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Series GSE125053 Query DataSets for GSE125053
Status Public on Feb 12, 2019
Title High-resolution analysis of chromatin structure by Mnase-SSP
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Contributor(s) Ramani V
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NIH grant(s)
Grant ID Grant title Affiliation Name
DP1 HG007811 Interpreting Genetic Variants of Uncertain Significance UNIVERSITY OF WASHINGTON JAY ASHOK SHENDURE
Submission date Jan 14, 2019
Last update date Mar 25, 2019
Contact name Vijay Ramani
Organization name UCSF
Department Biochemistry & Biophysics
Lab Ramani Lab
Street address 600 16th St, GH-S312B
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (14)
GSM3561968 Male mESC SSP rep 1
GSM3561969 Female mESC SSP rep1
GSM3561970 Male mESC SSP rep 2
BioProject PRJNA515040
SRA SRP179064

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE125053_RAW.tar 52.4 Gb (http)(custom) TAR (of BAI, BAM)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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