|
| Status |
Public on Sep 05, 2019 |
| Title |
Input_KO_LGMP_1 |
| Sample type |
SRA |
| |
|
| Source name |
KO LGMP cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
chip-antibody: None
genotype: Prkaa1 and Prkaa2 double knockout
cell type: leukemia-GMP
|
| Treatment protocol |
L-GMP cells were isolated from AMPK WT and KO mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 WT or KO L-GMP cells were sorted and treated with Mnase, histone-DNA complexes were isolated with antibody
ChIP DNA was purified for end repair, adapter ligation, and amplification using a NEB Ultra II library preparation kit following the manufacturer’s protocols (New England BioLabs, Ipswich, MA)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Reads were trimmed for quality using Trimmomatic (version 0.36)
Trimmed reads were aligned to mm10 using bowtie2 (version 2.2.6)
bedGraph files were generated using deepTools (version 3.1.0; bamCoverage)
Peak calling, enhancer, and super-enhancer predictions were performed using HOMER (version 4.10)
Genome_build: mm10
Supplementary_files_format_and_content: UCSC formatted bedGraph files, generated using deepTools (bamCoverage); scores are CPM normalized.
|
| |
|
| Submission date |
Mar 07, 2019 |
| Last update date |
Sep 07, 2019 |
| Contact name |
Daisuke Nakada |
| E-mail(s) |
[email protected]
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Human Genetics
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE128000 |
AMPK links acetyl-coA homeostasis to BET recruitment in acute myeloid leukemia: ChIP-seq |
| GSE128001 |
AMPK links acetyl-coA homeostasis to BET recruitment in acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN11082594 |
| SRA |
SRX5492021 |
