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Series GSE140276 Query DataSets for GSE140276
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.
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.
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
Organization name New England Biolabs
Street address 240 County Road
City Ipswich
State/province MA
ZIP/Postal code 01938
Country USA
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (28)
GSM4158691 HCT116_5mC_OnBead
GSM4158692 HCT116_C_OnBead
GSM4158693 HCT116_5mC_offBead
BioProject PRJNA589075
SRA SRP229617

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Supplementary file Size Download File type/resource
GSE140276_RAW.tar 13.6 Gb (http)(custom) TAR (of BW, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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