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| Status |
Public on May 25, 2022 |
| Title |
SK-MEL-28, S (RNA-seq) |
| Sample type |
SRA |
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| Source name |
melanoma cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-MEL-28
cell type: melanoma
treatment: untreated
phenotype: vemurafenib-sensitive
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| Treatment protocol |
Cells were treated with vemurafenib to gain acquired resistance.
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| Growth protocol |
Cells were grown in DMEM with 10% FBS.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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.
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| Submission date |
May 22, 2022 |
| Last update date |
May 25, 2022 |
| Contact name |
Hensin Tsao |
| E-mail(s) |
htsao@mgh.harvard.edu
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| Organization name |
Massachusetts General Hospital
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| Street address |
50 Blossom St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN28590852 |
| SRA |
SRX15408710 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6176118_SK-MEL-28_S_fpkm.csv.gz |
320.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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