cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24198234
title: Autophagy-mediated control of ribosome homeostasis in oncogene-induced senescence- Reverse phase pos part

description: Oncogene-induced senescence (OIS) is a persistent anti-proliferative response regarded as a fail-safe mechanism, which protects against malignant transformation. Yet OIS has pro-tumorigenic effects through the secretion of a diverse group of inflammatory factors, commonly referred to as the senescence-associated secretory phenotype (SASP). During OIS, cells undergo dynamic remodeling, which involves alterations in protein and organelle homeostasis through autophagy. The interplay between autophagy and senescence is complex, and recent evidence suggests a role for selective substrate degradation by autophagy in coordinating the senescent state.<br>Here we show that ribosomes, the complex macromolecular machines central for genetic interpretation in all cells, are selectively targeted for degradation by autophagy during OIS. Using a model system of BRAF-induced OIS in human primary fibroblasts, we find that both small- and large ribosomal subunits are efficiently recruited to autophagosomes and subsequently degraded in lysosomes during OIS. To gain insight into the molecular control of this process, we characterized the ribosome interactomes of proliferative and senescent human fibroblasts. Among the identified senescence-dependent alterations in the ribosome interactome, we found the de-ubiquitinase USP10. While USP10 is present at the ribosome in proliferating cells, its loss from the ribosome upon entry to OIS leads to an enhanced ribosome ubiquitination, particularly of small subunit proteins. Among these are mono-ubiquitination of Lysine 275 on RPS2, which is sufficient to signal for selective uptake of both small and large subunits by the autophagy-lysosomal system during OIS. This occurs, at least in part, via the autophagy cargo receptor protein p62. Both re-enforcement of the USP10-ribosome interaction or mutation of RPS2 K275 could selectively abrogate ribosomal delivery to lysosomes, without impacting bulk autophagy. We show that while ribophagic flux is not required for the establishment of senescence per se, it contributes to senescence-associated metabolome reprogramming and facilitates the SASP response.See 10.6084/m9.figshare.24203823 for reverse phase neg dataSee 10.6084/m9.figshare.24203847 for HILIC neg data<br>
DOI: 10.6084/m9.figshare.24198234.v2
title: Loss of USP10 from the ribosome interactome triggers autophagy-mediated degradation of ribosomes during oncogene-induced senescence - Reverse phase pos part

description: Oncogene-induced senescence (OIS) is a persistent anti-proliferative response regarded as a fail-safe mechanism, which protects against malignant transformation. Yet OIS has pro-tumorigenic effects through the secretion of a diverse group of inflammatory factors, commonly referred to as the senescence-associated secretory phenotype (SASP). During OIS, cells undergo dynamic remodeling, which involves alterations in protein and organelle homeostasis through autophagy. The interplay between autophagy and senescence is complex, and recent evidence suggests a role for selective substrate degradation by autophagy in coordinating the senescent state.<br>Here we show that ribosomes, the complex macromolecular machines central for genetic interpretation in all cells, are selectively targeted for degradation by autophagy during OIS. Using a model system of BRAF-induced OIS in human primary fibroblasts, we find that both small- and large ribosomal subunits are efficiently recruited to autophagosomes and subsequently degraded in lysosomes during OIS. To gain insight into the molecular control of this process, we characterized the ribosome interactomes of proliferative and senescent human fibroblasts. Among the identified senescence-dependent alterations in the ribosome interactome, we found the de-ubiquitinase USP10. While USP10 is present at the ribosome in proliferating cells, its loss from the ribosome upon entry to OIS leads to an enhanced ribosome ubiquitination, particularly of small subunit proteins. Among these are mono-ubiquitination of Lysine 275 on RPS2, which is sufficient to signal for selective uptake of both small and large subunits by the autophagy-lysosomal system during OIS. This occurs, at least in part, via the autophagy cargo receptor protein p62. Both re-enforcement of the USP10-ribosome interaction or mutation of RPS2 K275 could selectively abrogate ribosomal delivery to lysosomes, without impacting bulk autophagy. We show that while ribophagic flux is not required for the establishment of senescence per se, it contributes to senescence-associated metabolome reprogramming and facilitates the SASP response.See 10.6084/m9.figshare.24203823 for reverse phase neg dataSee 10.6084/m9.figshare.24203847 for HILIC neg data<br>
DOI: 10.6084/m9.figshare.24198234.v3
title: Autophagy-mediated control of ribosome homeostasis in oncogene-induced senescence- Reverse phase pos part

description: Oncogene-induced senescence (OIS) is a persistent anti-proliferative response regarded as a fail-safe mechanism, which protects against malignant transformation. Yet OIS has pro-tumorigenic effects through the secretion of a diverse group of inflammatory factors, commonly referred to as the senescence-associated secretory phenotype (SASP). During OIS, cells undergo dynamic remodeling, which involves alterations in protein and organelle homeostasis through autophagy. The interplay between autophagy and senescence is complex, and recent evidence suggests a role for selective substrate degradation by autophagy in coordinating the senescent state.<br>Here we show that ribosomes, the complex macromolecular machines central for genetic interpretation in all cells, are selectively targeted for degradation by autophagy during OIS. Using a model system of BRAF-induced OIS in human primary fibroblasts, we find that both small- and large ribosomal subunits are efficiently recruited to autophagosomes and subsequently degraded in lysosomes during OIS. To gain insight into the molecular control of this process, we characterized the ribosome interactomes of proliferative and senescent human fibroblasts. Among the identified senescence-dependent alterations in the ribosome interactome, we found the de-ubiquitinase USP10. While USP10 is present at the ribosome in proliferating cells, its loss from the ribosome upon entry to OIS leads to an enhanced ribosome ubiquitination, particularly of small subunit proteins. Among these are mono-ubiquitination of Lysine 275 on RPS2, which is sufficient to signal for selective uptake of both small and large subunits by the autophagy-lysosomal system during OIS. This occurs, at least in part, via the autophagy cargo receptor protein p62. Both re-enforcement of the USP10-ribosome interaction or mutation of RPS2 K275 could selectively abrogate ribosomal delivery to lysosomes, without impacting bulk autophagy. We show that while ribophagic flux is not required for the establishment of senescence per se, it contributes to senescence-associated metabolome reprogramming and facilitates the SASP response.See 10.6084/m9.figshare.24203823 for reverse phase neg dataSee 10.6084/m9.figshare.24203847 for HILIC neg data<br>
DOI: 10.5281/zenodo.8432989
title: trash

description: TRASH
description: This is the anonymized version to support peer review
DOI: 10.5281/zenodo.8432955
title: trash

description: TRASH
description: This is the anonymized version to support peer review
DOI: 10.7270/q241706j
title: BindingDB Entry 1993: Histone demethylase inhibitors

description: Small molecule binding data for protein Lysine-specific demethylase 4C, Uniprot Q9H3R0
DOI: 10.5067/iir/calipso/cal_iir_l2_track-standard-v4-51
title: CALIPSO Infrared Imaging Radiometer (IIR) Level 2 Track, V4-51
DOI: 10.6084/m9.figshare.24295078
title: i715n-2dpmf.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295078.v1
title: i715n-2dpmf.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295081
title: wt-pmf_firsthalf.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295081.v1
title: wt-pmf_firsthalf.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.5281/zenodo.8415038
title: Code repository for: Base editing mutagenesis maps functional alleles to tune human T cell activity

description: Jupyter notebook and supplemental datasets required to created critical figures for the publication.
DOI: 10.5281/zenodo.8415037
title: Code repository for: Base editing mutagenesis maps functional alleles to tune human T cell activity

description: Jupyter notebook and supplemental datasets required to created critical figures for the publication.
DOI: 10.6084/m9.figshare.24295087
title: wt-2dpmf.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295087.v1
title: wt-2dpmf.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295093
title: wt-water-density-run3.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295084
title: i715n-pore-profile.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295084.v1
title: i715n-pore-profile.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295090.v1
title: wt-pmf_secondhalf.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295099
title: i715-pmf-firsthalf.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295099.v1
title: i715-pmf-firsthalf.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295090
title: wt-pmf_secondhalf.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295093.v1
title: wt-water-density-run3.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295096.v1
title: i715n-water-coor.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295102.v1
title: i715-pmf-secondhalf.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295105
title: wt-water-density-run1.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295108
title: wt-water-coor.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295096
title: i715n-water-coor.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295102
title: i715-pmf-secondhalf.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295105.v1
title: wt-water-density-run1.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295111.v1
title: wt-pore-profile.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24292078
title: figure1-lowerpore.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24292078.v1
title: figure1-lowerpore.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295108.v1
title: wt-water-coor.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295111
title: wt-pore-profile.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295114
title: wt-water-density-run2.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.6084/m9.figshare.24295114.v1
title: wt-water-density-run2.datAll data files for the main figures in the manuscript

description: Hyrophobic gating in TRPV4 ion channel
DOI: 10.7270/q20z75km
title: BindingDB Entry 2507: Histone demethylase inhibitors

description: Small molecule binding data for protein Lysine-specific demethylase 4C, Uniprot Q9H3R0
DOI: 10.5517/ccdc.csd.cc211rsn
title: CCDC 1878531: Experimental Crystal Structure Determination

description: Related Article: Jie Zhou, Jun-Wei Xiong, Yu Zhao|2019|Phosphorus,Sulfur,Silicon,Relat.Elem.|194|829|doi:10.1080/10426507.2018.1550643
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc21pvxj
title: CCDC 1897848: Experimental Crystal Structure Determination

description: Related Article: Xiu-Heng Qi, Zhen-Ming Wu, Shuai-Bing Wang, Bao-Xin Wang, Ling-Ling Wang, Haiyan Li, Qian Guo|2019|J.Coord.Chem.|72|2310|doi:10.1080/00958972.2019.1647535
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc21pvyk
title: CCDC 1897849: Experimental Crystal Structure Determination

description: Related Article: Xiu-Heng Qi, Zhen-Ming Wu, Shuai-Bing Wang, Bao-Xin Wang, Ling-Ling Wang, Haiyan Li, Qian Guo|2019|J.Coord.Chem.|72|2310|doi:10.1080/00958972.2019.1647535
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc21pvzl
title: CCDC 1897850: Experimental Crystal Structure Determination

description: Related Article: Xiu-Heng Qi, Zhen-Ming Wu, Shuai-Bing Wang, Bao-Xin Wang, Ling-Ling Wang, Haiyan Li, Qian Guo|2019|J.Coord.Chem.|72|2310|doi:10.1080/00958972.2019.1647535
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc223dzl
title: CCDC 1909909: Experimental Crystal Structure Determination

description: Related Article: Di Li, Li-Fei Li, Zhi-Fang Zhang, Dong Xue, Lei Pan, Yang Liu|2020|J.Coord.Chem.|73|266|doi:10.1080/00958972.2020.1727895
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2245l0
title: CCDC 1910641: Experimental Crystal Structure Determination

description: Related Article: Yu-Xu Li, Gang Chen, Qiang Xiao, Jin-Hui Cheng, Zhi-Sheng Long, Liang Deng, Ling Ma, Fei-Peng Gong|2019|J.Coord.Chem.|72|2586|doi:10.1080/00958972.2019.1659963
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc22bqy3
title: CCDC 1916945: Experimental Crystal Structure Determination

description: Related Article: Wei He, Qinghui Yuan, Haibo Zeng|2019|J.Coord.Chem.|72|3471|doi:10.1080/00958972.2019.1700234
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc22f91w
title: CCDC 1919397: Experimental Crystal Structure Determination

description: Related Article: Xiaozheng Li, Baoyi Li, Xiaowan Jin, Fengquan Dong, Haiying Li|2020|J.Coord.Chem.|73|297|doi:10.1080/00958972.2020.1729980
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc23rr4s
title: CCDC 1959235: Experimental Crystal Structure Determination

description: Related Article: Cong Chen,  Bu-Fei Wang,  Chao-Sheng Zeng,  Min Chen,  Lin Chen,  Qing-Jie Su,  Huai-Jie Xing|2021|Inorg.Nano-Metal Chem.|51|1396|doi:10.1080/24701556.2020.1835979
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc23rr5t
title: CCDC 1959236: Experimental Crystal Structure Determination

description: Related Article: Cong Chen,  Bu-Fei Wang,  Chao-Sheng Zeng,  Min Chen,  Lin Chen,  Qing-Jie Su,  Huai-Jie Xing|2021|Inorg.Nano-Metal Chem.|51|1396|doi:10.1080/24701556.2020.1835979
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.24293758
title: Uy Jeanelle - Can gut size be inferred from ribcage form?

description: Ribcage form data from Homo, Gorilla, Hylobates, Pongo, Macaca, and Cebus. Modern human gut size data from CT scans.
DOI: 10.6084/m9.figshare.24293758.v1
title: Uy Jeanelle - Can gut size be inferred from ribcage form?

description: Ribcage form data from Homo, Gorilla, Hylobates, Pongo, Macaca, and Cebus. Modern human gut size data from CT scans.
DOI: 10.5517/ccdc.csd.cc24230c
title: CCDC 1968221: Experimental Crystal Structure Determination

description: Related Article: Ying Liu,  Peng Mao,  Yu Wu,  Guo-Feng Ma,  Wen Xue,  Wei-Dong Tang|2021|Inorg.Nano-Metal Chem.|51|1492|doi:10.1080/24701556.2020.1841233
description: Related Article: Meng Qinghua|2019|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.8433008
title: cinnycerthia_olivascens_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.8433007
title: cinnycerthia_olivascens_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5517/ccdc.csd.cc24mzc4
title: CCDC 1985406: Experimental Crystal Structure Determination

description: Related Article: Yuan Zhang, Shu-An Dong, Tian-Yu Yu, Jian-Bo Yu, Mu Rui, Ci Li, Jin Wang|2020|J.Mol.Struct.|1220|128708|doi:10.1016/j.molstruc.2020.128708
description: Related Article: haitao Yuan|2020|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc24mzd5
title: CCDC 1985407: Experimental Crystal Structure Determination

description: Related Article: Yuan Zhang, Shu-An Dong, Tian-Yu Yu, Jian-Bo Yu, Mu Rui, Ci Li, Jin Wang|2020|J.Mol.Struct.|1220|128708|doi:10.1016/j.molstruc.2020.128708
description: Related Article: haitao Yuan|2020|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc24th6p
title: CCDC 1990702: Experimental Crystal Structure Determination

description: Related Article: LI-Ying Yan,  Hong-Chao Zhu,  Yan-Qu Ma,  Ling Tao,  Ling-Li Quan,  Qing Zhang|2021|J.Coord.Chem.|74|714|doi:10.1080/00958972.2020.1870683
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc24v089
title: CCDC 1991200: Experimental Crystal Structure Determination

description: Related Article: haitao Yuan|2020|CSD Communication|||
description: Related Article: Wei Li, Jia-Shuai Tan|2021|J.Mol.Struct.|1237|130359|doi:10.1016/j.molstruc.2021.130359
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.