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EpiProfile specifications

Information


Unique identifier OMICS_31505
Name EpiProfile
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Programming languages MATLAB
License GNU General Public License version 3.0
Computer skills Medium
Version 2.0
Stability Stable
Requirements
Xcalibur
Maintained Yes

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  • person_outline Benjamin Garcia <>

Publications for EpiProfile

EpiProfile citations

 (13)
library_books

Characterization of histone acylations links chromatin modifications with metabolism

2017
PMCID: 5656686
PMID: 29070843
DOI: 10.1038/s41467-017-01384-9

[…] with an agc target of 3 × 104 using an injection time limit of 30 or 60 ms. all acquisitions were performed in positive mode polarity., data analysis was performed using our in-house software epiprofile with a 10-ppm tolerance for extracting peak areas from raw files. the relative abundances of acyl-ptms were calculated by dividing the intensity the modified peptide by the sum […]

library_books

Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b

2017
PMCID: 5506665
PMID: 28701172
DOI: 10.1186/s13072-017-0143-3

[…] orbitrap was operated in data-dependent mode essentially as previously described []. relative abundances of peptide species were calculated by chromatographic peak integration of full ms scans using epiprofile []. where necessary, peptide and ptm identity were verified by manual inspection of ms/ms spectra., isolated es cells were resuspended in pbs and crosslinked with 1% formaldehyde for 5 min […]

library_books

Metabolic labeling in middle down proteomics allows for investigation of the dynamics of the histone code

2017
PMCID: 5501349
PMID: 28683815
DOI: 10.1186/s13072-017-0139-z

[…] the precursor ion signal was split between the isobaric forms according to the relative intensities of the fragment ion signals. peak area was extracted from raw files by using our in-house software epiprofile [], which includes a pre-compiled list of peptides for quantification. the relative abundance of a given ptm was calculated by dividing its intensity by the sum of all modified […]

library_books

Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription

2017
PMCID: 5576860
PMID: 28682306
DOI: 10.1038/nature23267

[…] mode in the ion trap with sequential isolation windows of 50 m/z with an agc target of 3×104, a cid collision energy of 35 and a maximum injection time of 50 msec. the data was searched using epiprofile with schizosaccharomyces pombe database. the peptide relative ratio was calculated using the total area under the extracted ion chromatograms of all peptides with the same amino acid […]

library_books

Quantitative chromatin proteomics reveals a dynamic histone post translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites

2017
PMCID: 5428830
PMID: 28377601
DOI: 10.1038/s41598-017-00687-7

[…] translational repression seen for histones., we performed a quantitative assessment of histone samples using high-resolution nanolc-ms/ms; data processing/peak area extraction was performed by using epiprofile, and spectra identification was performed by using proteome discoverer (thermo). this enabled confident identification and quantification of histone ptms, as well as horizontal comparison […]

library_books

Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells

2017
PMCID: 5209743
PMID: 28051095
DOI: 10.1038/srep39406

[…] in the ion trap. the relative abundance of each modification, expressed as a percentage on a histone peptide sequence, was quantified by analyzing its ms and ms/ms spectra via an in-house software, epiprofile., dna oligonucleotide sequences () were designed to target slightly upstream of the promoter region of the genes of interest. these sequences were obtained from integrated dna technologies […]


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EpiProfile institution(s)
Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, USA
EpiProfile funding source(s)
Supported by NIH grants GM110174, AI118891, and CA196539; DOD grant W81XWH-113-1-0426; an UPenn Epigenetics Institute pilot grant and NIH grants TL1TR001880 and T32GM008275.

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