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| Status |
Public on Oct 02, 2020 |
| Title |
Universal NicE-seq for high resolution accessible chromatin profiling for native and formaldehyde fixed cells and tissues |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling method that negate the optimization step and is suited to a variety of mammalian cells and tissues. Addition of 5-methyldeoxycytidine triphosphate during accessible chromatin labeling and an on-bead library making step substantially improved the signal to noise ratio while protecting the accessible regions from repeated nicking in cell lines, mouse T cells, mouse kidney, and human frozen and FFPE tissue sections. These refinements allowed reliable mapping of accessible chromatin for high resolution genomic feature studies.
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| Overall design |
Open-chromatin profile of various samples from cultured cancer cell lines, mouse tissue and human tissue section using nicking enzyme, NtCviPII based NicE-seq library were generated and sequenced. Depending on the experiments some samples were sequenced once, in duplicate or triplicate.
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| |
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| Contributor(s) |
Chin HG, Sun Z, Hao C, Pradhan S |
| Citation(s) |
32962734 |
| Submission date |
Nov 12, 2019 |
| Last update date |
Oct 02, 2020 |
| Contact name |
Sriharsa Pradhan |
| E-mail(s) |
pradhan@neb.com
|
| Organization name |
New England Biolabs
|
| Street address |
240 County Road
|
| City |
Ipswich |
| State/province |
MA |
| ZIP/Postal code |
01938 |
| Country |
USA |
| |
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| Platforms (3) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (28)
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| Relations |
| BioProject |
PRJNA589075 |
| SRA |
SRP229617 |
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