|
| Status |
Public on Jan 06, 2023 |
| Title |
LP-1_DMSO_10min_GRO-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
LP-1_DMSO_10min
|
| 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 10 min, or with 0.5 μM JQ1 for 30 min.
|
| 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 |
Briefly, nuclei were isolated and nuclear run-on reactions were performed in the presence of ATP, GTP, CTP and BrdU. RNA was isolated and base hydrolyzed to ~100 nt. Nascent RNA was isolated using anti-BrdU antibodies conjugated to agarose beads.
Briefly, A poly A tail was added to each nascent RNA and used to prime first strand cDNA synthesis that added Illumina adaptors to one end of each nascent RNA. First strand cDNA was circularized and digested to give linear cDNAs flanked by adaptor sequences. Linear cDNAs were PCR amplified for 16 cycles. Libraries were size selected (175-400 bp) on a 2% agarose gel.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
nascent RNA
|
| Data processing |
Library strategy: GRO-seq
Reads from GRO-seq were mapped to the hg19 version of the human genome using BWA version 0.7.10. Duplicate reads were removed using samtools’ sort and rmdup functions.
GRO-seq data was normalized to reads per kilobase of measured interval, per million mappable bases. Normalized reads over the interval from +1 kb to +11 kb downstream of the TSS was used to define expression and log2 fold change expression.
IGVTools count was run with an extension of 100 and a window size of 25 bp to generate coverage signal in TDF and WIG formats. The WIG files were scaled to a mean of 1.0 assuming an effective genome size of 2,700,000,000 bases.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including normalized expression data and log fold change values for treated vs. untreated, Groseq signal in enhancers and wig files
|
| |
|
| 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) |
| GSE70449 |
BRD4 loading at the transcription start site mediates pause-release and underlies the disproportionate transcriptional response to BET bromodomain inhibition [GRO-Seq] |
| GSE70450 |
BRD4 loading at the transcription start site mediates pause-release and underlies the disproportionate transcriptional response to BET bromodomain inhibition |
|
| Relations |
| BioSample |
SAMN03835681 |
| SRA |
SRX1078952 |
