@data{ 
    title = "Processed Images and Summary Files for \"Phsyiological Adaptability and Parametric Versatility in a Simple Genetic Circuit\"",
    authors = "Chure, Griffin andKaczmarek, Zofii A. andPhillips, Rob",
    
    abstract ="This data set contains  Matlab `clist` files that are derived from segmentation and lineage tracking of bacterial cells growing under a microscope. This data set can be used to extract information about segmented cells, but contains no images.",
    year = "2019",
}


@data{ 
    title = "Tethered Particle Motion Measurements used in \"Sequence Dependent Dynamics of Synthetic and Endogenous RSSs in V(D)J Recombination.\"",
    authors = "Hirokawa, Soichi andChure, Griffin andBelliveau, Nathan M. andLovely, Goeffrey A andAnaya, Michael andSchatz, David G.  andBaltimore, David andPhillips, Rob",
    
    abstract ="This data set contains an array of .mat files that contain various statistics and classifications of single-molecule events from tethered particle motion experiments. More detail can be found at https://rpgroup.caltech.edu/vdj_recombination",
    year = "2019",
}


@data{ 
    title = "Raw flow cytometry data for \"Predictive shifts in free energy couple mutations to their phenotypic consequences\"\"",
    authors = "Chure, Griffin  andRazo-Mejia, Manuel andBelliveau, Nathan M. andEinav, Tal andKaczmarek, Zofii A. andBarnes, Stephanie L. andLewis, Mitchell andPhillips, Rob",
    
    abstract ="This data set contains raw flow cytometry files for the publication \"The Energetics of Molecular Adaptation in Transcriptional Regulation\". Please see the included README for details of the files and missing data sets. ",
    year = "2019",
}


@data{ 
    title = "Channel capacity bootstrap inferences from experimental data for \"First-principles prediction of the information processing capacity of a simple genetic circuit.\"",
    authors = "Razo-Mejia, Manuel andPhillips, Rob andMarzen, Sarah andChure, Griffin andTaubman, Rachel andMorrison, Muir",
    
    abstract ="The series of CSVs contain the channel capacity bootstrap estimates for each experimental set used on \"First-principles prediction of the information processing capacity of a simple genetic circuit.\" Each dataset was analyzed twice, one where the expression data matches the inducer concentration at which the cells were grown, and another where the data were shuffled. For more details please see the corresponding website for the article: https://www.rpgroup.caltech.edu/chann_cap/",
    year = "2019",
}


@data{ 
    title = "Microscopy image files for \"First-principles prediction of the information processing capacity of a simple genetic circuit.\"",
    authors = "Razo-Mejia, Manuel andPhillips, Rob andMarzen, Sarah andTaubman, Rachel andMorrison, Muir andChure, Griffin",
    
    abstract ="These data correspond to the raw microscopy images used to quantify fluorescence and compute gene expression distributions due to the activity of the Lac repressor molecule in E. coli cells. These images were passed through an image analysis pipeline which segmented individual cells and computed the mean pixel value for each cell. These data are separated by the operator we examined. A single strain was measured in twelve different inducer concentrations for each dataset with a total of 9 different strains imaged among all datasets. Please see the main text or the paper website at https://www.rpgroup.caltech.edu/chann_cap/ for more information.",
    year = "2019",
}


@data{ 
    title = "Cell intensities extracted from microscopy images for \"First-principles prediction of the information processing capacity of a simple genetic circuit.\"",
    authors = "Razo-Mejia, Manuel andPhillips, Rob andMarzen, Sarah andChure, Griffin andTaubman, Rachel andMorrison, Muir",
    
    abstract ="These data correspond to the single-cell mean intensity values obtained from microscopy images used to quantify fluorescence and compute gene expression distributions due to the activity of the Lac repressor molecule in E. coli cells. This information was used to compute the information processing capacity of the simple repression motif. These data are separated by the operator and repressor copy number we examined. Please see the main text or the paper website at https://mrazomej.github.io/chann_cap/analysis for more information.",
    year = "2019",
}


@data{ 
    title = "Raw mass spectrometry Thermo data from \"Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria\"",
    authors = "Belliveau, Nathan andPhillips, Rob",
    
    abstract ="This contains all Thermo .raw files.  The LacI target purification experiments were performed on a nanoflow LC system, EASY-nLC II coupled to a hybrid linear ion trap Orbitrap Classic mass spectrometer equipped with a Nanospray Flex Ion Source (Thermo Fisher Scientific). All other measurements were performed on a hybrid ion trap-Orbitrap Elite mass spectrometer (Thermo Fisher Scientific), which provided greater detection sensitivity and other fragmentation\ntechniques as described. The Orbitrap was operated in data-dependent acquisition mode to automatically alternate between a full scan (m/z=400–1,800) in the Orbitrap (resolution 120,000) and subsequent 5 MS/MS scans also acquired in Orbitrap with 15,000 resolution. The MS/MS spectra were acquired for the top 5 ions alternating between higher collision dissociation (HCD) and electron transfer dissociation (ETD) fragmentations that are well suited for higher charge peptides. Higher collision dissociation was performed at a normalized collision energy of 30% and electron transfer dissociation reaction time was set to 100 msec. ",
    year = "2018",
}


@data{ 
    title = "Processed sequence data as .fastq from \"Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria\"",
    authors = "Belliveau, Nathan andPhillips, Rob",
    
    abstract ="This contains all quality filtered sequence data as .fastq files (lac data are .fasta), with each sequencing bin as a unique file.",
    year = "2018",
}


@data{ 
    title = "Processed sequence data as .csv from \"Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria\"",
    authors = "Belliveau, Nathan andPhillips, Rob",
    
    abstract ="This contains all quality filtered sequence data as .csv files with each set of sequencing bins contained in a unique file.",
    year = "2018",
}


@data{ 
    title = "Processed data, code, and Jupiter notebooks from \"Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria\"",
    authors = "Belliveau, Nathan andBarnes, Stephanie andIreland, William andRob Phillips",
    
    abstract ="This contains all processed data sets used to construct expression shift plots and energy matrices, as well as several Jupiter notebooks associated with supplemental information of the work. Scripts used for data processing (in particular for .fastq files) are also included.",
    year = "2018",
}


@data{ 
    title = "Microscopy images analyzed in \"Connecting the dots between mechanosensitive channel abundance, osmotic shock, and survival at single-cell resolution\"",
    authors = "Griffin Chure andHeun Jin Lee andRob Phillips",
    
    abstract ="This data set contains all images, metadata, and marker positions  for the calibration and osmotic shock experiments. This set does not include the growth series from which survivors were identified. ",
    year = "2018",
}