|
| Status |
Public on Dec 01, 2020 |
| Title |
SUDHL6 DMSO D4 R1 |
| Sample type |
SRA |
| |
|
| Source name |
Diffuse large B cell lymphoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUDHL6
treatment: DMSO
|
| Treatment protocol |
96 hours of treatment with iEZH
|
| Growth protocol |
HT and SUDHL6 cell lines were grown in Roswell Park Memorial Institute (RPMI) GlutaMAX medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing was performed on the HiSeq 2000.
Tophat 1.4.1 was used to perform sequence alignment, with UCSC human (hg19) as the reference genome.
The Normalized counts of sequence reads (FPKM) mapped to annotated UCSC genes were determined using Cufflinks software.
The data was filtered to keep genes with at least one sample above a 50-read threshold. Samples with fewer than 10 reads FPKM are replaced with the average across samples of 10 reads FPKM, to generate the final gene counts for each sample and gene.
Data processing was performed by Ocean Ridge Biosystems.
Genome_build: hg19
|
| |
|
| Submission date |
Aug 29, 2012 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Barbara M Bryant |
| E-mail(s) |
barbara.bryant@constellationpharma.com
|
| Organization name |
Constellation Pharmaceuticals
|
| Street address |
215 First Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE40475 |
Selective lymphoma cell killing by a PRC2 small molecule inhibitor (RNA-Seq) |
| GSE40476 |
Selective lymphoma cell killing by a PRC2 small molecule inhibitor |
|
| Relations |
| SRA |
SRX181467 |
| BioSample |
SAMN01141438 |
