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Protocols

MM-ChIP specifications

Information


Unique identifier OMICS_27916
Name MM-ChIP
Alternative name Model-based Meta-analysis of ChIP data
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Liu Shirley

Publication for Model-based Meta-analysis of ChIP data

MM-ChIP citations

 (13)
library_books

Sorting cells by their density

2017
PLoS One
PMCID: 5516969
PMID: 28723908
DOI: 10.1371/journal.pone.0180520

[…] ements in separation efficiency with increased channel length are fairly modest. To understand why, we used our density_sorter.py software to simulate the behavior of beads in the 8-turn channel (207 mm) chip. The simulation results () show that, as mentioned earlier, in fluid of uniform density the larger and less-dense polyethylene bead floats to the ceiling of the channel after only 1 mm of tra […]

library_books

Compact SAW aerosol generator

2017
PMCID: 5269460
PMID: 28127655
DOI: 10.1007/s10544-017-0152-9

[…] zoelectric substrate, interdigital transducers (IDTs) and the polymer microchannel/s, all produced by conventional lift-off photolithography. On the chips used in this study (128°YX-LiNbO3, 8 mm × 19 mm chip size), pairs of IDTs (λ/4, λ = 90 μm, 46 finger pairs, 0.5 mm aperture, f0 ≅ 42.9 MHz) matched to 50 Ω impedance by design and consisting of subsequent layers of Ti (5 nm) and highly-textured […]

library_books

Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR γ

2017
eLife
PMCID: 5429093
PMID: 28425913
DOI: 10.7554/eLife.21697.044

[…] e with the MACS version 1.4.1. Peaks of the methylation and hydroxymethylation datasets were determined similarly. For histone marks, MACS version two was used with parameters –broad, -q 0.01, and –g mm. ChIP-seq peaks were annotated using the annotatePeaks.pl script of the HOMER suite (version 4.6) () using the UCSC mm10 annotation. The coverage depths of different ChIP-seq experiments at specifi […]

library_books

RNA editing generates cellular subsets with diverse sequence within populations

2016
Nat Commun
PMCID: 4947178
PMID: 27418407
DOI: 10.1038/ncomms12145

[…] To generate single-cell libraries, wild-type bone marrow-derived macrophages were flowed into a C1 IFC for mRNA seq (10–17 μm) chip using the Fluigidm system. Lysis, RT and PCR were performed using the SMARTer Kit designed for the C1 (Clontech, Mountain View, CA). The efficiency of chip loading (capture) was confirmed by […]

library_books

A Detailed Protocol to Enable Safe Handling, Preemptive Detection, and Systematic Surveillance of Rat Vectored Pathogens in the Urban Environment

2016
PMCID: 4945852
PMID: 27471725
DOI: 10.3389/fpubh.2016.00132

[…] ses, and connections for isoflurane unit. Isoflurane unit is on, all tubes connected. Table is clean. Instruments, microchips, and collection tubes on table.(2.3)Scan a selected microchip (Trovan® 12 mm chip is appropriate) to provide initial data point.(2.4)Place dry ice on two Pyrex 8″-roasting pans. One for ectorparasite collection and the other for body fluid collections. Anal swab (Swubes®) s […]

call_split

Urinary Kininogen 1 and Retinol binding protein 4 respond to Acute Kidney Injury: predictors of patient prognosis?

2016
Sci Rep
PMCID: 4726181
PMID: 26792617
DOI: 10.1038/srep19667
call_split See protocol

[…] formic acid in MilliQ water). A 6460 Triple Quadrupole mass spectrometer was used on-line connected to nano-chromatography in a Chip-format configuration (ChipCube interface, ProtID Zorbax 300B-C18-5 μm chip, 43 × 0.075-mm analytical column and 40 nL enrichment column, Agilent Technologies). The system was controlled by Mass Hunter Software (v4.0 Agilent Technologies). Theoretical SRM transitions […]

Citations

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MM-ChIP institution(s)
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA; Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China; Department of Statistics, Harvard University, Cambridge, MA, USA
MM-ChIP funding source(s)
Supported by NIH grants HG004069 and DK62434.

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