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Sample GSM2359190 Query DataSets for GSM2359190
Status Public on Oct 23, 2017
Title A375-C3 Combo_THZ1_Vem [lab: Hammerman-DFCI]
Sample type SRA
 
Source name Melanoma
Organism Homo sapiens
Characteristics cell line: A375
tissue: Skin
drug: Vemurafenib / THZ1
concentration: 1 uM / 50 nM
treatment duration: 48h
Treatment protocol Cells were treated with Vemurafenib / THZ1 (1 uM / 50 nM) for 48h prior to harvesting
Growth protocol A375 cells were cultured in DMEM media, supplemented with 10% FBS, and penicillin/streptomycin/L-glutamine. Cells were cultured at 37 °C in a humidified chamber in the presence of 5% CO2.
Extracted molecule total RNA
Extraction protocol RNA was isolated using the RNeasy micro kit (Qiagen). cDNA libraries were prepared using the NEBNext Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. Library integrity was assessed on an Agilent 2100 Bioanalyzer (Agilent).
RNeasy micro kit (Qiagen)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Aligned using bowtie2 v2.2.1 and quantified using RSEM v1.2.12.
hg19 prepared using RSEM with bowtie2 and transcript annotations from Gencode release12.
Genome_build: hg19
Supplementary_files_format_and_content: matrix file with expression counts for each sample
 
Submission date Oct 24, 2016
Last update date May 15, 2019
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL11154
Series (2)
GSE89127 Suppression of adaptive responses to targeted cancer therapy by transcriptional repression [RNA-seq]
GSE89129 Suppression of adaptive responses to targeted cancer therapy by transcriptional repression
Relations
BioSample SAMN05937363
SRA SRX2266573

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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