cnidii Rhizoma (High dose)_rep1

description:
sample 12-1-1
RCM_tonifying_HT29.txt

value: Cnidii Rhizoma ethanol extract 500 μg/mL


title: HT29_BatchD_ethanol extract of Angelicae Gigantis Radix (Low dose)_rep2

description:
sample 11-2-3
RCM_tonifying_HT29.txt


title: HC2, NS


title: HT29_BatchD_ethanol extract of Paeoniae Radix (High dose)_rep2

description:
sample 11-2-4
RCM_tonifying_HT29.txt


title: HC2, IL2


title: 159TPulmonI


title: HC2, IFNa

value: IFNa


title: 159TPulmonD


title: HT29_BatchD_ethanol extract of Angelicae Gigantis Radix (Medium dose)_rep2

description:
sample 11-2-2
RCM_tonifying_HT29.txt


title: HT29_BatchD_ethanol extract of Angelicae Gigantis Radix (High dose)_rep2

description:
sample 11-2-1
RCM_tonifying_HT29.txt


title: HT29_BatchD_ethanol extract of Paeoniae Radix (Low dose)_rep1

description:
sample 11-1-6
RCM_tonifying_HT29.txt


title: HC1, NS


title: HT29_BatchD_Vehicle(DMSO)_rep3

description:
sample D1-3-1
RCM_tonifying_HT29.txt

value: 0.1% DMSO


title: HC1, IL2


title: HT29_BatchD_ethanol extract of Paeoniae Radix (High dose)_rep1

description:
sample 11-1-4
RCM_tonifying_HT29.txt


title: 153TTraquea


title: 156T3


title: HC3, IFNa


title: HC1, IFNa


title: HT29_BatchD_Vehicle(DMSO)_rep1

description:
sample D1-1-1
RCM_tonifying_HT29.txt


title: CTL187PulmonI

source_name: normal lung

value: normal lung


title: D1, NS


title: HT29_BatchC_ethanol extract of Angelicae Gigantis Radix (Low dose)_rep1

description:
sample 11-1-3
RCM_tonifying_HT29.txt


title: HT29_BatchC_ethanol extract of Angelicae Gigantis Radix (Medium dose)_rep1

description:
sample 11-1-2
RCM_tonifying_HT29.txt


title: CTL146


title: D1, IL2


title: HT29_BatchC_ethanol extract of Angelicae Gigantis Radix (High dose)_rep1

description:
sample 11-1-1
RCM_tonifying_HT29.txt


title: HT29_BatchC_ethanol extract of Panax Ginseng (Low dose)_rep3

description:
sample 10-3-6
RCM_tonifying_HT29.txt

value: Panax Ginseng ethanol extract 20 μg/mL


title: CTL144


title: D1, IFNa


title: HT29_BatchC_ethanol extract of Panax Ginseng (Medium dose)_rep3

description:
sample 10-3-5
RCM_tonifying_HT29.txt

value: Panax Ginseng ethanol extract 100 μg/mL


title: HT29_BatchC_ethanol extract of Panax Ginseng (High dose)_rep3

description:
sample 10-3-4
RCM_tonifying_HT29.txt

value: Panax Ginseng ethanol extract 500 μg/mL


title: CTL117


title: C1, NS


title: HT29_BatchC_ethanol extract of Glycyrrhizae Radix (Low dose)_rep3

description:
sample 10-3-3
RCM_tonifying_HT29.txt

value: Glycyrrhizae Radix ethanol extract 14 μg/mL


title: HT29_BatchC_ethanol extract of Glycyrrhizae Radix (Medium dose)_rep3

description:
sample 10-3-2
RCM_tonifying_HT29.txt

value: Glycyrrhizae Radix ethanol extract 70 μg/mL


title: HT29_BatchC_ethanol extract of Glycyrrhizae Radix (High dose)_rep3

description:
sample 10-3-1
RCM_tonifying_HT29.txt

value: Glycyrrhizae Radix ethanol extract 350 μg/mL


title: CTL116


title: C1, IL2


title: C1, IFNa


title: HT29_BatchC_ethanol extract of Panax Ginseng (Medium dose)_rep2

description:
sample 10-2-5
RCM_tonifying_HT29.txt


title: HT29_BatchD_Vehicle(DMSO)_rep2

description:
sample D1-2-1
RCM_tonifying_HT29.txt


title: HT29_BatchC_ethanol extract of Panax Ginseng (High dose)_rep2

description:
sample 10-2-4
RCM_tonifying_HT29.txt


title: HT29_BatchE_Vehicle(DMSO)_rep3

description:
sample E1-3-1
RCM_tonifying_HT29.txt


title: HT29_BatchC_ethanol extract of Glycyrrhizae Radix (Low dose)_rep2

description:
sample 10-2-3
RCM_tonifying_HT29.txt


title: B1, NS


title: BM1_spm_I_3h

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone marrow derived macropahges

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

value: Bone marrow derived macropahges

value: macrophage


title: BM2_spm_I_0h


title: BM2_spm_I_3h


title: HT29_BatchC_ethanol extract of Panax Ginseng (Low dose)_rep1

description:
sample 10-1-6
RCM_tonifying_HT29.txt


title: BM1_spm_I_0h


title: HT29_BatchC_ethanol extract of Glycyrrhizae Radix (Medium dose)_rep2

description:
sample 10-2-2
RCM_tonifying_HT29.txt


title: HT29_BatchD_ethanol extract of Samul-tang (Medium dose)_rep1

description:
sample 14-1-5
RCM_tonifying_HT29.txt

value: Samul-tang ethanol extract 100 μg/mL


title: B1, IFNa

value: Activated T cells


title: HT29_BatchC_ethanol extract of Panax Ginseng (High dose)_rep1

description:
sample 10-1-4
RCM_tonifying_HT29.txt


title: HT29_BatchC_ethanol extract of Panax Ginseng (Medium dose)_rep1

description:
sample 10-1-5
RCM_tonifying_HT29.txt


title: A2, NS


title: HT29_BatchC_ethanol extract of Glycyrrhizae Radix (Low dose)_rep1

description:
sample 10-1-3
RCM_tonifying_HT29.txt


title: BM2_PBS_I_3h


title: BM1_PBS_I_3h


title: HT29_BatchD_ethanol extract of Paeoniae Radix (Medium dose)_rep1

description:
sample 11-1-5
RCM_tonifying_HT29.txt

value: Paeoniae Radix ethanol extract 100 μg/mL


title: HT29_BatchC_ethanol extract of Glycyrrhizae Radix (High dose)_rep1

description:
sample 10-1-1
RCM_tonifying_HT29.txt


title: HT29_BatchC_ethanol extract of Panax Ginseng (Low dose)_rep2

description:
sample 10-2-6
RCM_tonifying_HT29.txt


title: HT29_BatchC_ethanol extract of Glycyrrhizae Radix (Medium dose)_rep1

description:
sample 10-1-2
RCM_tonifying_HT29.txt


title: A2, IFNa


title: HT29_BatchC_ethanol extract of Atractylodis Rhizoma (High dose)_rep3

description:
sample 9-3-4
RCM_tonifying_HT29.txt

value: Atractylodis Rhizoma ethanol extract 500 μg/mL


title: BM2_PBS_I_0h


title: HT29_BatchC_ethanol extract of Atractylodis Rhizoma (Medium dose)_rep3

description:
sample 9-3-5
RCM_tonifying_HT29.txt

value: Atractylodis Rhizoma ethanol extract 100 μg/mL


title: A2, IL2


title: HT29_BatchC_ethanol extract of Atractylodis Rhizoma (Low dose)_rep3

description:
sample 9-3-6
RCM_tonifying_HT29.txt

value: Atractylodis Rhizoma ethanol extract 20 μg/mL


title: A1, NS

value: NS


title: HT29_BatchC_ethanol extract of Glycyrrhizae Radix (High dose)_rep2

description:
sample 10-2-1
RCM_tonifying_HT29.txt


title: BM1_PBS_I_0h


title: HT29_BatchC_ethanol extract of Poria Cocos (Medium dose)_rep3

description:
sample 9-3-2
RCM_tonifying_HT29.txt

value: Poria Cocos ethanol extract 100 μg/mL


title: B1, IL2


title: T_cells, monocultured, scRNA-seq, bechmark2

city: Philadelphia

first: Bo

last: Li

state: PA

address: 3501 Civic Center Blvd

department: Department of Pathology and Laboratory Medicine

institute: The Children’s Hospital of Philadelphia, University of Pennsylvania

description: 5' gene expression library (10X Genomics)

data_processing:
The Cell Ranger (v6.0.0) Software Suite was used to process the raw sequence data into gene expression profiles. The fastq files for each sample were processed with Cell Ranger count, which was used to align to mm10 reference genome, filter and quantify.
The Cell Ranger ATAC pipeline (v2.0.0)  was used to process the raw .fastq.gz data of  mtscATAC-seq data. The raw data from mtscATAC-seq libraries underwent alignment with the mm10 reference via the cellranger-atac count command
MERCI-mtSNP (v1.3.0）was used to call mitochondrial variants from the bam files generated by  cellranger count  or cellranger-atac count command
Seurat was used to deal with scRNA-seq data, high-quality cell were remained with < 10% MT percentage
Used MERCI pacakge to get the high-quality cell with high coverage in MT genome
Assembly: mm10
Supplementary files format and content: cell_information is .txt file, providing the cell annotations.
Supplementary files format and content: mtSNV_profile is a .txt file and generated by MERCI-mtSNP , providing the cell-level mitochondrial variants for high-quality cells of each sample.
Supplementary files format and content: MT_covearge_cells  is a .txt file and generated by MERCI-mtSNP, providing the read coverage inforamtion in the MT gnome for each cell.
Supplementary files format and content: normalized_exp_matrix is .txt file and generated by Seurat pipeline, providing the normalized gene expression data for each scRNA-seq sample.

molecule: polyA RNA

source_name: Spleen

extract_protocol:
10x Genomic single cell 5’ VDJ library, , Gel Bead & Multiplex Kit and Chip Kit; 10x Chromium Controller and the Chromium Next GEM Single Cell ATAC Kit v2 (PN-1000406)  (CG000496 Rev-B)
Single-cell gene expression and TCR libraries were generated according to the manufacturer’s instructions.

value: Spleen

value: CD8 T cells


title: A1, IL2


title: HT29_BatchC_ethanol extract of Poria Cocos (High dose)_rep3

description:
sample 9-3-1
RCM_tonifying_HT29.txt

value: Poria Cocos ethanol extract 500 μg/mL


title: HT29_BatchC_ethanol extract of Poria Cocos (Low dose)_rep3

description:
sample 9-3-3
RCM_tonifying_HT29.txt

value: Poria Cocos ethanol extract 20 μg/mL


title: KP_cells, monocultured, scRNA-seq, bechmark2

source_name: KrasG12D/p53ko (KP)

value: KrasG12D/p53ko (KP)

value: lung cancer cells


title: A1, IFNa

value: IFNa


title: HT29_BatchC_ethanol extract of Atractylodis Rhizoma (Medium dose)_rep2

description:
sample 9-2-5
RCM_tonifying_HT29.txt


title: HT29_BatchC_ethanol extract of Atractylodis Rhizoma (Low dose)_rep2

description:
sample 9-2-6
RCM_tonifying_HT29.txt


title: HT29_BatchC_ethanol extract of Poria Cocos (Low dose)_rep2

description:
sample 9-2-3
RCM_tonifying_HT29.txt


title: KP_cells, cocultured, scRNA-seq, bechmark2


title: WD39, iPSC-derived motor neurons from healthy control, ROPI, 84h

city: Kanagawa

first: Satoru

last: Morimoto

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

department: Keio Regenerative Medicine Research Center (KRM)

country: Japan

institute: Keio University

description: SMART-seq

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

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

value: WT

value: ROPI


title: HT29_BatchC_ethanol extract of Poria Cocos (Medium dose)_rep2

description:
sample 9-2-2
RCM_tonifying_HT29.txt


title: WD39, iPSC-derived motor neurons from healthy control, ROPI, 36h

description: SMART-seq


title: HT29_BatchC_ethanol extract of Atractylodis Rhizoma (Low dose)_rep1

description:
sample 9-1-6
RCM_tonifying_HT29.txt


title: HT29_BatchC_ethanol extract of Poria Cocos (High dose)_rep2

description:
sample 9-2-1
RCM_tonifying_HT29.txt


title: KP_cells, monocultured, mtscRNA-seq, bechmark2

description: revised Chromium Next GEM Single Cell ATAC library (10x Genomics)


title: HT29_BatchC_ethanol extract of Atractylodis Rhizoma (Medium dose)_rep1

description:
sample 9-1-5
RCM_tonifying_HT29.txt


title: WD39, iPSC-derived motor neurons from healthy control, ROPI, 12h

description: SMART-seq


title: WD39, iPSC-derived motor neurons from healthy control, ROPI, 6h

description: SMART-seq


title: HT29_BatchC_ethanol extract of Atractylodis Rhizoma (High dose)_rep1

description:
sample 9-1-4
RCM_tonifying_HT29.txt


title: KP_cells, cocultured, mtscATAC-seq, bechmark2


title: T_cells, monocultred, scRNA-seq, benchmark1


title: HT29_BatchC_ethanol extract of Atractylodis Rhizoma (High dose)_rep2

description:
sample 9-2-4
RCM_tonifying_HT29.txt


title: HT29_BatchC_water extract of Sibjeondaebo-tang (Low dose)_rep3

description:
sample 8-3-6
RCM_tonifying_HT29.txt

value: Sibjeondaebo-tang water extract 20 μg/mL


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

description:
sample 9-1-1
RCM_tonifying_HT29.txt


title: WD39, iPSC-derived motor neurons from healthy control, non, 84h

description: SMART-seq

value: non


title: WD39, iPSC-derived motor neurons from healthy control, non, 72h

description: SMART-seq


title: HT29_BatchC_water extract of Sibjeondaebo-tang (High dose)_rep3

description:
sample 8-3-4
RCM_tonifying_HT29.txt

value: Sibjeondaebo-tang water extract 500 μg/mL


title: KP_cells, cocultured, scRNA-seq, bechmark1


title: T_cells, monocultred, mtscATAC-seq, benchmark2


title: WD39, iPSC-derived motor neurons from healthy control, non, 60h

description: SMART-seq


title: KP_cells, monocultured, scRNA-seq, bechmark1


title: HT29_BatchC_water extract of Sibjeondaebo-tang (Medium dose)_rep3

description:
sample 8-3-5
RCM_tonifying_HT29.txt

value: Sibjeondaebo-tang water extract 100 μg/mL


title: HT29_BatchC_water extract of Palmul-tang (Low dose)_rep3

description:
sample 8-3-3
RCM_tonifying_HT29.txt

value: Palmul-tang water extract 20 μg/mL


title: WD39, iPSC-derived motor neurons from healthy control, non, 48h

description: SMART-seq


title: MC3T3-E1 cells, Untreated, 1hr [SAM225]

city: Chiba

first: Chisato

last: Sampei

address: Yamazaki 2641

institute: Tokyo university of science

data_processing:
Illumina Novaseq software used for basecalling
Sequence reads were trimmed for adaptor sequence, and mapped to mm10 whole genome using Hisat2.
Rea count extraction and normalization were perormed using python2.7.
Supplementary files format and content: mm10
Supplementary files format and content: Matrix table with gene counts for every gene and every sample after TMM normalization.

growth_protocol: MC3T3-E1 osteoblastic cells were maintained in α-MEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using FastGene RNA Basic Kit (NIPPON genetics).
RNA libraries were prepared for sequencing using standard illumina protocols.

treatment_protocol: 25,000 cells/cm2 were seeded  in 12-well plates. After 24hr, we treated with 10 nM PTH (Med Chem Express).

value: osteoblasts

value: Untreated


title: WD39, iPSC-derived motor neurons from healthy control, non, 36h

description: SMART-seq


title: MC3T3-E1 cells, PTH, 1hr [SAM226]

value: PTH


title: HT29_BatchC_water extract of Sibjeondaebo-tang (Low dose)_rep2

description:
sample 8-2-6
RCM_tonifying_HT29.txt


title: HT29_BatchC_water extract of Sibjeondaebo-tang (High dose)_rep2

description:
sample 8-2-4
RCM_tonifying_HT29.txt


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

description:
sample 9-1-2
RCM_tonifying_HT29.txt

value: Poria Cocos ethanol extract 100 μg/mL


title: HT29_BatchC_water extract of Palmul-tang (Low dose)_rep2

description:
sample 8-2-3
RCM_tonifying_HT29.txt


title: HT29_BatchC_water extract of Sibjeondaebo-tang (Medium dose)_rep2

description:
sample 8-2-5
RCM_tonifying_HT29.txt


title: biol rep 5 : Ifnar1-/-_PBS_d6_5

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Peripheral blood

value: Peripheral blood

value: whole blood

value: PBS/priatane induced day6


title: WD39, iPSC-derived motor neurons from healthy control, non, 24h

description: SMART-seq


title: HT29_BatchC_water extract of Palmul-tang (Medium dose)_rep2

description:
sample 8-2-2
RCM_tonifying_HT29.txt

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

value: Palmul-tang water extract 100 μg/mL


title: biol rep 4 : Ifnar1-/-_PBS_d6_4


title: HT29_BatchC_water extract of Palmul-tang (High dose)_rep2

description:
sample 8-2-1
RCM_tonifying_HT29.txt

value: Palmul-tang water extract 500 μg/mL


title: WD39, iPSC-derived motor neurons from healthy control, non, 12h

description: SMART-seq


title: HT29_BatchC_water extract of Sibjeondaebo-tang (Low dose)_rep1

description:
sample 8-1-6
RCM_tonifying_HT29.txt


title: WD39, iPSC-derived motor neurons from healthy control, non, 0h

description: SMART-seq


title: HT29_BatchC_water extract of Sibjeondaebo-tang (Medium dose)_rep1

description:
sample 8-1-5
RCM_tonifying_HT29.txt


title: HT29_BatchC_water extract of Palmul-tang (Medium dose)_rep3

description:
sample 8-3-2
RCM_tonifying_HT29.txt


title: HT29_BatchC_water extract of Palmul-tang (High dose)_rep3

description:
sample 8-3-1
RCM_tonifying_HT29.txt


title: biol rep 2 : Ifnar1-/-_PBS_d6_2


title: HT29_BatchC_water extract of Sibjeondaebo-tang (High dose)_rep1

description:
sample 8-1-4
RCM_tonifying_HT29.txt


title: HT29_BatchC_water extract of Palmul-tang (Low dose)_rep1

description:
sample 8-1-3
RCM_tonifying_HT29.txt


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

description: SMART-seq


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

description: SMART-seq


title: biol rep 1 : Ifnar1-/-_PBS_d6_1


title: HT29_BatchC_water extract of Palmul-tang (Medium dose)_rep1

description:
sample 8-1-2
RCM_tonifying_HT29.txt


title: HT29_BatchC_Vehicle(DMSO)_rep3

description:
sample C1-3-1
RCM_tonifying_HT29.txt

value: 0.1% DMSO


title: HT29_BatchC_Vehicle(DMSO)_rep2

description:
sample C1-2-1
RCM_tonifying_HT29.txt


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

description: SMART-seq

value: WT


title: biol rep 5 : Ifnar1-/-_PBS_d4_5

value: PBS/priatane induced day4


title: HT29_BatchC_water extract of Palmul-tang (High dose)_rep1

description:
sample 8-1-1
RCM_tonifying_HT29.txt