NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6176120 Query DataSets for GSM6176120
Status Public on May 25, 2022
Title K4, S (RNA-seq)
Sample type SRA
 
Source name melanoma cell line
Organism Homo sapiens
Characteristics cell line: K4
cell type: melanoma
treatment: untreated
phenotype: vemurafenib-sensitive
Treatment protocol Cells were treated with vemurafenib to gain acquired resistance.
Growth protocol Cells were grown in DMEM with 10% FBS.
Extracted molecule total RNA
Extraction protocol Total cell RNA was extracted using TRIzol Reagent (Invitrogen; Thermo Fisher Scientific, Waltham, MA) and RNeasy Mini kit (Qiagen, Hilden, Germany). RNA quality was examined by Qubit 3 (Thermo Fisher Scientific) and Fragment Analysis (Whitehead Institute Genome Technology Core, Massachusetts Institute of Technology, Cambridge, MA).
Sequencing libraries were prepared following the NEBNext Ultra II RNA Library Prep kit (New England Biolabs, MA) protocol and sequenced at Admera Health (South Plainfield, NJ) using the Illumina platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing fastqc to QC fastq file
StringTie was used to assemble RNA-Seq alignments into potential transcripts.
Using STAR aligner, read counts were converted to FPKM (Fragments per kilobase of transcript per million read pairs). FPKMs are calculated from the number of reads mapped to each particular gene sequence taking into account the gene length and the sequencing depth.
Assembly: hg38
Supplementary files format and content: comma-separated text files include FPKM fold change values for each sensitive-resistant pair.
 
Submission date May 22, 2022
Last update date May 25, 2022
Contact name Hensin Tsao
E-mail(s) htsao@mgh.harvard.edu
Organization name Massachusetts General Hospital
Street address 50 Blossom St
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL16791
Series (2)
GSE203545 Divergent BRAF Inhibitor Resistance Mechanisms Revealed through Epigenetic Mapping [RNA-seq]
GSE203546 Divergent BRAF Inhibitor Resistance Mechanisms Revealed through Epigenetic Mapping
Relations
BioSample SAMN28590850
SRA SRX15408712

Supplementary file Size Download File type/resource
GSM6176120_K4_S_fpkm.csv.gz 322.0 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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