|
| Status |
Public on Oct 08, 2017 |
| Title |
A375 cell RNA-seq with ERK inhibitor treatment plus EGF stimulation |
| Sample type |
SRA |
| |
|
| Source name |
Skin
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
genetic background: BRAF mutation
culture medium: Starvation: Culture in 0.5% FBS medium for 2 days
agent: ERK inhibitor 3 hours at 1uM
egf stimulation: EGF stimulation: 20 min, 100ng/ml
|
| Treatment protocol |
The inhibitor treatment was carried out by incubating cells with drug containing medium for 3 hours.
|
| Growth protocol |
The cells were cultured in 37 degree incubator with 5% CO2. The growth medium contains 10% FBS and 1X L-gultamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Chromatin associate RNA were extracted from cultured cells for RNA-seq. DNA was immuno-precipitated with antibody from sonicated cell lysate.
RNA and CHIP libraries were prepared with NEBNext Library Prep Kits for Illumina using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
A375_ERKinh-EGF
|
| Data processing |
Illumina NextSeq 500 system was used to do sequencing and generate FASTQ files
For RNA-seq, reads were aligned to human hg19 genome assembly using BaseSpace apps_TopHat Alignment (version 1.0.0) by selecting trim TruSeq Adapters option.
For CHIP-seq, Sequenced reads were processed using trimmomatic/0.32 with parameter LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 and also trimmed adaptor sequence; and then were aligned to human hg19 genome assembly using bowtie2/2.2.6.
For both RNA-seq and CHIP-seq, aligned reads were processed with samtools to get .bam and .bam.bai files. Python bam2wig tools were used to generate bigwig files in order to visualize sequencing tracks on UCSC genome browser.
Genome_build: Human hg19
Supplementary_files_format_and_content: bigwig files for UCSC genome browser visualization
|
| |
|
| Submission date |
Aug 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jingyin Yue |
| E-mail(s) |
jxy154@med.miami.edu
|
| Phone |
305-243-7394
|
| Organization name |
University of Miami
|
| Department |
Sylvester Comprehensive Cancer Center
|
| Lab |
Shiekhattar, Ramin
|
| Street address |
1501 NW 10th Ave
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE85089 |
Integrator orchestrates RAS/ERK1/2 signaling transcriptional programs |
|
| Relations |
| BioSample |
SAMN05504845 |
| SRA |
SRX1994771 |
