|
| Status |
Public on Sep 30, 2023 |
| Title |
MUTZ3 - RNA-seq - PLASS control Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone marrow
cell line: MUTZ3
cell type: acute myelomonocytic leukemia
genotype: p50MX-3xFLAG-3xNLS-4xPLASS-Zeo
treatment: PLASS_control
timepoint: 72hrs
replicate: Rep1
|
| Treatment protocol |
Samples were transduced with a retroviral construct containg either of these three: a) PLDLS peptide that inhibits interaction between EVI1 and CTBP proteins, a PLASS peptide that has no such effect, an empty vector.
|
| Growth protocol |
MUTZ3 cells were cultured in αMEM with 20% FCS and 20% conditioned 5637 medium
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated by phenol chloroform extraction followed by DNase digestion. The SuperScript II Reverse Transcriptase kit (Invitrogen) was used for synthesis of cDNA.
The cDNA was sheared with the Covaris device and further processed according to the TruSeq RNA Sample Preparation v2 Guide (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling was conducted with bcl2fastq v1.8.4 with the settings --no-eamss --mismatches 1
Transcript abundance was quantified using Salmon v0.3.1 for pseudoalignment against RefSeq gene transcripts of the hg38 human reference build
Assembly: hg38
Supplementary files format and content: quant.sf contain transcript abundance and transcripts per million (TPM) quantified by Salmon
|
| |
|
| Submission date |
Sep 20, 2023 |
| Last update date |
Sep 30, 2023 |
| Contact name |
Ruud Delwel |
| E-mail(s) |
[email protected]
|
| Organization name |
Erasmus MC
|
| Street address |
Dr. Molewaterplein 40
|
| City |
Rotterdam |
| ZIP/Postal code |
3015 GD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE243620 |
Oncogene EVI1 Drives Acute Myeloid Leukemia Via a Targetable Interaction with CTBP2 [RNA-seq] |
| GSE243621 |
Oncogene EVI1 Drives Acute Myeloid Leukemia Via a Targetable Interaction with CTBP2 |
|
| Relations |
| BioSample |
SAMN37475611 |
| SRA |
SRX21838331 |
