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| Status |
Public on Jun 21, 2024 |
| Title |
BatchB_water extract of Rehmanniae Radix Preparata (Medium dose)_rep1 |
| Sample type |
SRA |
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| Source name |
SW1783
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SW1783
treatment: Rehmanniae Radix Preparata water extract 100 microg/mL
time: 24hr
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| Treatment protocol |
Leibovitz's L-15, phosphate-buffered saline (PBS), TrypLE Express, penicillin-streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO) and QIAzol lysis reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA) and Qiagen (Germantown, MD, USA), respectively. The dried medicinal plants, prepared in compliance with the Korean Pharmacopoeia, were supplied from Kwangmyung-dang Medicinal Herbs Co. (Ulsan, Republic of Korea). The samples used in the experiment underwent organoleptic examination by Dr. Choi Goya, an herbal medicine organoleptic examination expert appointed by the Korea Food and Drug Administration, and were additionally identified at the species level by analyzing the DNA barcode region sequences. Voucher specimen were deposited in the Korean Herbarium of Standard Herbal Resources, Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Republic of Korea . All herbs and extracts can be obtained from the Oriental Medicine Resources Research Center (KIOM, https://oasis.kiom.re.kr/herblib). A hot water and 70% ethanol extract of each plant was prepared and supplied by KOC Biotech Co. (Daejeon, Republic of Korea). Briefly, dried plants (1,000 g) were pulverized and extracted in hot distilled water (10 L) for 3 h under a reflux extraction system (MS-DM609; MTOPS, Seoul, Republic of Korea) or in 70% ethanol (15L) for 1 h under ultrasonication system (VCP-20, Lab companion, Dajeon, Republic of Korea) twice. The extract solution was filtered through a 5 µm cartridge filter, concentrated in a rotary evaporator (Ev-1020, SciLab, Seoul, Republic of Korea), and then lyophilized in a freeze dryer (LP-20, Ilshin-Bio-Base, Dongduchen, Republic of Korea) to obtain the final extract. The extract was finely homogenized and packed in a glass bottle containing a desiccant silica gel. The decoction was prepared by mixing each extract, considering the composition ratio and extract yield of a single medicinal herb, and homogenized, according to the Korean Pharmacopoeia. For the in vitro treatment, extracts (100 mg) were vigorously vortexed for 30 min in 10 mL phosphate-buffered saline (PBS; Thermo Fisher Scientific, Rockford, IL, USA) containing 2% DMSO and then sterilized by filtering through a 0.22 µm membrane to obtain a stock solution (10 mg/mL); the stock solution was aliquoted in small volumes and stored at -80°C until use.
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| Growth protocol |
Human astrocytoma cell line, SW1783 (HTB-13) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). SW1783 cells were maintained in Leibovitz's L-15 medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 0% CO2 incubator. The cell was subcultured every 3 or 4 days, depending on the cell density.
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| Extracted molecule |
total RNA |
| Extraction 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MGISEQ-2000RS |
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| Description |
sample 5-1-5
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| 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
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| Submission date |
Oct 20, 2023 |
| Last update date |
Jun 21, 2024 |
| Contact name |
Musun Park |
| E-mail(s) |
bmusun@kiom.re.kr
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| Organization name |
Korean Institute of Oriental Medicine
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| Street address |
1672 Yuseong-daero, Yuseong-gu
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| City |
Daejeon |
| ZIP/Postal code |
34054 |
| Country |
South Korea |
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| Platform ID |
GPL30209 |
| Series (2) |
| GSE245898 |
Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_SW1783_batchB |
| GSE245912 |
Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_Tonifying_SW1783 |
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| Relations |
| BioSample |
SAMN37907494 |
| SRA |
SRX22157395 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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