NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4193227 Query DataSets for GSM4193227
Status Public on Nov 27, 2019
Title Metformin [RNA-seq]
Sample type SRA
 
Source name H1299 cells
Organism Homo sapiens
Characteristics cell line: H1299
cell type: Non-small cell lung cancer cell line
passages: 10-15
treatment: Metformin
Treatment protocol The cells were treated with or without 5mM metformin (D150959, Sigma-Aldrich, St. Louis, MO).
Growth protocol The lung cancer cell line H1299 (ATCC, CRL-5803) was obtained from the American Type Culture Collection (ATCC). The cells were cultured in RPMI 1640 medium (Lonza, Allendale, NJ) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin, at 37°C in a humidified atmosphere with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cultured H1299 cells using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA). DNA contamination was removed using DNase, and the remaining RNA was broken into short fragments. The RNA fragments were reverse transcribed into cDNA, ligated with adaptors, and PCR amplified. The amplified cDNAs were then selected by a range of sizes and sequenced using a next-generation sequencing device (NovaSeq 6000 System).
The sequence library was mapped to the reference genome UCSC hg19 using the Bowtie2 program.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing After sequencing, the low-quality reads and PCR duplicates were removed by Trimmomatic 0.38.
The trimmed sequences were then assembled into reference transcripts using the HISAT2 program.
The read count was normalized into a value of FPKM (Fragments Per Kilobase of transcript per Million mapped reads), and the reads with a value of zero were excluded.
Significantly up- or down-regulated genes were identified by cutoff value of |FC| >= 1.5.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.gene_abund.anno.tab: Tab-delimited text files include FPKM and TPM values.
 
Submission date Nov 26, 2019
Last update date Nov 27, 2019
Contact name Dongho Kim
E-mail(s) jindonghao2001@hotmail.com
Phone 82312996440
Organization name Sungkyunkwan University School of Medicine
Department Samsung Biomedical Research Institute
Lab Molecular Cell Biology
Street address #300 Chunchun-dong, Jangan-Ku, Suwon, Kyungggi-do
City Suwon
ZIP/Postal code 440-746
Country South Korea
 
Platform ID GPL24676
Series (2)
GSE141052 Effect of metformin on mRNA expression in lung cancer cells
GSE141060 Effect of metformin on mRNA expression, histone modifications, and chromatin accessibility in lung cancer cells
Relations
BioSample SAMN13390302
SRA SRX7218342

Supplementary file Size Download File type/resource
GSM4193227_Metformin.gene_abund.anno.tab.gz 628.1 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap