cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3662777
title: Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes

description: <strong>Data download</strong><br> http://resources-molpara.vetmed.lmu.de/Kraus_et_al_2019_sequencing_analysis.tar.gz <strong>Contents of the tar.gz archive:</strong><br> upload_sequencing/<br> ├── bin/<br> │ ├── scripts necessary to run the pipeline<br> ├── input/<br> │ ├── input files<br> ├── output/<br> │ ├── output files for ChIP and RNA-seq<br> └── output2/<br> └── output files for ATAC-seq <strong>Abstract</strong><br> Despite histone H2A variants and acetylation of histones occurring in almost every eukaryotic organism, it has been difficult to establish direct functional links between canonical histone or H2A variant acetylation, deposition of H2A variants and transcription. To disentangle these complex interdependent processes, we devised a highly sensitive strategy for quantifying histone acetylation levels at specific genomic loci. Taking advantage of the unusual genome organization in <em>Trypanosoma brucei</em>, we identify 58 histone modifications enriched at transcription start sites (TSSs). Furthermore, we find TSS-associated H4 and H2A.Z acetylation to be mediated by two different histone acetyltransferases, HAT2 and HAT1, respectively. Whereas depletion of HAT2 decreases H2A.Z deposition and shifts the site of transcription initiation, depletion of HAT1 does not affect H2A.Z deposition but reduces total mRNA levels by 50%. Thus, specifically reducing H4 or H2A.Z acetylation levels enabled us to reveal distinct roles for these modifications in H2A.Z deposition and RNA transcription.
description: We thank all current and former members of the Siegel and Janzen laboratories for valuable discussions and for assistance with experiments. We thank Joana Correia-Faria for sharing protocols for the isolation of the chromatin-associated protein fractions. We thank Felix Müller-Planitz, Stan Gorski, Kirsty McWilliam and Raúl Cosentino for critically reading the manuscript. We thank Konrad U. Förstner and Raúl O. Cosentino for suggestions regarding data analysis and the Core Unit Systems Medicine of the University of Würzburg for the high-throughput sequencing. We acknowledge the support and resources from the Bioinformatics Core Facility at the Biomedical Center Munich. We thank Beate Vogt and Christiane Winkler for their help in sample preparation for FIPQuant. This work was funded by the Young Investigator Program of the Research Center for Infectious Diseases (ZINF) at the University of Würzburg, Germany, a grant from the German Research Foundation (SI 1610/2-1) and an ERC Starting Grant (3D_Tryps 715466).
DOI: 10.5281/zenodo.3662776
title: Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes

description: This repository contains the run scripts for this publication. <strong>Complete data download</strong><br> http://resources-molpara.vetmed.lmu.de/Kraus_et_al_2019_sequencing_analysis.tar.gz <strong>Contents of the tar.gz archive:</strong><br> upload_sequencing/<br> ├── bin/<br> │ ├── scripts necessary to run the pipeline<br> ├── input/<br> │ ├── input files<br> ├── output/<br> │ ├── output files for ChIP and RNA-seq<br> └── output2/<br> └── output files for ATAC-seq <strong>Abstract</strong><br> Despite histone H2A variants and acetylation of histones occurring in almost every eukaryotic organism, it has been difficult to establish direct functional links between canonical histone or H2A variant acetylation, deposition of H2A variants and transcription. To disentangle these complex interdependent processes, we devised a highly sensitive strategy for quantifying histone acetylation levels at specific genomic loci. Taking advantage of the unusual genome organization in <em>Trypanosoma brucei</em>, we identify 58 histone modifications enriched at transcription start sites (TSSs). Furthermore, we find TSS-associated H4 and H2A.Z acetylation to be mediated by two different histone acetyltransferases, HAT2 and HAT1, respectively. Whereas depletion of HAT2 decreases H2A.Z deposition and shifts the site of transcription initiation, depletion of HAT1 does not affect H2A.Z deposition but reduces total mRNA levels by 50%. Thus, specifically reducing H4 or H2A.Z acetylation levels enabled us to reveal distinct roles for these modifications in H2A.Z deposition and RNA transcription.
description: We thank all current and former members of the Siegel and Janzen laboratories for valuable discussions and for assistance with experiments. We thank Joana Correia-Faria for sharing protocols for the isolation of the chromatin-associated protein fractions. We thank Felix Müller-Planitz, Stan Gorski, Kirsty McWilliam and Raúl Cosentino for critically reading the manuscript. We thank Konrad U. Förstner and Raúl O. Cosentino for suggestions regarding data analysis and the Core Unit Systems Medicine of the University of Würzburg for the high-throughput sequencing. We acknowledge the support and resources from the Bioinformatics Core Facility at the Biomedical Center Munich. We thank Beate Vogt and Christiane Winkler for their help in sample preparation for FIPQuant. This work was funded by the Young Investigator Program of the Research Center for Infectious Diseases (ZINF) at the University of Würzburg, Germany, a grant from the German Research Foundation (SI 1610/2-1) and an ERC Starting Grant (3D_Tryps 715466).
DOI: 10.17632/4jjv75y45m.1
title: Data for: Influence of sediment organic carbon on toxicity depends on organism’s ecology

description: Density of each nematode genus
DOI: 10.5285/9e4a232d-b59e-7e87-e053-6c86abc0f29f
title: Arctic PRIZE mission three near-real time glider dataset in the Barents Sea Spring 2018.

description: Data were collected by a slocum glider (unit 399) in the Barents Sea for the Arctic PRIZE project as part of the wider Changing Arctic Ocean programme during spring 2018. The two deployments were the final glider mission of three in the Barents Sea for the project. The gliders had a pumped CTD, a Wetlabs triplet ECO puck (CDOM, chla and optical backscatter) and an oxygen optode. This dataset contains the near-real time data from this glider deployment.
DOI: 10.5281/zenodo.3666116
title: 44444-digits Automorphic Numbers

description: In this folder, you can find the two 44444-digits automorphic numbers I computed to solve a riddle in my lab. Even if it was a purely funny exercise, I believe these numbers can be useful for both researchers and practitioners. There are two files: number-of-5-sequence.txt number-of-6-sequence.txt The first file contains the 44444-digits number of the 5-sequence, whilst the second contains the number of the 6-sequence. Both files start with the most significant digit and end with the least significant digit, respectively 5 and 6. In this blog post, I describe more in detail the approach I used to compute those numbers: https://www.salatino.org/wp/computing-automorphic-numbers/
DOI: 10.5281/zenodo.3666117
title: 44444-digits Automorphic Numbers

description: In this folder, you can find the two 44444-digits automorphic numbers I computed to solve a riddle in my lab. Even if it was a purely funny exercise, I believe these numbers can be useful for both researchers and practitioners. There are two files: number-of-5-sequence.txt number-of-6-sequence.txt The first file contains the 44444-digits number of the 5-sequence, whilst the second contains the number of the 6-sequence. Both files start with the most significant digit and end with the least significant digit, respectively 5 and 6. In this blog post, I describe more in detail the approach I used to compute those numbers: https://www.salatino.org/wp/computing-automorphic-numbers/
DOI: 10.5281/zenodo.3968153
title: Surveyed terrace profiles and terrace radiocarbon ages, western Jumgal basin, Tien Shan, Kyrgyz Republic

description: This archive contains survey data and radiocarbon ages from deformed terraces in the western Jumgal basin, Kyrgyz Republic. These data support analysis by Coddington and Burgette (2020) to be published in <em>Tectonics</em>: “Fold kinematics and fault slip rates from progressively deformed terraces: Implications for structural evolution of basins in the Kyrgyz Tien Shan”
DOI: 10.5281/zenodo.3666129
title: IO Islamic 2544. Muntakhab-i-Lubâb, History of the Tîmûrides in India

description: IO Islamic 2544. Muntakhab-i-Lubâb, History of the Tîmûrides in India
DOI: 10.5281/zenodo.3666130
title: IO Islamic 2544. Muntakhab-i-Lubâb, History of the Tîmûrides in India

description: IO Islamic 2544. Muntakhab-i-Lubâb, History of the Tîmûrides in India
DOI: 10.5281/zenodo.3968152
title: Surveyed terrace profiles and terrace radiocarbon ages, western Jumgal basin, Tien Shan, Kyrgyz Republic

description: This archive contains survey data and radiocarbon ages from deformed terraces in the western Jumgal basin, Kyrgyz Republic. These data support analysis by Coddington and Burgette (2020) to be published in <em>Tectonics</em>: “Fold kinematics and fault slip rates from progressively deformed terraces: Implications for structural evolution of basins in the Kyrgyz Tien Shan”
DOI: 10.17632/6tb68dv2jr.1
title: Data for: Accelerated CPU-GPUs Implementations for Quaternion Polar Harmonic Transform of Color Images
DOI: 10.5281/zenodo.3666143
title: IO Islamic 246. Muntakhab-i-Lubâb, History of the Tîmûrides in India (Selections)

description: IO Islamic 246. Muntakhab-i-Lubâb, History of the Tîmûrides in India (Selections)
DOI: 10.6084/m9.figshare.11845551.v5
title: Simulated zero-crossing wave period (3-hourly, 150a) from FIO-ESM v2.0 1pctCO2 experiment r1i1p1f1

description: Simulated zero-crossing wave period (3-hourly, 150a) from FIO-ESM v2.0 1pctCO2 experiment (CO2 prescribed to increase at 1% per year) r1i1p1f1, which is branch from Jan 1, 301 of piControl experiment. The grid, named gx1v6, is the displaced pole (the North Pole displaced to the Greenland) grid with 1.1 degree in longitude and 0.27-0.54 degree in latitude.
DOI: 10.5285/9c949855-dbd5-6e9e-e053-6c86abc0f145
title: TELEMAC-3D numerical model results used for plume dispersion experiments during cruise JC142 to Tropic Seamount, Northeast Atlantic, as part of the MarineE-tech project (October-December 2016).

description: This dataset includes results and input files from the open source TELEMAC-3D numerical model (version 6.3 release 2), used for prediction of currents during plume dispersion experiments on 17-18 November 2016 and 1 December 2016, during RRS James Cook cruise JC142 to Tropic Seamount in the Northeast Atlantic Ocean. The November flow model run lasted seven days starting at 00:00am on 14 November 2016, whilst the December flow model run lasted 9 days starting at 00:00am 27 on November 2016. Oceanographic data from this cruise was used as verification data for the numerical model runs. These data were used to test hypotheses for the dispersal of sediment plumes that may arise during any future crust extraction for industrial purposes. The impact of these plumes on sessile fauna are of particular concern for the protection of seamount ecosystems and the prospect of ecologically sustainable deep-sea mining. These data were collected as part of the MarineE-tech project, one of four consortium projects of the NERC SoS Minerals research programme. The work was undertaken by scientists at the National Oceanography Centre, Southampton, HR Wallingford, and the University of Sao Paolo, Brazil.
DOI: 10.5281/zenodo.3666131
title: IO Islamic 305. Muntakhab-i-Lubâb, History of the Tîmûrides in India

description: IO Islamic 305. Muntakhab-i-Lubâb, History of the Tîmûrides in India
DOI: 10.5281/zenodo.3666132
title: IO Islamic 305. Muntakhab-i-Lubâb, History of the Tîmûrides in India

description: IO Islamic 305. Muntakhab-i-Lubâb, History of the Tîmûrides in India
DOI: 10.5281/zenodo.3234794
title: Gullspång Pull-out Test Data Set

description: This data set contains the outcome of a series of pull-out tests (and 3D scan analysis) in the investigation of the bond behavior of naturally-corroded, plain reinforcement sourced from a decommissioned structure. The contents of this data set includes 1) photos and test measurements for all tested rebars; 2) an SQL database containing all pullout (unprocessed) data; and 3) an SQL database containing processed data. Data is provided in SQL format to permit querying of entries across the otherwise large, and parametrically diverse, data set. A "Read Me" file is also provided for additional descriptions of the content within.
description: Funding Sources: 1) Trafikverket (TRV 2017/39084) -- Professor Karin Lundgren' 2) Svenska Forskningsrådet Formas (2016-00568) -- Professor Karin Lundgren
DOI: 10.5281/zenodo.3234793
title: Gullspång Pull-out Test Data Set

description: This data set contains the outcome of a series of pull-out tests (and 3D scan analysis) in the investigation of the bond behavior of naturally-corroded, plain reinforcement sourced from a decommissioned structure. The contents of this data set includes 1) photos and test measurements for all tested rebars; 2) an SQL database containing all pullout (unprocessed) data; and 3) an SQL database containing processed data. Data is provided in SQL format to permit querying of entries across the otherwise large, and parametrically diverse, data set. A "Read Me" file is also provided for additional descriptions of the content within.
description: Funding Sources: 1) Trafikverket (TRV 2017/39084) -- Professor Karin Lundgren' 2) Svenska Forskningsrådet Formas (2016-00568) -- Professor Karin Lundgren
DOI: 10.5281/zenodo.3666118
title: IO Islamic 2400. Muntakhab-i-Lubâb, History of the Tîmûrides in India

description: IO Islamic 2400. Muntakhab-i-Lubâb, History of the Tîmûrides in India
DOI: 10.5281/zenodo.3666119
title: IO Islamic 2400. Muntakhab-i-Lubâb, History of the Tîmûrides in India

description: IO Islamic 2400. Muntakhab-i-Lubâb, History of the Tîmûrides in India
DOI: 10.5281/zenodo.3666140
title: IO Islamic 2992. Muntakhab-i-Lubâb, History of the Tîmûrides in India (Selections)

description: IO Islamic 2992. Muntakhab-i-Lubâb, History of the Tîmûrides in India (Selections)
DOI: 10.5281/zenodo.3666139
title: IO Islamic 2992. Muntakhab-i-Lubâb, History of the Tîmûrides in India (Selections)

description: IO Islamic 2992. Muntakhab-i-Lubâb, History of the Tîmûrides in India (Selections)
DOI: 10.5525/gla.researchdata.854
title: Twin-Airy point-spread function for extended-volume particle localization
DOI: 10.5281/zenodo.3666138
title: IO Islamic 3054. Muntakhab-i-Lubâb, History of the Tîmûrides in India

description: IO Islamic 3054. Muntakhab-i-Lubâb, History of the Tîmûrides in India
DOI: 10.17632/4jjv75y45m.2
title: Data for: Influence of sediment organic carbon on toxicity depends on organism’s ecology

description: Density of each nematode genus
DOI: 10.5281/zenodo.3666137
title: IO Islamic 3054. Muntakhab-i-Lubâb, History of the Tîmûrides in India

description: IO Islamic 3054. Muntakhab-i-Lubâb, History of the Tîmûrides in India
DOI: 10.5281/zenodo.3666145
title: IO Islamic 84. Muntakhab-i-Lubâb, History of the Minor Dynasties in India

description: IO Islamic 84. Muntakhab-i-Lubâb, History of the Minor Dynasties in India
DOI: 10.5281/zenodo.3666146
title: IO Islamic 84. Muntakhab-i-Lubâb, History of the Minor Dynasties in India

description: IO Islamic 84. Muntakhab-i-Lubâb, History of the Minor Dynasties in India
DOI: 10.5281/zenodo.3666144
title: IO Islamic 246. Muntakhab-i-Lubâb, History of the Tîmûrides in India (Selections)

description: IO Islamic 246. Muntakhab-i-Lubâb, History of the Tîmûrides in India (Selections)
DOI: 10.15129/b253a0ec-9232-47fd-9aa9-b62d721c0975
title: Replication data for: "Finding political capital for monetary tightening: unemployment insurance and monetary cycles"

description: Data on Inflation, Short-term Interest rates, Employment Protection and Social Welfare Indicators in 18 industrialised Democracies from 1970 to 1997. These data were compiled to test the whether partisan monetary cycles exist in the presence of employment protection or unemployment insurance.
DOI: 10.5281/zenodo.3666147
title: IO Islamic 852. Extracts from Historical Works

description: IO Islamic 852. Extracts from Historical Works
DOI: 10.5281/zenodo.3666148
title: IO Islamic 852. Extracts from Historical Works

description: IO Islamic 852. Extracts from Historical Works
DOI: 10.17632/j6sdxytt46.10
title: 3D reconstruction data used to perform selection task

description: In the selection task, participants had to select the region of interest (a specified vessel segment) as explained in the "Experiment_description.pdf" file. They were asked to manipulate (i.e., translate, rotate and scale) a 3D box widget, initially positioned such that the region of interest covered all vessel structures displayed on the screen. Three 3D model files ("level1.vtk", "level2.vtk" and "level.3 vtk") were used to define three complexity levels of the selection task: Level 1 (simple) — one vessel; Level 2 (average) — two closely located vessels; Level 3 (complex) — three vessels, where two vessels are located close to each other. This project was funded by the University of Amsterdam and NWO.
DOI: 10.25573/data.10042595.v3
title: Culebra_Wind Speed

description: Punta Culebra Nature Center meteorological station. Established in 2002. <br>Location: 8.910718°N, -79.528919°Wind Speed, interval max/min/avg
DOI: 10.25573/data.10042610.v3
title: Culebra_Air Temperature

description: Punta Culebra Nature Center meteorological station. Established in 2002. <br>Location: 8.910718°N, -79.528919°<br>Temperature, interval max/min/avg<br>
DOI: 10.25573/data.10042598.v3
title: Culebra_Relative Humidity

description: Punta Culebra Nature Center meteorological station. Established in 2002. <br>Location: 8.910718°N, -79.528919°<br>Relative Humidity, interval max/min/avg<br>
DOI: 10.25573/data.10042586.v3
title: Culebra_Precipitation

description: Punta Culebra Nature Center meteorological station. Established in 2002. <br>Location: 8.910718°N, -79.528919°<br>Precipitation, interval total
DOI: 10.25573/data.10042640.v3
title: Galeta_Wind Direction

description: Galeta Island marine laboratory. Pier Tower and ReefTwo sensors: pier tower and pylon on outer reef<br>Location: 9.402742°, -79.860837°<br>Wind direction, Interval mean vector and standard deviation<br><br>Galeta Island Marine Laboratory physical monitoring station established in 1974<br>Galeta station is located 6 km North East of the city of Colon. Established in the 1960’s.
DOI: 10.25573/data.10042604.v3
title: Culebra_Solar Radiation, Pyranometer

description: Punta Culebra Nature Center meteorological station. Established in 2002. <br>Location: 8.910718°N, -79.528919°<br>Solar Radiation (Pyranometer), interval max/min/avg<br>
DOI: 10.25573/data.10042622.v3
title: Culebra_Wind Direction

description: Punta Culebra Nature Center meteorological station. Established in 2002. <br>Location: 8.910718°N, -79.528919°<br>Wind Direction, interval mean vector, standard deviation<br>
DOI: 10.25573/data.10042643.v3
title: Galeta_Relative Humidity

description: Galeta Island marine laboratory. Pier Tower<br>Location: 9.402742°, -79.860837°<br>Relative Humidity, interval max/min/avg<br><br>Galeta Island Marine Laboratory physical monitoring station established in 1974<br>Galeta station is located 6 km North East of the city of Colon. Established in the 1960’s.
DOI: 10.25573/data.10042625.v3
title: Galeta_Air Temperature

description: Galeta Island marine laboratory. Pier Tower<br>Location: 9.402742°, -79.860837°<br>Air Temperature, interval max/min/avg<br><br>Galeta Island Marine Laboratory physical monitoring station established in 1974<br>Galeta station is located 6 km North East of the city of Colon. Established in the 1960’s.
DOI: 10.25573/data.10042637.v3
title: Galeta_Water Temperature

description: Galeta Island marine laboratory. below Pier Tower <br>Location: 9.402742°, -79.860837°<br>Water Temperature, interval average<br>Galeta Island Marine Laboratory physical monitoring station established in 1974<br>Galeta station is located 6 km North East of the city of Colon. Established in the 1960’s.
DOI: 10.25573/data.10042688.v3
title: San Lorenzo Crane_Wind Speed

description: San Lorenzo (Formerly know as Fort Sherman) Canopy Access Crane. <br><br>Wind speed, interval max/min/avg<br>Established in 1997, the San Lorenzo canopy crane (9.281031°, -79.974518°) is located approximately 11 km South West from the city of Colon, in the middle the Parque Natural San Lorenzo (formerly known as Fort Sherman) and is surrounded by 300-year old, low-land tropical rainforest
DOI: 10.5519/qd.vy0kn7r6
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (219 records)
DOI: 10.25573/data.10042664.v3
title: Galeta_Precipitation

description: Galeta Island marine laboratory. <br>Location: 9.402742°, -79.860837°Location of gauge has change, but is currently located on the pier tower<br><br>Precipitation, interval total<br>Galeta Island Marine Laboratory physical monitoring station established in 1974<br>Galeta station is located 6 km North East of the city of Colon. Established in the 1960’s.
DOI: 10.5281/zenodo.3666191
title: Surface rupture dataset of 18 normal and strike-slip events

description: Fault displacement hazard assessment is based on the analysis of empirical datasets. Here, I present a dataset of surface ruptures related to 18 normal and strike-slip events occurred between 1905 and 2011, with a magnitude range of Mw 5.9 – 8.3. Rupture traces were digitized from published maps at a variable scale, dependent on the resolution of the original map. Earthquakes are from Iran (7 events), Mongolia, China, Turkey, Greece (2 events for each country), Italy, Kenya and Japan (1 event). The dataset aligns with the recent efforts to constitute a worldwide and unified fault displacement database (e.g., SURE database, Baize et al., 2019). The Table “events” contains details on the analyzed dataset, in a format similar to that proposed by SURE. The shapefile contains the ruptured segments, coordinate system: WGS84.
DOI: 10.25573/data.10042691.v3
title: San Lorenzo Crane_Relative Humidity

description: San Lorenzo (Formerly know as Fort Sherman) Canopy Access Crane. <br><br>Relative humidity, interval max/min/avg<br>Established in 1997, the San Lorenzo canopy crane (9.281031°, -79.974518°) is located approximately 11 km South West from the city of Colon, in the middle the Parque Natural San Lorenzo (formerly known as Fort Sherman) and is surrounded by 300-year old, low-land tropical rainforest
DOI: 10.25573/data.10059536.v5
title: Monthly summary_Parque Natural Metropolitano Crane

description: Monthly and daily summaries from Parque Natural Metropolitano (PNM) crane station. <br>Location: 8.994410°, - 79.543000°<br>Parameters: air temperature, relative humidity, wind speed and direction, precipitation, solar radiation (pyranometer)<br>Established in 1995, the PNM canopy crane is located at the North Western edge of Panama City, at the eastern edge of the Parque Natural Metropolitano (Metropolitan Nature Park) and is surrounded by 80-year old, lowland semi-deciduous forest. The crane is 42 meters tall. <br><br>The original station was located on the side of the tower at approximately 25m. Some sensors were later moved to the top of the tower.
DOI: 10.25573/data.10059530.v4
title: Monthly summary_Galeta Station

description: Monthly and daily summary from Galeta Island marine laboratory<br>Location: 9.402742°, -79.860837°<br>Parameters: air temperature, relative humidity, wind speed and direction, precipitation, sea surface temperature, solar radiation (pyranometer)<br><br>Galeta Island Marine Laboratory physical monitoring station established in 1974<br>Galeta station is located 6 km North East of the city of Colon. Established in the 1960’s.