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Status |
Public on Aug 19, 2021 |
Title |
Batch2 Saikosaponin B4 0.4uM rep3 |
Sample type |
SRA |
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Source name |
A549
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Organism |
Homo sapiens |
Characteristics |
treatment: Saikosaponin B4 treatment dose: 0.4uM treatment_time: 24h
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Treatment protocol |
We obtained lyophilized powder of water extract of Bupleuri Radix (W-BR; 3-10-0054) and ethanol extract of Bupleuri Radix (E-BR; 3-10-0097) from Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine (KIOM; Naju, Korea). Each powder was dissolved in 2% dimethyl sulfoxide (DMSO; Sigma, St Louis, MO, USA) to a final concentration of 10 mg/mL, filtered, and stored at -20°C until use.
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Growth protocol |
Human lung cancer A549 cell line (CCL-185) was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in RPMI1640 (Gibco, Grand Island, NY, USA) containing 10% heat-inactivated fetal bovine serum (FBS, Gibco), 100 IU/mL penicillin/100 mg/mL streptomycin (P/S; Gibco).
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from tissue using Maxwell (Promega) based method. One 1 mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction. The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved in the RT directional buffer, followed by second strand cDNA synthesis. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library. The double stranded library is quantified using QauntiFluor ONE dsDNA System (Promega). The library is circularized at 37 °C for 30 min, and then digested at 37 °C for 30 min, followed by cleanup of circularization product. To make DNA nanoball (DNB), the library is incubated at 30 °C for 25 min using DNB enzyme. Finally, Library was quantified by QauntiFluor ssDNA System (Promega). Sequencing of the prepared DNB was conducted on the MGIseq system (MGI) 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 |
Saikosaponin B4 0.4uM rep3 Batch2
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Data processing |
Quality check and adapter trimming of RNA-seq data were conducted using FastQC and TrimGalore (https://www.bioinformatics.babraham.ac.uk/), respectively. The cleaned reads were mapped to human genome assembly GRCh38 (hg38) via the STAR aligner (v2.7.3a). Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) with human gene annotation GRCh38.84. Genome_build: hg38 Supplementary_files_format_and_content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample
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Submission date |
Aug 12, 2021 |
Last update date |
Aug 21, 2021 |
Contact name |
Haeseung Lee |
E-mail(s) |
haeseung@pusan.ac.kr
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Organization name |
Pusan National University
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Department |
College of Pharmacy
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Street address |
63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu
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City |
Busan |
ZIP/Postal code |
46241 |
Country |
South Korea |
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Platform ID |
GPL30209 |
Series (1) |
GSE182007 |
Identification of novel efficacy of Bupleuri Radix based on the transcriptome analysis |
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Relations |
BioSample |
SAMN20749564 |
SRA |
SRX11730448 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5516146_Batch2_433.clean.STAR.RSEM.genes.results.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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