|
| Status |
Public on Jun 29, 2016 |
| Title |
27-TRIMA1-M4B1-UT |
| Sample type |
SRA |
| |
|
| Source name |
Acute myeloid leukemia (AML) driven by Tet-regulated MLL-AF9 and an oncogenic form of NRAS (Tet-Off MLL-AF9 AML)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Tet-Off MLL-AF9 AML cells
protocol: untreated
origin: MLL-AF9 primary AML cells obtained from the spleen of terminally sick mice
strain: C57/BL6
|
| Treatment protocol |
Tet-Off MLL-AF9 AML cells were treated in vitro with doxycycline (DOX) for 4 days to inactivate MLL-AF9 expression or left untreated (UT); or transduced in vitro with an Id2-GFP or a control-GFP retroviral vector and GFP-positive cells were FACS-sorted 2 days after transduction.
|
| Growth protocol |
Primary Tet-Off MLL-AF9 AMLs were generated by reconstituting lethally irradiated congenic mice with foetal liver cells co-transduced with a Tet-Off-MLL-AF9-dRED retroviral vector and a second vector co-expressing NRASG12D together with the Tet-Off responsive transcriptional activator. AML cells were harvested form the spleen of leukemic animals.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysated and total RNA was extracted using Trizol reagent. Illumina TruSeq V2 RNA-seq kit was used with 400 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
27-TRIMA1-M4B1-UT
NormalizedMatrix_TRIMA4dDOX_Paper.txt
|
| Data processing |
Illumina Casava 1.8.2 software used for basecalling.
Reads were mapped to the mouse reference genome (mm10) using Tophat2 with default parameters.
Counts per gene were obtained using HTSeq with mode intersection-nonempty and Ensembl gtf. Counts were normalised using the limma-voom method.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing limma-voom normalised log2 values for each Sample
|
| |
|
| Submission date |
May 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Margherita Ghisi |
| E-mail(s) |
margherita.ghisi@gmail.com
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Department |
Research
|
| Lab |
Gene Regulation
|
| Street address |
St Andrews Place
|
| City |
Melbourne |
| State/province |
Victoria |
| ZIP/Postal code |
3002 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE68462 |
RNA sequencing expression analysis of murine Tet-off MLL-AF9;NRAS acute myeloid leukemia cells over-expressing Id2 and upon MLL-AF9 withdrawal |
| GSE68463 |
Id2 and E proteins orchestrate the initiation and maintenance of MLL-rearranged acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN03579661 |
| SRA |
SRX1015879 |
