|
| Status |
Public on Apr 26, 2022 |
| Title |
AG636_2_ATACseq |
| Sample type |
SRA |
| |
|
| Source name |
Acute myeloid leukemia
|
| Organism |
Mus musculus |
| Characteristics |
background: C57BL/6
genotype: MLL-AF9; KrasG12D
cell type: MN 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 |
genomic DNA |
| Extraction protocol |
Cells were isolated from bone marrow and spleen of experimental mice by fluorescence-based cell sorting. ATAC-seq was performed as previously published (Buenrostro, 2015).
Chromatin was tagmented using TDE1 Enzyme (Illumina), then adapters ligated and library amplified with HotStart KAPA readymix.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
JS12-8_S12
drug_merged_bin50_smooth150_e200_CPM_rmBlacklist.bw
|
| 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 Bowtie2 to the mouse reference genome (GRCm38/mm10).
Bigwigs were generated and data was visualised with deeptools (v2.5.3).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig
|
| |
|
| 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) |
| GSE181660 |
Inhibition of pyrimidine biosynthesis targets protein translation in AML [ATAC-seq_MN-2] |
| GSE181666 |
Inhibition of pyrimidine biosynthesis targets protein translation in AML |
|
| Relations |
| BioSample |
SAMN20667269 |
| SRA |
SRX11672340 |
