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SRX5247938: GSM3561971: Female mESC SSP rep 2; Mus musculus; MNase-Seq
1 ILLUMINA (Illumina MiSeq) run: 7.7M spots, 1.2G bases, 577.2Mb downloads

Submitted by: NCBI (GEO)
Study: High-resolution analysis of chromatin structure by Mnase-SSP
show Abstracthide Abstract
Proof-of-concept for Mnase-SSP: a variant of Mnase-seq. Mnase-SSP dramatically increases the representation of short fragments of nucleolytically-digested DNA, enabling simultaneous analysis of transcription factor binding and nucleosome occupancy using the same assay. We used MNase-SSP to demarcate chromatin architecture at murine promoters and at transcription factor binding sites in murine embryonic stem cells. Are results reveal heterogeneity in the binding mode of C2H2 zinc fingers like Ctcf and Rest, demonstrating that Mnase-SSP, and SSP in general, as a flexible platform for profiling nucleolytically digested DNA for MNase-seq, MNase-ChIP, or CUT&RUN with reduced bias. Overall design: Nuclei are purified, treated with varying amounts of micrococcal nuclease, and then DNA fragments are purified. DNA is melted, ligated to a 3' single-strand adapter, and then subjected to second-strand synthesis, adaptor ligation, and PCR. Please note that these libraries are non-traditional in the sense that the library prep is very different from standard Illumina protocols, and so the raw fastqs have been subjected to non-standard adaptor trimming + read filtration (in addition to read deduplication), generating BAM files as only processed data.
Sample: Female mESC SSP rep 2
SAMN10741203 • SRS4250194 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina MiSeq
Strategy: MNase-Seq
Source: GENOMIC
Selection: MNase
Layout: PAIRED
Construction protocol: Cells are lysed using a standard phenol-choloroform-isoamyl alcohol purification Mnase-SSP is performed using the single-stranded library prep of Gansauge and Meyer (Nature Prot. 2013) Libraries are sequenced with a custom read 1 primer on Illumina MiSeq or NextSeq instruments
Experiment attributes:
GEO Accession: GSM3561971
Links:
Runs: 1 run, 7.7M spots, 1.2G bases, 577.2Mb
Run# of Spots# of BasesSizePublished
SRR84405857,668,0891.2G577.2Mb2019-02-13

ID:
7084004

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