|
| Status |
Public on Nov 16, 2022 |
| Title |
MLLr-MLL3-Mut_AML-PDX_RNA_VTP50469_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
MLLr; MLL3-Mut AML PDX
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MLL3 Mutant PDX
cell type: Acute myeloid leukemia
genotype: MLL-rearranged; MLL3 mutant
treatment: VTP50469
|
| Growth protocol |
Serially transplanted in NSG mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NEBNext Ultra II RNA
Leukemia cells were treated with either vehicle or Menin-MLL inhibitor for 4 days. Cells were harvested, washed with PBS, and flash frozen in liquid nitrogen. RNA was isolated using QIAGEN RNeasy kit. NEBNext Ultra II RNA Library Prep Kit was used with 1ug of total RNA for construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Transcript abundance was computed from FASTQ files using Salmon (v0.8.2) and the GENCODE reference transcript sequences, transcript counts were imported into R with the tximport R Bioconductor package, and differential gene expression was determined with the DESeq2 R Bioconductor package
Genome_build: mm10/hg38
Supplementary_files_format_and_content: Counts tables contain the raw counts quantified by Salmon and DESeq2.
|
| |
|
| Submission date |
Oct 27, 2021 |
| Last update date |
Nov 16, 2022 |
| Contact name |
Douglas Barrows |
| E-mail(s) |
dbarrows@rockefeller.edu
|
| Phone |
7749940981
|
| Organization name |
Rockefeller University
|
| Street address |
1230 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE186709 |
A molecular switch between mammalian MLL complexes dictates response to Menin-MLL inhibition [RNA-seq] |
| GSE186711 |
A molecular switch between mammalian MLL complexes dictates response to Menin-MLL inhibition |
|
| Relations |
| BioSample |
SAMN22604644 |
| SRA |
SRX12799869 |
