|
| Status |
Public on Oct 19, 2020 |
| Title |
A375_Drugs=Vem+Cobimetinib_EGF_time=0.5_h (S53) |
| Sample type |
SRA |
| |
|
| Source name |
A375_Drugs=Vem+Cobimetinib_EGF_time=0.5_h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375 melanoma
vemurafenib for 24 hrs (um): 1
cobimetinib for 24 hrs (um): 1
egf at 100 ng/ml (h): 0.5
set id: 3
|
| Treatment protocol |
24 hours after seeding cells, DMSO, or the RAF inhibitor Vemurafenib alone or with Cobimetinib were added to cells that were at 50-60% confluency. After 24 hours in the drug treatment, cells were either lysed in plates or, when define by experimental design, stimulated with EGF (100 ng/mL) for the defined amount of time and then lysed in the plates. The procedure was repeated on two different days for each of the two experimental designs (Vemurafenib doses or EGF addition time course), giving a total of four replicates per conditions (two day-to-day replicates with two technical replicates each). Technical replicates obtained on the same day have the same Set ID.
|
| Growth protocol |
A375 cells were plated in 24-well plates (Corning, #353047) with 475 uL of growth media (DMEM with 4.5 g/l glucose, l‐glutamine, and sodium pyruvate from Corning supplemented with 5% FBS) and allowed to adhere for 24 hours before perturbations.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Applied Biosystems MagMax 96 total RNA isolation kit (AM1830) with DNAse digestion according to the manufacturer’s protocol.
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kit (RS-122-2103) from 500 ng of purified total RNA according to the manufacturer’s protocol in a reduced reaction volume.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
S53
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Bcbio-nextgen software with the following configuration parameters: analysis=RNA-seq genome_build=hg38 algorithm=transcriptome_fasta=./Homo_sapiens_dnarna/Homo_sapiens.GRCh38.allRCNA.fa transcriptome_gtf=./Homo_sapiens_dnarna/Homo_sapiens.GRCh38.93.gtf aligner=hisat2 strandedness=firststrand spikein_fasta=./Homo_sapiens_dnarna/ERCC92/ERCC92.fa
RPM (reads per milion) were calculated and genes with RPM of 0 in all of the samples were discarded.
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing RPM (reads per milion) mean and standard deviation for each gene (rows, N=18261 with ENSG identifiers and gene names) and conditions including the RPM of each individual sample replicate (columns, N=140 made of 22 means, 22 standard deviations for aggregate replicates and 96 individual samples)
|
| |
|
| Submission date |
Mar 07, 2019 |
| Last update date |
Oct 19, 2020 |
| Contact name |
Luca Gerosa |
| Organization name |
Harvard Medical School
|
| Department |
Laboratory of Systems Pharmacology
|
| Lab |
Peter Sorger Lab
|
| Street address |
200 Longwood Avenue Warren Alpert Bldg, Apt2
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE127988 |
Gene expression of the A375 melanoma cell line treated with RAF inhibitors Vemurafenib and time-course with EGF stimulation during Vemurafenib RAF inhibitor treatment alone or with the MEK inhibitor Cobimetinib |
|
| Relations |
| BioSample |
SAMN11082127 |
| SRA |
SRX5491648 |
