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| Status |
Public on Jun 30, 2024 |
| Title |
Chromatin accessibility in B16 and 4T1 cell lines with decitabine treatment [ATAC-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The goal of ATAC-seq is to identify the open chromatin regions in the B16 and 4T1 cells after Decitabine treatment. Three biological replicates were assigned for each group and in total 12 groups were prepared for ATAC-seq libraries. We mapped about 30-100 million reads per sample to M.musculus (mm10) with bowtie2 workflow. Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. Our results showed M.Musculus have dispartate chromatin accessibility after Decitabine treatment
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| Overall design |
Nuclei from B16 and 4T1 cells were extacted and transposed, and cDNA libraries were generated for deep sequencing, in triplicate, using HiSeq 4000 or NovaSeq S4
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| Contributor(s) |
Zhang Y, Wang SY |
| Citation(s) |
39169233 |
| |
| Submission date |
Aug 25, 2022 |
| Last update date |
Sep 30, 2024 |
| Contact name |
Eric Greer |
| E-mail(s) |
Eric.Greer@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital/Harvard Medical School
|
| Department |
Newborn Medicine/Department of Pediatrics
|
| Lab |
Greer Lab
|
| Street address |
320 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE212029 |
B16 and 4T1 cell lines with decitabine treatment |
|
| Relations |
| BioProject |
PRJNA873588 |
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