|
| Status |
Public on Jan 06, 2023 |
| Title |
LP-1_500nM_JQ1_4h_RNA-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
LP-1_500nM_JQ1_4h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LP-1
cell type: multiple myeloma
|
| Treatment protocol |
LP-1 cells were treated with DMSO or 0.5 μM JQ1 for 4 hours.
|
| Growth protocol |
LP-1 cells were cultured at 37 ˚C under 5% CO2 in IMDM medium supplemented with 10% fetal bovine serum, 100U/mL penicillin and 100 µg/mL streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were counted using a Countess Automated Cell Counter (Life Technologies). Equal numbers of cells for each sample were used for total RNA isolation: Cells were harvested, lysed directly in 1 mL Trizol Reagent (Life Technologies) and incubated for 5 minutes at room temperature. 200 µL chloroform was added to each sample, and samples were shaken for 15 seconds, followed by a 3 minute incubation at room temperature. Samples were spun at 15,000 x g for 15 minutes at 4 ˚C. The aqueous layer was removed and RNA was purified using an RNeasy Mini Kit (QIAGEN) with on-column DNase digestion. Equal amounts of ERCC RNA spike-in mix 1 (Life Technologies) were added to each sample, to give the same amount of synthetic spike-in RNA per cell equivalent across samples
500 ng of total RNA were used for library construction using the TruSeq RNA Sample Preparation Kit v2 (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads from RNA-seq were mapped to the hg19 version of the human genome using TopHat v1.4.1 with parameters –p 2 --library-type fr-unstranded. The hg19 bowtie genome index was downloaded from ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/. Duplicate read pairs were removed prior to further processing.
Cufflinks was run against reference transcriptome Homo_sapiens.GRCh37.73.chr.gtf, obtained from ftp://ftp.ensembl.org/pub/release-73/gtf/homo_sapiens/Homo_sapiens.GRCh37.73.gtf.gz, with parameters --no-effective-length-correction and --library-type fr-unstranded. Failed expression estimate attempts were set to NA and ignored for the rest of the analyses. We worked with regularized log expression data, calculated by adding 1.0 to Cufflink’s RPKM expression estimates and taking the log base 2. Log fold change values were then calculated by taking the difference between regularized log expression values.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes regularized log expression data and log fold change values for treated vs. untreated
|
| |
|
| Submission date |
Jul 01, 2015 |
| Last update date |
Jan 06, 2023 |
| 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 |
GPL16791 |
| Series (2) |
| GSE70447 |
BRD4 loading at the transcription start site mediates pause-release and underlies the disproportionate transcriptional response to BET bromodomain inhibition [RNA-Seq] |
| GSE70450 |
BRD4 loading at the transcription start site mediates pause-release and underlies the disproportionate transcriptional response to BET bromodomain inhibition |
|
| Relations |
| BioSample |
SAMN03835668 |
| SRA |
SRX1078939 |
