|
| Status |
Public on Jan 19, 2022 |
| Title |
RNA-seq in MLL-AF4 patient derived xenograft cells - control_2 |
| Sample type |
SRA |
| |
|
| Source name |
MLL-AF4+ acute lymphoblastic leukemia, patient derived xenograft
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lymphoblasts (CD19+) - patient derived xenograft cells
tissue: spleen
treatment: vehicle (60percent Phosal 50PG; 30percent PEG400; 10percent Ethanol – by oral gavage) for 3 weeks
|
| Treatment protocol |
Mice were treated with vehicle (60% Phosal 50PG; 30% PEG400; 10% Ethanol) or with 100 mg/kg of venetoclax for 3 weeks (5 days on/2 says off schedule)
|
| Growth protocol |
MLL-AF4+ ALL patient derived xenograft cells were injected intravenously to NSG mice (0.5 x 106/mouse)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Following the last dose, spleens were harvested and CD19+ leukemic cells were isolated using EasySep™ Human CD19 Positive Selection Kit II (STEMCELL, cat. # 17854). RNA was isolated from Trizol preserved cells according to manufacturer’s protocol (Ambion, Life Technologies) followed by loading the ethanol-precipitated sample into an RNeasy column (RNeasy Mini Kit; QIAGEN) and DNase digestion with an RNase-Free DNase Set (QIAGEN).
RNA sequencing was performed using TruSeq Stranded mRNA Library Prep (Illumina) according to the manufacturers' protocol. 1 μg of RNA was purified, fragmented and transcribed into cDNA, then samples were indexed with TruSeq RNA CD Index Plate (cat. no 20019792) and amplified. Quantification of DNA libraries using DNA 1000 chip on an Agilent Technologies 2200 TapeStation System was performed, then DNA libraries were normalized to 4 nM and then pooled in equal volumes.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
RNA-seq reads were aligned to the hg19 genome using STAR
Duplicate reads were removed using picard-tools MarkDuplicates
Read counts were determined using featureCounts (Subread package)
Differential gene expression analysis was conducted using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: feature counts
Supplementary_files_format_and_content: contrast table
|
| |
|
| Submission date |
Dec 15, 2020 |
| Last update date |
Jan 19, 2022 |
| Contact name |
Malgorzata Firczuk |
| E-mail(s) |
[email protected]
|
| Organization name |
Medical University of Warsaw
|
| Department |
Department of Immunology
|
| Street address |
Nielubowicza 5 Street
|
| City |
Warsaw |
| State/province |
masovian |
| ZIP/Postal code |
02-097 |
| Country |
Poland |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE163227 |
Potent, p53-independent induction of NOXA sensitizes MLL-rearranged B-cell acute lymphoblastic leukemia cells to venetoclax [RNA-Seq] |
| GSE163229 |
Potent, p53-independent induction of NOXA sensitizes MLL-rearranged B-cell acute lymphoblastic leukemia cells to venetoclax |
|
| Relations |
| BioSample |
SAMN17083533 |
| SRA |
SRX9686491 |
