|
| Status |
Public on Sep 07, 2020 |
| Title |
L540_C2_100nM_6h |
| Sample type |
SRA |
| |
|
| Source name |
L-540 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: L-540
cell type: Hodgkin lymphoma cell line
treatment group: vehicle-treated Control 6 hr
sequencing library pool: RP6530 100nM
|
| Treatment protocol |
L-540 and KM-H2 Hodgkin lymphoma cell lines were treated with the novel PI3Kδ/γ inhibitor RP6530 (100nM and 10uM) for 6 hours and RP6530 (10uM) for 24 hours
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using RNeasy Mini Kit (Qiagen), and treated with DNase according to the manufacture’s protocol.
Total RNA quality was evaluated using the Agilent Bioanalyzer and the RNA Nano kit: only samples with RIN score ≥ 8 were processed further. RNA-seq libraries were sequenced using the TruSeq mRNA stranded kit (Illumina) according manufacturer’s indications. Briefly, the polyA fraction was isolated starting form 300 ng of high quality total RNA. All libraries were quantified using Qubit (Thermo Fisher Scientific Logo) and Bioanalyzer 2100 (Agilent) instruments. According to index compatibility, the libraries were grouped into pools at a concentration of 8 pM to obtain ~15 million clusters for each sample, for single run.
Single end sequence reads (75-bp in length) were generated on an Illumina NextSeq 500 (Sample 1 to 24)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-seq reads were aligned to the hg38 genome assembly using STAR v2.5 (PMID: 23104886)
Transcript abundance was obtained using the internally developed RNA read counter of STAR v2.5 (PMID: 23104886)
Differentially expressed genes were identified using R and edgeR (PMID: 19910308)
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig were generated using bam2wig.py module in RSeQC v2.6.3 (PMID: 22743226)
|
| |
|
| Submission date |
Jul 26, 2018 |
| Last update date |
Sep 08, 2020 |
| Contact name |
Simone Serio |
| E-mail(s) |
[email protected]
|
| Organization name |
Humanitas Research Hospital
|
| Department |
Cardiovascular Medicine
|
| Street address |
Via Alessandro Manzoni, 56
|
| City |
Rozzano |
| State/province |
Milano |
| ZIP/Postal code |
20089 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE105439 |
Effects of the novel PI3K δ/γ inhibitor RP6530 on global gene expression in Hodgkin Lymphoma cell lines. |
|
| Relations |
| BioSample |
SAMN09722088 |
| SRA |
SRX4466349 |
