|
| Status |
Public on Dec 06, 2018 |
| Title |
SUDHL6_VEH_24H_R2 |
| Sample type |
SRA |
| |
|
| Source name |
SUDHL6 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUDHL6
treatment: Vehicle (0.01% DMSO)
time of treatment: 24 h
|
| Treatment protocol |
Cells were treated with vehicle (0.01%DMSO) or 200nM GSK591 for 24 h or 96 h.
|
| Growth protocol |
Cells were grown in RPMI 1640 medium with 10% FBS, 10 mM Hepes, 2 mM glutamine, and pen/strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using the Trizol (Life Technologies).
Genomic DNA was eliminated with DNase treatment, and mRNA was isolated using two rounds of poly-T oligo attached magnetics beads. Sequencing libraries were generated with the Illumina TruSeq RNA sample prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PolyA RNA
processed data file: SUDHL6_GSK591_24H_counts.txt
processed data: TopTags_SUDHL6_GSK591_24hr.txt
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Reads that passed filter were aligned to hg19 using STAR (Dobin et al., 2012).
Gene expression values were calculated by counting how many reads map uniquely to the union of all gene exons using HTseq-count.
Differentially expressed genes were identified with the edgeR package (Robinson et al., 2010). Genes with a logCPM < -3 and FDR < 0.05 were considered differentially expressed.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Read counts that map uniquely to the union of all gene exons using HTseq-count and topTags output from EdgeR is provided as .txt files.
|
| |
|
| Submission date |
Jul 11, 2018 |
| Last update date |
Dec 06, 2018 |
| Contact name |
Tharu M Fernando |
| E-mail(s) |
[email protected]
|
| Phone |
646-962-6728
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Medicine, Heme-Onc
|
| Lab |
Ari Melnick
|
| Street address |
413 East 69th St BB1462
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE116963 |
PRMT5 Interacts with the BCL6 Oncoprotein and is Required for Germinal Center Formation and Lymphoma Cell Survival |
|
| Relations |
| BioSample |
SAMN09643681 |
| SRA |
SRX4381886 |
