|
Status |
Public on Dec 01, 2017 |
Title |
MEKDD.TRE.1.1.A |
Sample type |
SRA |
|
|
Source name |
Melanoma
|
Organism |
Homo sapiens |
Characteristics |
cell line: A375 replicate: 4
|
Treatment protocol |
Expression of ERK alleles was induced with 1ug/ml doxycycline. Twenty-four hours post induction, half of replicates were treated for 4 hours with 4nM trametinib.
|
Growth protocol |
A375 cells were grown in RPMI media supplemented with 10% FBS and 1% penicillin/streptomycin.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted using the Qiagen RNeasy kit per the manufacturer's instructions. Illumina TruSeq
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Parental cell line with MEKDD ERK2 over-expression treated with trametinib
|
Data processing |
Illumina RNASeq libraries were prepared from 100 ng of bulk RNA using the TruSeq RNA Sample Prep Kit (v2, Illumina). mRNA-seq libraries were sequenced on an Illumina NextSeq 500 sequencer, as 75bp paired-end reads Reads were mapped with STAR aligner (Dobin et al. 2013) Genome_build: hg19 of the human genome and build 12 of the GENCODE human genome annotation Supplementary_files_format_and_content: csv file with raw counts
|
|
|
Submission date |
Jul 20, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Ofir Cohen |
E-mail(s) |
ofirc@broadinstitute.org
|
Phone |
617-714-7301
|
Organization name |
Broad Institute
|
Department |
Cancer Program
|
Street address |
415 Main St, Cambridge, MA 02142
|
City |
Cambridge |
State/province |
Massachusetts |
ZIP/Postal code |
02142 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE79989 |
Massively-parallel functional characterization of MAPK1 missense mutants |
|
Relations |
BioSample |
SAMN05420197 |
SRA |
SRX1961816 |