 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 08, 2022 |
| Title |
SU-DHL-4 AZD N2 |
| Sample type |
SRA |
| |
|
| Source name |
Peritoneal effusion
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Peritoneal effusion
cell line: SU-DHL-4
cell type: B cell lymphoma
genotype: wt
treatment: AZD
|
| Treatment protocol |
SU-DHL-4 cells were exposed to 1µM Entospletinib (Absource Diagnostics GmbH, München, Germany), 0.01µM AZD5153 (Absource Diagnostics GmbH, München, Germany), the combination (1µM Ento+ 0.01µM AZD) or DMSO as control for 72h.
|
| Growth protocol |
SU-DHL-4 cell line were maintained in RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum (FBS) and and 100 µg/ml penicillin and streptomycin in a humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were resuspended in QIAzol Lysis Reagent (QIAGEN, Venlo, Netherlands) and RNA Isolation was performed with miRNeasy Mini Kit (QIAGEN, Venlo, Netherlands) according to the manufacturer’s instructions
Poly-A RNA was enriched from 1 µg total RNA using the NEBNext Poly (A) mRNA Magnetic Isolation Module (New England Bioabs, Ipswich, USA) and sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (New England Bioabs, Ipswich, USA). Sequencing was conducted on an Illumina NextSeq500 (Illumina, San Diego, USA) as single reads with 75 bp length with a total of 480 million reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calling with Illumina Software bcl2fastq v2.19; parameters: bcl2fastq --minimum-trimmed-read-length 25 --input-dir {path} --output-dir {path}; all others: default
The RNAseq data were processed as follows. The raw reads from different lanes were concatenated before being trimmed and quality controlled using CutAdapt via TrimGalore!
Trimmed reads were aligned to the human genome (GRCh38.p13) and feature counts were performed using Rsubread
The technical replicates were then averaged, and edgeR was used to filter low read counts using the filterByExpr() function, normalize using the TMM method, and perform a differential expression analysis using the GLM method to fit a generalized linear model, specifying no intercept and with treatment group as the only covariate
All contrasts were tested using the glmQLFTest() function of edgeR, which performs an empirical Bayes quasi-likelihood F-test for each gene, and the results were corrected for multiplicity using the Benjamini-Hochberg correction
A gene was deemed significantly differentially expressed if it had a corrected p-value of < 0.05 and a fold-change > 2
Gene Ontology (GO) enrichment analysis was performed using the “weight01” algorithm of topGO with GO terms with a p-value of < 0.05 being taken as significant.
Assembly: hg19
Supplementary files format and content: TMM_values.txt File containg the normalized read counts
Supplementary files format and content: count_table.txt file containing the read counts
|
| |
|
| Submission date |
Jul 01, 2022 |
| Last update date |
Aug 31, 2022 |
| Contact name |
Sina Sender |
| E-mail(s) |
[email protected]
|
| Organization name |
Rostock University Medical Center
|
| Department |
Department of Medicine, Clinic III
|
| Lab |
Hematology/Oncology
|
| Street address |
Schillingallee 70
|
| City |
Rostock |
| State/province |
Mecklenburg Vorpommern |
| ZIP/Postal code |
18059 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE207382 |
Evaluation of the synergistic potential of simultaneous pan- or isoform specific BET and SYK inhibition in B-cell lymphoma (RNA-Seq) |
| GSE207383 |
Evaluation of the synergistic potential of simultaneous pan- or isoform specific BET and SYK inhibition in B-cell lymphoma |
|
| Relations |
| BioSample |
SAMN29474323 |
| SRA |
SRX15970417 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
