cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/tktd6bz2t4.1
title: Mapping subcellular localizations of unannotated microproteins with MicroID

description: Identification of translated small open reading frames using proteogenomic approaches and ribosomal profiling has revealed thousands of previously unannotated cellular microproteins, or polypeptides of less than 150 amino acids, and alternative proteins (alt-proteins) that are co-encoded with canonical proteins and can be longer than 150 amino acids. The majority of microproteins and alt-proteins remain uncharacterized, in part because their short lengths preclude analysis of homology to known protein domains. The subcellular localizations of microproteins and alt-proteins remain largely unknown but can have significant implications for their functions. Proximity-dependent biotinylation has provided an attractive approach to define the canonical protein composition of subcellular compartments in living cells and animals. Here, we developed a high-throughput technology for global mapping of unannotated microproteins and alt-proteins to subcellular localizations by proximity-dependent biotinylation with TurboID (MicroID). We showed that more than 150 microproteins and alt-proteins are associated with subnuclear organelles and with complexes that carry out critical cellular functions. One of these novel microproteins, alt-LAMA3, localizes to the nucleolus and functions in pre-rRNA transcription. As a demonstration of its in vivo utility, we applied MicroID in a mouse model, identifying a conserved nuclear microprotein translated from a pseudogene, and establishing the foundation for use of this technology in discovery and characterization of microproteins in animals.
DOI: 10.17632/wjhtzjyy45.1
title: Blotting analysis of wild type (WT) HaCaT and p53 knockdown HaCaT cells

description: Here we present the experimental data of blotting and immunosorbent analysis of wild type (WT) HaCaT and p53 knockdown HaCaT cells. Provided results were obtained to confirm the knockdown of p53 in HaCaT keratinocytes. 
HaCaT cells were obtained from Bank of DKFZ, Heidelberg and cultured in DMEM/F:12 medium (1:1, Gibco, USA) supplemented with 1% GlutaMAX (Thermo Fisher Scientific, USA), penicillin/streptomycin (100 UI/mL and 100 μg/mL, Gibco, USA) and 10% v/v fetal bovine serum (Gibco, USA). Cells were grown in 60 mm Petri dishes (Corning, USA) and harvested by trypsinization. The culture medium was replaced by fresh every other day.
The knockdown was performed using shRNA designed to knockdown TP53 expression. To perform the knockdown, we applied lentiviral particles (LVPs) encoding anti-TP53 shRNA pLKO-p53-shRNA (Addgene, #25637). To assemble the LVPs, the pLKO-p53-shRNA was delivered in HEK293T cells using PEI transfection. The condition medium was collected 48-72 hours post transfection and purified from cell debris via centrifugation (45 min at 4500g and 4° C).  HaCaT cells were grown until 70% confluence, then the cultivation medium was replaced with condition medium containing LPVs for 1.5 hours. The cells were cultured for 4 days under standard conditions, afterwards the medium was replaced with puromycin-containing medium (1 µg/ml). As a control, we used HaCaT cells transduced with lego-ig2 (Addgene, #27341), which does not contain the puromycin resistance gene. After 10 days of puromycin selection 100% of control cells were dead. The obtained cells were used for further experiments. 

For the immunosorbent assay, the cells were seeded at density of 1×104 cells per well 48 hours prior analysis. ELISA was performed via Abcam’s assay (ab205713) for semi-quantitative p53 determination in accordance with the supplier's manual. 
For blotting analysis, the cells were grown until confluence of 70% at 60 mm Petri dishes under standard conditions. The cells were rinsed with DPBS and lysed in RIPA buffer (150 mM NaCl, 1% Triton X-100, 0.5% sodium deoxycholate, 0.1% SDS, 50 mM Tris, pH 8.0). Then 4x Laemmli buffer was mixed with the samples to 1x followed by 10 min incubation at 90C. The proteins were separated in 8% sodium SDS-PAGE and transfered to PVDF membrane. The immunodetection was performed with antibodies to human p53 (clone BP-53-12, PrimeBioMed, Russia) and β-actin (Bio-rad, VMA00048). 
Alkaline phosphatase (AP)-conjugated secondary antibodies (Bio-rad, STAR108A) were used for the immunodetection. The chemiluminescence was detected with DNR LumiBis Gel Imaging System 3.2. The images were obtained using GelCapture software. 
Here we deposit the results of immunoblotting assay confirming the decrease of p53 level in p53 knockdown HaCaT cells. The provided data includes the results of 3 independent experiments. Also, we present the raw data obtained from the ELISA assay.
DOI: 10.5517/ccdc.csd.cc2bgc4b
title: CCDC 2158751: Experimental Crystal Structure Determination

description: Related Article: Andreas Lorbach, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgc5c
title: CCDC 2158752: Experimental Crystal Structure Determination

description: Related Article: Andreas Lorbach, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgc6d
title: CCDC 2158753: Experimental Crystal Structure Determination

description: Related Article: Andreas Lorbach, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgc7f
title: CCDC 2158754: Experimental Crystal Structure Determination

description: Related Article: Andreas Lorbach, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgc8g
title: CCDC 2158755: Experimental Crystal Structure Determination

description: Related Article: Andreas Lorbach, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgc9h
title: CCDC 2158756: Experimental Crystal Structure Determination

description: Related Article: Andreas Lorbach, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgd9j
title: CCDC 2158787: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgdcl
title: CCDC 2158789: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgddm
title: CCDC 2158790: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgdhq
title: CCDC 2158793: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgdjr
title: CCDC 2158794: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgdlt
title: CCDC 2158796: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5066/p9txlt1x
title: Modeling accumulated surface runoff and water availability for aquifer storage and recovery in the MENA region from 1984-2015

description: The Middle East and North Africa (MENA) region is the most water-scarce region with only two percent of the global average annual rainfall, hence underground aquifers are the major source of water. The need to improve water productivity and increase aquifer storage and recovery (ASR) is driving the efforts for this acceleration of aquifer storage and recovery project. The objective was to model runoff in the study area using multi-source satellite data and identify regions of runoff retention and recharge. Daily runoff is simulated using a saturation excess principle with the VegET model (Senay 2008). It is a spatially explicit (500m grid cell), one-dimensional root-zone water balance model that is driven by precipitation, operating on a control volume defined by the root zone (1 m deep) using soil water holding capacity (WHC) to define the size of the ?bucket?, and the Normalized Difference Vegetation Index (NDVI) is used to parameterize daily actual Evapotranspiration (ETa) rates. The datasets included in this Data Release are: daily, and annual precipitation, daily NDVI, daily reference evapotranspiration, daily, monthly, and annual surface runoff, annual actual evapotranspiration, average annual accumulated runoff including the corresponding coefficient of variance, the VegET model Python scripts, and auxiliary data such as vector watershed file and elevation. For detailed description of each dataset please see the individual meta data files.
DOI: 10.6084/m9.figshare.19529995
title: A Survey on Sustainable Software Ecosystems to Support Experimental and Observational Science at Oak Ridge National Laboratory

description: This archive contains the survey data underlying the paper (official citation to be added when available):<br>David E Bernholdt, Mathieu Doucet, William F Godoy, Addi Malviya-Thakur, and Gregory R Watson, A Survey on Sustainable Software Ecosystems to Support Experimental and Observational Science at Oak Ridge National Laboratory, in International Conference on Computational Science, thematic track 2022 International Workshop on Software Engineering for Computational Science,London, United Kingdom, June 2022.
DOI: 10.5517/ccdc.csd.cc25j8nn
title: CCDC 2011641: Experimental Crystal Structure Determination

description: Related Article: Semyon V. Dudkin, Alexander S. Chuprin, Svetlana A. Belova, Anna V. Vologzhanina, Yan V. Zubavichus, Polina M. Kaletina, Inna K. Shundrina, Elena G. Bagryanskaya, Yan Z. Voloshin|2022|Dalton Trans.|51|5645|doi:10.1039/D1DT04187H
DOI: 10.5517/ccdc.csd.cc25j8pp
title: CCDC 2011642: Experimental Crystal Structure Determination

description: Related Article: Semyon V. Dudkin, Alexander S. Chuprin, Svetlana A. Belova, Anna V. Vologzhanina, Yan V. Zubavichus, Polina M. Kaletina, Inna K. Shundrina, Elena G. Bagryanskaya, Yan Z. Voloshin|2022|Dalton Trans.|51|5645|doi:10.1039/D1DT04187H
DOI: 10.5517/ccdc.csd.cc25j8qq
title: CCDC 2011643: Experimental Crystal Structure Determination

description: Related Article: Semyon V. Dudkin, Alexander S. Chuprin, Svetlana A. Belova, Anna V. Vologzhanina, Yan V. Zubavichus, Polina M. Kaletina, Inna K. Shundrina, Elena G. Bagryanskaya, Yan Z. Voloshin|2022|Dalton Trans.|51|5645|doi:10.1039/D1DT04187H
DOI: 10.5517/ccdc.csd.cc25j8rr
title: CCDC 2011644: Experimental Crystal Structure Determination

description: Related Article: Semyon V. Dudkin, Alexander S. Chuprin, Svetlana A. Belova, Anna V. Vologzhanina, Yan V. Zubavichus, Polina M. Kaletina, Inna K. Shundrina, Elena G. Bagryanskaya, Yan Z. Voloshin|2022|Dalton Trans.|51|5645|doi:10.1039/D1DT04187H
DOI: 10.5517/ccdc.csd.cc28nkj1
title: CCDC 2105133: Experimental Crystal Structure Determination

description: Related Article: Zi-Jian Chen, Hsiu-Feng Lu, Ito Chao, Jye-Shane Yang|2022|J.Org.Chem.|87|5029|doi:10.1021/acs.joc.2c00140
DOI: 10.5517/ccdc.csd.cc28pbw6
title: CCDC 2105888: Experimental Crystal Structure Determination

description: Related Article: Zi-Jian Chen, Hsiu-Feng Lu, Ito Chao, Jye-Shane Yang|2022|J.Org.Chem.|87|5029|doi:10.1021/acs.joc.2c00140
DOI: 10.5517/ccdc.csd.cc28tmzq
title: CCDC 2110014: Experimental Crystal Structure Determination

description: Related Article: Madan D. Ambhore, Santosh P. Panchal, Arpan Mondal, Sanjit Konar, Venkataramanarao G. Anand|2022|Org.Biomol.Chem.|20|2818|doi:10.1039/D1OB02230J
DOI: 10.5517/ccdc.csd.cc1q9p5w
title: CCDC 1588228: Experimental Crystal Structure Determination

description: Related Article: Madan D. Ambhore, Santosh P. Panchal, Arpan Mondal, Sanjit Konar, Venkataramanarao G. Anand|2022|Org.Biomol.Chem.|20|2818|doi:10.1039/D1OB02230J
DOI: 10.5517/ccdc.csd.cc28wzz4
title: CCDC 2112277: Experimental Crystal Structure Determination

description: Related Article: Xin Jin, Sifan Li, Lifang Guo, Jianli Hua, Da-Hui Qu, Jianhua Su, Zhiyun Zhang, He Tian|2022|J.Am.Chem.Soc.|144|4883|doi:10.1021/jacs.1c12610
DOI: 10.5517/ccdc.csd.cc28x007
title: CCDC 2112278: Experimental Crystal Structure Determination

description: Related Article: Xin Jin, Sifan Li, Lifang Guo, Jianli Hua, Da-Hui Qu, Jianhua Su, Zhiyun Zhang, He Tian|2022|J.Am.Chem.Soc.|144|4883|doi:10.1021/jacs.1c12610
DOI: 10.5517/ccdc.csd.cc28x018
title: CCDC 2112279: Experimental Crystal Structure Determination

description: Related Article: Xin Jin, Sifan Li, Lifang Guo, Jianli Hua, Da-Hui Qu, Jianhua Su, Zhiyun Zhang, He Tian|2022|J.Am.Chem.Soc.|144|4883|doi:10.1021/jacs.1c12610
DOI: 10.5517/ccdc.csd.cc2900gt
title: CCDC 2115175: Experimental Crystal Structure Determination

description: Related Article: Haidi Yang, Jinyao Liu, Pan Hu, Liang Gao, Zedu Huang, Fener Chen|2022|Org.Biomol.Chem.|20|2909|doi:10.1039/D2OB00384H
DOI: 10.5517/ccdc.csd.cc29fr9t
title: CCDC 2128376: Experimental Crystal Structure Determination

description: Related Article: Ya-Qian Zhang, Ning Xu, Yu Liu, Xiao-Sa Zhang, Wen-Ze Li, Hong-Tian Zhao, Jian Luan|2022|RSC Advances|12|9363|doi:10.1039/D1RA09309F
DOI: 10.5517/ccdc.csd.cc28z9wg
title: CCDC 2114506: Experimental Crystal Structure Determination

description: Related Article: Jeremy A. Intrator, Nicholas M. Orchanian, Andrew J. Clough, Ralf Haiges, Smaranda C. Marinescu|2022|Dalton Trans.|51|5660|doi:10.1039/D1DT03404A
DOI: 10.5281/zenodo.6425013
title: COSTCO Snapshots

description: Constrained Simulations of the COSMOS field (COSTCO). Snapshots for z=2.3 and z=0
DOI: 10.5281/zenodo.6425012
title: COSTCO Snapshots

description: Constrained Simulations of the COSMOS field (COSTCO). Snapshots for z=2.3 and z=0
DOI: 10.6084/m9.figshare.19552588
title: Coupled abiotic-biotic cycling of nitrous oxide in tropical peatlands

description: Atmospheric nitrous oxide (N2O) is a potent greenhouse gas thought to be mainly derived from microbial metabolism as part of the denitrification pathway. Here, we report that in unexplored peat soils of Central and South America, N2O production can be driven by abiotic reactions (≤ 98 %) highly competitive to their enzymatic counterparts. Extracted soil iron positively correlated with <em>in-situ</em> abiotic N2O production determined by isotopic tracers. Moreover, we found that microbial N2O reduction accompanied abiotic production, essentially closing a coupled abiotic-biotic N2O cycle. Anaerobic N2O consumption occurred ubiquitously (pH 6.4-3.7), with proportions of diverse clade II N2O-reducers increasing with consumption rates. Our findings show denitrification in tropical peat soils is not a purely biological process, but rather a “mosaic” of abiotic and biotic reduction reactions. We predict hydrological and temperature fluctuations differentially affect abiotic and biotic drivers and further contribute to the high N2O flux variation in the region.
DOI: 10.5517/ccdc.csd.cc2bgdmv
title: CCDC 2158797: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgdnw
title: CCDC 2158798: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgdpx
title: CCDC 2158799: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgdqy
title: CCDC 2158800: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgdrz
title: CCDC 2158801: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgds0
title: CCDC 2158802: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgdt1
title: CCDC 2158803: Experimental Crystal Structure Determination

description: Related Article: Christian Reus, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgmwb
title: CCDC 2159022: Experimental Crystal Structure Determination

description: Related Article: Steffen Pospiech, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgmxc
title: CCDC 2159023: Experimental Crystal Structure Determination

description: Related Article: Steffen Pospiech, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgmyd
title: CCDC 2159024: Experimental Crystal Structure Determination

description: Related Article: Steffen Pospiech, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgmzf
title: CCDC 2159025: Experimental Crystal Structure Determination

description: Related Article: Steffen Pospiech, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgn1j
title: CCDC 2159027: Experimental Crystal Structure Determination

description: Related Article: Steffen Pospiech, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgn3l
title: CCDC 2159029: Experimental Crystal Structure Determination

description: Related Article: Steffen Pospiech, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgn4m
title: CCDC 2159030: Experimental Crystal Structure Determination

description: Related Article: Steffen Pospiech, Michael Bolte, Matthias Wagner|2022|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc2bgqj2
title: CCDC 2159104: Experimental Crystal Structure Determination

description: Related Article: Frank R. Fronczek|2022|CSD Communication|||
DOI: 10.5281/zenodo.6425852
title: A 21st century high-resolution glacier and ice sheet fractional area dataset: Code and Data

description: This resource contains code and input data to develop a high-resolution (0.1°) gridded global glacier and ice sheet fractional area dataset, which is also available in this resource. The dataset is developed from Randolph Glacier Inventory v6.0 shapefiles and supplementary shapefiles for the Antarctic and Greenland ice sheets. The approach is adapted from Li et al., (2021; https://doi.org/10.1017/jog.2021.28). The dataset provides estimates of the fraction (0 to 1) of land cover that is glaciated in each 0.1° x 0.1° grid cell. The dataset was designed for use in the SPEAR model (https://www.gfdl.noaa.gov/spear/) from the NOAA Geophysical Fluid Dynamics Laboratory (GFDL), but may be useful for other applications as well. This work is documented in a NOAA Technical Memorandum (citation information to follow).
DOI: 10.5281/zenodo.6425851
title: A 21st century high-resolution glacier and ice sheet fractional area dataset: Code and Data

description: This resource contains code and input data to develop a high-resolution (0.1°) gridded global glacier and ice sheet fractional area dataset, which is also available in this resource. The dataset is developed from Randolph Glacier Inventory v6.0 shapefiles and supplementary shapefiles for the Antarctic and Greenland ice sheets. The approach is adapted from Li et al., (2021; https://doi.org/10.1017/jog.2021.28). The dataset provides estimates of the fraction (0 to 1) of land cover that is glaciated in each 0.1° x 0.1° grid cell. The dataset was designed for use in the SPEAR model (https://www.gfdl.noaa.gov/spear/) from the NOAA Geophysical Fluid Dynamics Laboratory (GFDL), but may be useful for other applications as well. This work is documented in a NOAA Technical Memorandum (citation information to follow).
DOI: 10.6084/m9.figshare.16663627.v2
title: Routable_rivers_International_Amazon_region

description: Dataset containing the routable version of the rivers of the International Amazon
DOI: 10.6084/m9.figshare.14622093
title: Dataset from the paper "Reviewing the effects of contamination on the biota of Brazilian coastal ecosystems: Scientific challenges for a developing country in a changing world"

description: This dataset is from a review on the knowledge status of contamination and the effects of contaminants on the biota of Brazilian coastal ecosystems. The spreadsheet contains the list of reviewed publications and the information extracted from each publication<br>
DOI: 10.6084/m9.figshare.14622093.v7
title: Dataset from the paper "Reviewing the effects of contamination on the biota of Brazilian coastal ecosystems: Scientific challenges for a developing country in a changing world"

description: This dataset is from a review on the knowledge status of contamination and the effects of contaminants on the biota of Brazilian coastal ecosystems. The spreadsheet contains the list of reviewed publications and the information extracted from each publication<br>
DOI: 10.6084/m9.figshare.14622093.v6
title: Dataset from the paper "Reviewing the effects of contamination on the biota of Brazilian coastal ecosystems: Scientific challenges for a developing country in a changing world"

description: This dataset is from a review on the knowledge status of contamination and the effects of contaminants on the biota of Brazilian coastal ecosystems. The spreadsheet contains the list of reviewed publications and the information extracted from each publication<br>
DOI: 10.5281/zenodo.6425902
title: Cellxgene VIP snRNA-seq demo dataset for visualization and DE analysis

description: H5ad file can be used as demo input for Cellxgene VIP. Dataset was the re-process from Schirmer et al Nature 2019 paper by using the raw fastq files. In order to reproduce the h5ad file, details could be found in https://github.com/interactivereport/cellxgene_VIP/blob/master/notebook/MS_Nature_Rowitch_snRNAseq.ipynb <br> Two rds files are also included here which are the input files for sample differential expression (DE) analysis scripts (glmmTMB and Nebula)
DOI: 10.5281/zenodo.6425901
title: Cellxgene VIP snRNA-seq demo dataset for visualization and DE analysis

description: H5ad file can be used as demo input for Cellxgene VIP. Dataset was the re-process from Schirmer et al Nature 2019 paper by using the raw fastq files. In order to reproduce the h5ad file, details could be found in https://github.com/interactivereport/cellxgene_VIP/blob/master/notebook/MS_Nature_Rowitch_snRNAseq.ipynb <br> Two rds files are also included here which are the input files for sample differential expression (DE) analysis scripts (glmmTMB and Nebula)