|
| Status |
Public on Feb 01, 2024 |
| Title |
VF-14_CTX-0391034 |
| Sample type |
SRA |
| |
|
| Source name |
CD34+ pro-erythroblasts
|
| Organism |
Mus musculus |
| Characteristics |
tissue: CD34+ pro-erythroblasts
treatment: CTX-0391034
dose: 100 mg/kg b.i.d. of drug
|
| Treatment protocol |
Female C57Bl6 mice 6-8 weeks of age, were divided into five groups (n=6 mice per group) and were treated for 11 days with either vehicle or CTX-0391034 at 10, 30 or 100 mg/kg b.i.d. via oral gavage. A fifth group of mice was treated with CTX-0391034 100 mg/kg b.i.d. for 11 days and then drug was withdrawn for seven days. All groups were harvested 12 h after the final dose. Human CD34+ cells were treated with either DMSO or CTX-034 (1 microM) for 72 hours before harvesting for RNA-seq analysis.
|
| Growth protocol |
Generation of Jak2V617F knockin mice is summarized here Mullally et al 2010. All animal experiments were approved by the AMREP (Alfred Medical Research and Education Precinct) Animal Ethics Committee. Bone marrow was isolated from Jak2VF (CD45.2) or WT (CD45.1) mice aged 6-12 weeks. Bone marrow cells were mixed at an ∼3:1 ratio (Jak2VF:WT) and injected into lethally irradiated C57BL/6-Ly5.1 (CD45.1 positive) recipient mice. Recipient mice received 950 Rads total body irradiation in equal divided doses, at least 3 hours apart within 24 hours of transplantation. All transplanted cells were injected by lateral tail vein. Chimerism was determined 5 weeks after injection. Mice were maintained on antibiotic (Neomycin) water for 3 weeks after transplantation. Human CD34+ cells were isolated from human bone marrow using a MiniMACS magnetic cell sorting system (Miltenyi Biotec) and maintained in StemSpan SFEM II (STEMCELL Technologies Inc.) supplemented with Penicillin/Streptomycin (10,000 µg/ml, Gibco), L-Glutamine (200 mM, Gibco) Human SCF (100 ng/ml, R&D systems), Human IL-3 (5 ng/ml, R&D systems) Epoetin alfa (3U/ml, EPREX) and Dexamethasone (2 µM, Sigma) for up to 14 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
bone marrow cells were recovered by flushing both femurs with 1 mL of ice-cold PBS and Total RNA was extracted using TriZol method according to manufacturer's instructions.
MGIEasy V2 Library preparation was performed as per manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
NonStrandedCounts-withNames-proteinCoding.txt
|
| Data processing |
Data was processed using Laxy (https://laxy.io)
Alignment and mapping was performed using STAR v.2.5.2b and to the mouse reference genome GRCm38 or hg19 for human samples
Read counting was performed using FeatureCounts
Differential Gene expression analysis was performed using Degust.
Genome_build: GRCm38 and hg19
Supplementary_files_format_and_content: text file containing matrix of genes and read counts
|
| |
|
| Submission date |
Feb 13, 2020 |
| Last update date |
Feb 01, 2024 |
| Contact name |
Nicholas C Wong |
| E-mail(s) |
nick.wong@monash.edu
|
| Organization name |
Monash University
|
| Department |
Monash Bioinformatics Platform, Central Clinical School
|
| Street address |
Wellington Road
|
| City |
Clayton |
| State/province |
Victoria |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE145285 |
Small-molecule inhibition of PRMT5 activates p53 in erythropoiesis through perturbation of mRNA processing, transport and protein translation |
|
| Relations |
| BioSample |
SAMN14101037 |
| SRA |
SRX7724203 |
