|
| Status |
Public on Sep 27, 2023 |
| Title |
SEM_PINO_RES_DOT1Li_biol rep 4 RNA |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line
cell line: Acute Lymphoblastic Leukemia cell line SEM
cell type: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation
genotype: t(4;11)(q21;q23) translocation
treatment: 50uM pinometostat for 7 days
|
| Treatment protocol |
SEM and SEMPINORES cells were cultured in the presence of 50 µM of the DOT1L inhibitor pinometostat (EPZ5676, Selleckchem) for 1 week, with passage of the cells after 3 days with fresh inhibitor
|
| Growth protocol |
SEM and SEMPINORES cells were continuously grown in in RPMI-1640 medium containing GlutaMAXTM supplemented with 10% fetal calf serum, 100 IU/ml Penicillin and Streptomycin, and 0.125µg/ml Amphotericin B (Life Technologies), at 37°C under a 5% CO2 containing atmosphere. Cell lines passed every 3-4 days and routinely tested for the absence of mycoplasma and DNA fingerprinted to assure cell line authenticity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from leukemic cells using the RNeasy Mini Kit (Qiagen)
Libraries were generated using the TruSeq Stranded mRNA library preparation kit (Illumina, RS-122-2103)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SEM_vs_PINO_RES_DEGs_CPM.txt
SEM_vs_PINO_RES_featureCounts.txt
|
| Data processing |
QC was performed with fastQC
reads were trimmed with trim_galore, then aligned against the human genome assembly (hg19) with STAR
read counts were used to identify differential gene expression using DESeq2 (v3.12)
Gene expression levels were quantified using the featureCounts function of the Subread package
Differential gene expression analysis was conducted using DEseq2
Assembly: hg19
Supplementary files format and content: logFC and CPM
Supplementary files format and content: featureCounts output
|
| |
|
| Submission date |
Apr 27, 2023 |
| Last update date |
Sep 27, 2023 |
| Contact name |
Ronald W. Stam |
| E-mail(s) |
r.w.stam@prinsesmaximacentrum.nl
|
| Organization name |
Prinses Maxima Centrum
|
| Street address |
Heidelberglaan 25
|
| City |
Utrecht |
| ZIP/Postal code |
3702 VK |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE230791 |
Modelling acquired resistance to DOT1L inhibition exhibits the adaptive potential of KMT2A-rearranged Acute Lymphoblastic Leukemia’ [RNA-seq] |
| GSE230807 |
Modelling acquired resistance to DOT1L inhibition exhibits the adaptive potential of KMT2A-rearranged Acute Lymphoblastic Leukemia’ |
|
| Relations |
| BioSample |
SAMN34411292 |
| SRA |
SRX20121270 |
