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SRX3644207: GSM2977180: F123 CAP-C No proteinase K; Mus musculus; OTHER
1 ILLUMINA (NextSeq 500) run: 473.2M spots, 47.3G bases, 18.9Gb downloads

Submitted by: NCBI (GEO)
Study: Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution
show Abstracthide Abstract
We introduce Chemical-crosslinking Assisted Proximity Capture (CAP-C), a method that utilizes multi-functional chemical crosslinkers with defined physical sizes to directly assess spatial distances between nuclear genomic sequences. CAP-C avoids limitations caused by extensive protein-DNA crosslinking in most in situ methods, and thus generates chromatin contact maps at high resolution with low background noise. Overall design: CAP-C utilizes a multifunctional PAMAM dendrimer platform instead of DNA-bound proteins to crosslink spatially adjacent DNA sequences, followed by restriction digestion and proximal ligation and high-throughput sequencing. We develop this method to examine the chromatin architecture of mouse embryonic stem cell F123, human HCT116 and drosophila S2 cell lines.
Sample: F123 CAP-C No proteinase K
SAMN08457658 • SRS2909024 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: NextSeq 500
Strategy: OTHER
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: For all CAP-C experiment, after dendrimer crosslinking, DNA bound protein was striped away by proteinase K and DNA was extracted by ethanol precopitation. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment ( exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA was PCR amplified with Illumina primers for 11 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Experiment attributes:
GEO Accession: GSM2977180
Links:
Runs: 1 run, 473.2M spots, 47.3G bases, 18.9Gb
Run# of Spots# of BasesSizePublished
SRR6667424473,198,75247.3G18.9Gb2020-08-24

ID:
5042933

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