|
| Status |
Public on Apr 26, 2022 |
| Title |
AG636_1_RNAseq_RUNX1 |
| Sample type |
SRA |
| |
|
| Source name |
Acute myeloid leukemia
|
| Organism |
Mus musculus |
| Characteristics |
background: C57BL/6
genotype: RUNX1-RUNX1T1
cell type: AML cells
treatment: AG636
|
| Treatment protocol |
AG636 was administered b.i.d. by oral gavage at a dose of 100mg/kg body weight.
|
| Growth protocol |
AML cells were transplanted into sub-lethal irradiated Ptprca recipients.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were isolated from bone marrow and spleen of experimental mice by fluorescence-based cell sorting and total RNA was extracted using the Direct-zol™ RNA miniprep kit (Zymo Research) according to manufacturer’s instructions.
cDNA libraries were prepared using QuantSeq 3' mRNA seq kit (Lexogen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
AG353_S41
RUNX1counts.txt
|
| Data processing |
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute).
The RNA sequencing reads were trimmed using cutadapt (v1.9.1) to remove poor quality ends.
Read data was then aligned using Hisat2 (2.0.4) to the mouse reference genome (GRCm38/mm10).
Read counting was performed with featureCounts from the subread package (v1.5.0-p3).
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RUNX1counts.txt: Count file generated by featureCounts.
|
| |
|
| Submission date |
Aug 08, 2021 |
| Last update date |
Apr 26, 2022 |
| Contact name |
Joan So |
| E-mail(s) |
[email protected]
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan St
|
| City |
Melbourne |
| State/province |
Victoria |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE181664 |
Inhibition of pyrimidine biosynthesis targets protein translation in AML [RNA-seq_RUNX1] |
| GSE181666 |
Inhibition of pyrimidine biosynthesis targets protein translation in AML |
|
| Relations |
| BioSample |
SAMN20667409 |
| SRA |
SRX11672666 |
