|
| Status |
Public on Jul 01, 2015 |
| Title |
Mel-RNA |
| Sample type |
SRA |
| |
|
| Source name |
Melanocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: non tumorigenic (Melanocytes)
genotype/variation: wild type
|
| Treatment protocol |
Cells were treated with 1µM of JQ1 or an enantiomer (control) for 6h
|
| Growth protocol |
SK-mel147 were grown with DMEM media with 10%FBS and antibiotics. Melanocytes were cultured in Melanocyte Growth Media 254 supplemented with Human Melanocyte Growth Supplement (Life Technologies)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
Sequencing libraries were prepared following the Illumina TruSeq Stranded Total RNA library prep protocol, with Ribo-Zero (RS-122-2201 or -2202), starting from 300-500ng of DNase I-treated total RNA, with the exception of 13 cycles of PCR amplification instead of 15. Amplified libraries were purified using AMPure beads, quantified by Qubit and qPCR, and visualized on an Agilent Bioanalyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Read alignment preformed using TopHat, version 2.0.12 (--transcriptome-only). Transcriptome assemblies in FPKM (fragments per kilo-base per million reads). For each RNA sample two technical replicates were merged
Differential expression preformed using Cufflinks 2.2.1
bigWig file generated using genomeCoverageBed and bg2bw.sh
Genome_build: UCSC-hg19
Supplementary_files_format_and_content: txt files containg FPKM values for all samples.
|
| |
|
| Submission date |
Apr 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Emily Bernstein |
| E-mail(s) |
emily.bernstein@mssm.edu
|
| Phone |
(212) 824-9335
|
| Organization name |
Mount Sinai School of Medicine
|
| Department |
Oncological Sciences
|
| Lab |
Bernstein Lab
|
| Street address |
1470 Madison Avenue, 6th floor Rm 302
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE68221 |
Histone variant H2A.Z.2 mediates proliferation and drug sensitivity of malignant melanoma [RNA-seq] |
|
| Relations |
| BioSample |
SAMN03566722 |
| SRA |
SRX1007710 |
