|
| Status |
Public on Dec 01, 2017 |
| Title |
P58L.1.4.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 P58L 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 |
SAMN05420365 |
| SRA |
SRX1961873 |
