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Sample GSM5516093 Query DataSets for GSM5516093
Status Public on Aug 19, 2021
Title Batch2 Wortmannin 1.95uM rep2
Sample type SRA
 
Source name A549
Organism Homo sapiens
Characteristics treatment: Wortmannin
treatment dose: 1.95uM
treatment_time: 24h
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.
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).
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model MGISEQ-2000RS
 
Description Wortmannin 1.95uM rep2
Batch2
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
 
Submission date Aug 12, 2021
Last update date Aug 21, 2021
Contact name Haeseung Lee
E-mail(s) haeseung@pusan.ac.kr
Organization name Pusan National University
Department College of Pharmacy
Street address 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu
City Busan
ZIP/Postal code 46241
Country South Korea
 
Platform ID GPL30209
Series (1)
GSE182007 Identification of novel efficacy of Bupleuri Radix based on the transcriptome analysis
Relations
BioSample SAMN20749520
SRA SRX11730395

Supplementary file Size Download File type/resource
GSM5516093_Batch2_122.clean.STAR.RSEM.genes.results.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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