2024 nature (Nature) agu ads article report on 02/04/2025 13:54:02


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32 of 3081 possible papers ( 1% ) contained references to SPDF keywords

Authors=Zhernakova, Daria V.; Wang, Daoming; Liu, Lei; Andreu-Sanchez, Sergio; Zhang, Yue; Ruiz-Moreno, Angel J.; Peng, Haoran; Plomp, Niels; Del Castillo-Izquierdo, Angela; Gacesa, Ranko; Lopera-Maya, Esteban A.; Temba, Godfrey S.; Kullaya, Vesla I.; van Leeuwen, Sander S.; Lifelines Cohort Study, Aguirre-Gamboa, Raul; Deelen, Patrick; Franke, Lude; Kuivenhoven, Jan A.; Kuivenhoven, Jan A.; Nolte, Ilja M.; Sanna, Serena; Snieder, Harold; Swertz, Morris A.; Visscher, Peter M.; Vonk, Judith M.; Vonk, Judith M.; Xavier, Ramnik J.; de Mast, Quirijn; Joosten, Leo A. B.; Riksen, Niels P.; Rutten, Joost H. W.; Netea, Mihai G.; Sanna, Serena; Wijmenga, Cisca; Weersma, Rinse K.; Zhernakova, Alexandra; Harmsen, Hermie J. M.; Fu, Jingyuan
Title=Host genetic regulation of human gut microbial structural variation, 2024, doi:10.1038/s41586-023-06893-w, ID=26789866
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =In brief, samples were genotyped on the Illumina HumanCoreExome-24 BeadChip Kit or the Illumina Infinium Omni-express chip. Imputation was carried out using the HRC v.1.1 reference panel 49 .

Authors=Li, Yaxu; Ran, Qiao; Duan, Qiuhui; Jin, Jiali; Wang, Yanjin; Yu, Lei; Wang, Chaojie; Zhu, Zhenyun; Chen, Xin; Weng, Linjun; Li, Zan; Wang, Jia; Wu, Qi; Wang, Hui; Tian, Hongling; Song, Sihui; Shan, Zezhi; Zhai, Qiwei; Qin, Huanlong; Chen, Shili; Fang, Lan; Yin, Huiyong; Zhou, Hu; Jiang, Xuejun; Wang, Ping
Title=7-Dehydrocholesterol dictates ferroptosis sensitivity, 2024, doi:10.1038/s41586-023-06983-9, ID=27091234
journal=Nature
Keywords found:iri
Sample usage ( ACK ) =Zhai for sharing information of the kidney IRI model; and H. Li for technical help. This study was supported by the National Key Research and Development Program of China (2022YFC3401500, 2021YFA1302200 and 2020YFA0803201), grants from the National Natural Science Foundation of China (31830053, 31920103007, 82341028, 82122056, 82073155, 82073153, 32030053, 22207084 and 32150710522), the Shanghai Sailing Program (22YF1433500), Shanghai Municipal Health Commission (20204Y0033), the Fundamental Research Funds for the Central Universities (22120220616 and PA2023000692), the fund from City University of Hong Kong (9380154, 7006046) and the Shanghai Rising-Star Program (23QA1407500).
Sample usage ( BODY ) =At this stage, we cannot rule out the possibility that metastasis promoted by 7-DHC may occur through a more complex mechanism, in addition to ferroptosis inhibition. 7-DHC protects the kidneys from IRI Ferroptosis has been implicated as the major form of cell death in IRI 5 , 6 .
Sample usage ( ABSTRACT ) =Ferroptosis, a form of regulated cell death that is driven by iron-dependent phospholipid peroxidation, has been implicated in multiple diseases, including cancer1-3, degenerative disorders4 and organ ischaemia-reperfusion injury (IRI)5,6. Here, using genome-wide CRISPR-Cas9 screening, we identified that the enzymes involved in distal cholesterol biosynthesis have pivotal yet opposing roles in regulating ferroptosis through dictating the level of 7-dehydrocholesterol (7-DHC)--an intermediate metabolite of distal cholesterol biosynthesis that is synthesized by sterol C5-desaturase (SC5D) and metabolized by 7-DHC reductase (DHCR7) for cholesterol synthesis.

Authors=Obara, Christopher J.; Nixon-Abell, Jonathon; Moore, Andrew S.; Riccio, Federica; Hoffman, David P.; Shtengel, Gleb; Xu, C. Shan; Schaefer, Kathy; Pasolli, H. Amalia; Masson, Jean-Baptiste; Hess, Harald F.; Calderon, Christopher P.; Blackstone, Craig; Lippincott-Schwartz, Jennifer
Title=Motion of VAPB molecules reveals ER-mitochondria contact site subdomains, 2024, doi:10.1038/s41586-023-06956-y, ID=27091463
journal=Nature
Keywords found:hdp
Sample usage ( BODY ) =Identification of latent states in single trajectories All trajectories longer than 500 steps (approximately 5.5 s) were analysed using a non-parametric Bayesian modelling technique (Hierarchical Dirichlet Process Modelling, HDP) coded using Python to estimate latent state changes in single-molecule behaviour 30 , 31 .

Authors=Taskiran, Ibrahim I.; Spanier, Katina I.; Dickmanken, Hannah; Kempynck, Niklas; Pancikova, Alexandra; Eksi, Eren Can; Hulselmans, Gert; Ismail, Joy N.; Theunis, Koen; Vandepoel, Roel; Christiaens, Valerie; Mauduit, David; Aerts, Stein
Title=Cell-type-directed design of synthetic enhancers, 2024, doi:10.1038/s41586-023-06936-2, ID=27091473
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =After 3 days the cells were split and expanded further. OmniATAC-seq Omni-assay for transposase-accessible chromatin using sequencing (OmniATAC-seq) was performed as described previously 78 .

Authors=Guzior, Douglas V.; Okros, Maxwell; Shivel, Madison; Armwald, Bruin; Bridges, Christopher; Fu, Yousi; Martin, Christian; Schilmiller, Anthony L.; Miller, Wendy M.; Ziegler, Kathryn M.; Sims, Matthew D.; Maddens, Michael E.; Graham, Stewart F.; Hausinger, Robert P.; Quinn, Robert A.
Title=Bile salt hydrolase acyltransferase activity expands bile acid diversity, 2024, doi:10.1038/s41586-024-07017-8, ID=27274988
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =Before analysis, phosphate buffered saline (Sigma) was added 3:1 (v/w) to faecal samples while 200 ml was added to caecum samples followed by homogenization through bead bashing at maximum speed for 10 min using a Bead Ruptor 96 (Omni International). Male and female C57BL/6Crl mice were bred inhouse and pups were weaned at 3 weeks of age.

Authors=Stokowski, Hubert S.; Dean, Devin J.; Hwang, Alexander Y.; Park, Taewon; Celik, Oguz Tolga; McKenna, Timothy P.; Jankowski, Marc; Langrock, Carsten; Ansari, Vahid; Fejer, Martin M.; Safavi-Naeini, Amir H.
Title=Integrated frequency-modulated optical parametric oscillator, 2024, doi:10.1038/s41586-024-07071-210.48550/arXiv.2307.04200, ID=27444206
journal=Nature
Keywords found:hdp
Sample usage ( BODY ) =We clad the entire chip with a layer of 700-nm thick SiO 2 deposited with a high-density plasma chemical vapour deposition using PlasmaTherm Versaline HDP CVD System (Extended Data Fig. 2f ) and open vias to access electrodes using inductively coupled plasma reactive ion etching (Extended Data Fig. 2g ).

Authors=Tufan, Turan; Comertpay, Gamze; Villani, Ambra; Nelson, Geoffrey M.; Terekhova, Marina; Kelley, Shannon; Zakharov, Pavel; Ellison, Rochelle M.; Shpynov, Oleg; Raymond, Michael; Sun, Jerry; Chen, Yitan; Bockelmann, Enno; Stremska, Marta; Peterson, Lance W.; Boeckaerts, Laura; Goldman, Seth R.; Etchegaray, J. Iker; Artyomov, Maxim N.; Peri, Francesca; Ravichandran, Kodi S.
Title=Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release, 2024, doi:10.1038/s41586-024-07172-y, ID=27606447
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =ATAC-seq library preparation ATAC-seq libraries were prepared following a modified version of the Omni-ATAC-seq protocol 51 . In brief, after efferocytosis, macrophages were washed three times with cold PBS to remove any unbound or uneaten apoptotic cells.

Authors=Moreno, Jorge A.; Dudchenko, Olga; Feigin, Charles Y.; Mereby, Sarah A.; Chen, Zhuoxin; Ramos, Raul; Almet, Axel A.; Sen, Harsha; Brack, Benjamin J.; Johnson, Matthew R.; Li, Sha; Wang, Wei; Gaska, Jenna M.; Ploss, Alexander; Weisz, David; Omer, Arina D.; Yao, Weijie; Colaric, Zane; Kaur, Parwinder; Leger, Judy St.; Nie, Qing; Mena, Alexandria; Flanagan, Joseph P.; Keller, Greta; Sanger, Thomas; Ostrow, Bruce; Plikus, Maksim V.; Kvon, Evgeny Z.; Aiden, Erez Lieberman; Mallarino, Ricardo
Title=Emx2 underlies the development and evolution of marsupial gliding membranes, 2024, doi:10.1038/s41586-024-07305-3, ID=28503751
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =Library preparation was performed according to the Omni-ATAC method 53 . In brief, cells were lysed for 3 min on ice. The transposition reaction on the permeabilized nuclei was performed using TDE1 transposase (Illumina) at 37 degC for 60 min, and then purified using the Zymo DNA Clean and Concentrator-5 kit (Zymo).

Authors=Zhao, Qinqin; Bertolli, Savannah; Park, Young-Jun; Tan, Yongjun; Cutler, Kevin J.; Srinivas, Pooja; Asfahl, Kyle L.; Fonesca-Garcia, Citlali; Gallagher, Larry A.; Li, Yaqiao; Wang, Yaxi; Coleman-Derr, Devin; DiMaio, Frank; Zhang, Dapeng; Peterson, S. Brook; Veesler, David; Mougous, Joseph D.
Title=Streptomyces umbrella toxin particles block hyphal growth of competing species, 2024, doi:10.1038/s41586-024-07298-z, ID=28503782
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =Cells were automatically segmented frame-by-frame using Omnipose (bact_phase_omni model) 61 . Spurious labels arising from plate defects, debris or pillars were manually removed in napari following automatic edge-based filtering in Python.

Authors=Baltgalvis, Kristen A.; Lamb, Kelsey N.; Symons, Kent T.; Wu, Chu-Chiao; Hoffman, Melissa A.; Snead, Aaron N.; Song, Xiaodan; Glaza, Thomas; Kikuchi, Shota; Green, Jason C.; Rogness, Donald C.; Lam, Betty; Rodriguez-Aguirre, Maria E.; Woody, David R.; Eissler, Christie L.; Rodiles, Socorro; Negron, Seth M.; Bernard, Steffen M.; Tran, Eileen; Pollock, Jonathan; Tabatabaei, Ali; Contreras, Victor; Williams, Heather N.; Pastuszka, Martha K.; Sigler, John J.; Pettazzoni, Piergiorgio; Rudolph, Markus G.; Classen, Moritz; Brugger, Doris; Claiborne, Christopher; Plancher, Jean-Marc; Cuartas, Isabel; Seoane, Joan; Burgess, Laurence E.; Abraham, Robert T.; Weinstein, David S.; Simon, Gabriel M.; Patricelli, Matthew P.; Kinsella, Todd M.
Title=Chemoproteomic discovery of a covalent allosteric inhibitor of WRN helicase, 2024, doi:10.1038/s41586-024-07318-y, ID=28803643
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =In vivo sample preparation Samples were lysed using Pierce radioimmunoprecipitation (RIPA) buffer (Thermo Fisher Scientific, catalogue no. 89900) containing HALT protease and phosphatase inhibitor cocktail, 1 mM MgSO 4 and benzonase nuclease, and homogenized using a Bead Mill homogenizer (OMNI International, SKU 19-042E). Following homogenization, samples were centrifuged at 4,000 g and 4 degC for 10 min.

Authors=Makova, Kateryna D.; Pickett, Brandon D.; Harris, Robert S.; Hartley, Gabrielle A.; Cechova, Monika; Pal, Karol; Nurk, Sergey; Yoo, DongAhn; Li, Qiuhui; Hebbar, Prajna; McGrath, Barbara C.; Antonacci, Francesca; Aubel, Margaux; Biddanda, Arjun; Borchers, Matthew; Bornberg-Bauer, Erich; Bouffard, Gerard G.; Brooks, Shelise Y.; Carbone, Lucia; Carrel, Laura; Carroll, Andrew; Chang, Pi-Chuan; Chin, Chen-Shan; Cook, Daniel E.; Craig, Sarah J. C.; de Gennaro, Luciana; Diekhans, Mark; Dutra, Amalia; Garcia, Gage H.; Grady, Patrick G. S.; Green, Richard E.; Haddad, Diana; Hallast, Pille; Harvey, William T.; Hickey, Glenn; Hillis, David A.; Hoyt, Savannah J.; Jeong, Hyeonsoo; Kamali, Kaivan; Pond, Sergei L. Kosakovsky; LaPolice, Troy M.; Lee, Charles; Lewis, Alexandra P.; Loh, Yong-Hwee E.; Masterson, Patrick; McGarvey, Kelly M.; McCoy, Rajiv C.; Medvedev, Paul; Miga, Karen H.; Munson, Katherine M.; Pak, Evgenia; Paten, Benedict; Pinto, Brendan J.; Potapova, Tamara; Rhie, Arang; Rocha, Joana L.; Ryabov, Fedor; Ryder, Oliver A.; Sacco, Samuel; Shafin, Kishwar; Shepelev, Valery A.; Slon, Viviane; Solar, Steven J.; Storer, Jessica M.; Sudmant, Peter H.; Sweetalana, Sweeten, Alex; Tassia, Michael G.; Thibaud-Nissen, Francoise; Ventura, Mario; Wilson, Melissa A.; Young, Alice C.; Zeng, Huiqing; Zhang, Xinru; Szpiech, Zachary A.; Huber, Christian D.; Gerton, Jennifer L.; Yi, Soojin V.; Schatz, Michael C.; Alexandrov, Ivan A.; Koren, Sergey; O'Neill, Rachel J.; Eichler, Evan E.; Phillippy, Adam M.
Title=The complete sequence and comparative analysis of ape sex chromosomes, 2024, doi:10.1038/s41586-024-07473-2, ID=29062641
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =To assist with assemblies, paired-end short-read sequencing was performed on Hi-C (Dovetail Omni-C from Cantata Bio) libraries sequenced on Illumina NovaSeq 6000, targeting 400 M pairs of 150-bp reads (>=30x depth) per sample.

Authors=Stankey, C. T.; Bourges, C.; Haag, L. M.; Turner-Stokes, T.; Piedade, A. P.; Palmer-Jones, C.; Papa, I.; Silva dos Santos, M.; Zhang, Q.; Cameron, A. J.; Legrini, A.; Zhang, T.; Wood, C. S.; New, F. N.; Randzavola, L. O.; Speidel, L.; Brown, A. C.; Hall, A.; Saffioti, F.; Parkes, E. C.; Edwards, W.; Direskeneli, H.; Grayson, P. C.; Jiang, L.; Merkel, P. A.; Saruhan-Direskeneli, G.; Sawalha, A. H.; Tombetti, E.; Quaglia, A.; Thorburn, D.; Knight, J. C.; Rochford, A. P.; Murray, C. D.; Divakar, P.; Green, M.; Nye, E.; MacRae, J. I.; Jamieson, N. B.; Skoglund, P.; Cader, M. Z.; Wallace, C.; Thomas, D. C.; Lee, J. C.
Title=A disease-associated gene desert directs macrophage inflammation through ETS2, 2024, doi:10.1038/s41586-024-07501-1, ID=29062651
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =ATAC-seq analysis ATAC-seq in ETS2 -edited and unedited TPP macrophages was performed using the Omni-ATAC protocol 67 with the following modifications: the cell number was increased to 75,000 cells; the cell lysis time was increased to 5 min; the volume of Tn5 transposase in the transposition mixture was doubled; and the duration of the transposition step was extended to 40 min.

Authors=Li, Kai; Chatterjee, Avradip; Qian, Chen; Lagree, Katherine; Wang, Yang; Becker, Courtney A.; Freeman, Michael R.; Murali, Ramachandran; Yang, Wei; Underhill, David M.
Title=Profiling phagosome proteins identifies PD-L1 as a fungal-binding receptor, 2024, doi:10.1038/s41586-024-07499-6, ID=29078558
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =Cells were disrupted by bead-beating with a bead ruptor 12-bead mill homogenizers (Omni) at a speed setting of high for six cycles of 30 s with 3 min of ice incubation in between.

Authors=Zhao, Sen; Jin, Fei-Fei; Stuecker, Malte F.; Thompson, Philip R.; Kug, Jong-Seong; McPhaden, Michael J.; Cane, Mark A.; Wittenberg, Andrew T.; Cai, Wenju
Title=Explainable El Nino predictability from climate mode interactions, 2024, doi:10.1038/s41586-024-07534-6, ID=29108010
journal=Nature
Keywords found:iri
Sample usage ( BODY ) =Red shading indicates the 10-90% ensemble spread of simulated 43 year segments, obtained from splitting a 43,000 year XRO simulation into 1,000 non-overlapping parts. m , All-months correlation skill of 3 month running mean Nino3.4 as a function of forecast lead for forecasts verified on 2002-2022 for the out-of-sample nRO (magenta) and XRO (red) fitted on 1950-1999, the AI model (blue), the XRO control fitted on 1979-2022 (black) and IRI operational models, the ensemble mean of dynamical models (dark purple curve) and ensemble mean of statistical models (dark cyan curve). n , Same as m , but for Nino3.4 forecast skills for nRO (magenta) and XRO (red) control forecasts, AI model forecasts (blue), and NMME dynamical model forecasts (multi-model ensemble mean in black, ensemble means from individual models in other colours).

Authors=Birkholz, Nils; Kamata, Kotaro; Feussner, Maximilian; Wilkinson, Max E.; Cuba Samaniego, Christian; Migur, Angela; Kimanius, Dari; Ceelen, Marijn; Went, Sam C.; Usher, Ben; Blower, Tim R.; Brown, Chris M.; Beisel, Chase L.; Weinberg, Zasha; Fagerlund, Robert D.; Jackson, Simon A.; Fineran, Peter C.
Title=Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein, 2024, doi:10.1038/s41586-024-07644-1, ID=29211507
journal=Nature
Keywords found:omni
Sample usage ( ACK ) =We gratefully acknowledge use of the Otago Micro and Nanoscale Imaging (OMNI) Flow Cytometry unit.

Authors=Bosch, Miriam; Kallin, Nina; Donakonda, Sainitin; Zhang, Jitao David; Wintersteller, Hannah; Hegenbarth, Silke; Heim, Kathrin; Ramirez, Carlos; Furst, Anna; Lattouf, Elias Isaac; Feuerherd, Martin; Chattopadhyay, Sutirtha; Kumpesa, Nadine; Griesser, Vera; Hoflack, Jean-Christophe; Siebourg-Polster, Juliane; Mogler, Carolin; Swadling, Leo; Pallett, Laura J.; Meiser, Philippa; Manske, Katrin; de Almeida, Gustavo P.; Kosinska, Anna D.; Sandu, Ioana; Schneider, Annika; Steinbacher, Vincent; Teng, Yan; Schnabel, Julia; Theis, Fabian; Gehring, Adam J.; Boonstra, Andre; Janssen, Harry L. A.; Vandenbosch, Michiel; Cuypers, Eva; Ollinger, Rupert; Engleitner, Thomas; Rad, Roland; Steiger, Katja; Oxenius, Annette; Lo, Wan-Lin; Klepsch, Victoria; Baier, Gottfried; Holzmann, Bernhard; Maini, Mala K.; Heeren, Ron; Murray, Peter J.; Thimme, Robert; Herrmann, Carl; Protzer, Ulrike; Bottcher, Jan P.; Zehn, Dietmar; Wohlleber, Dirk; Lauer, Georg M.; Hofmann, Maike; Luangsay, Souphalone; Knolle, Percy A.
Title=A liver immune rheostat regulates CD8 T cell immunity in chronic HBV infection, 2024, doi:10.1038/s41586-024-07630-7, ID=29448985
journal=Nature
Keywords found:

Authors=Franca, Gustavo S.; Baron, Maayan; King, Benjamin R.; Bossowski, Jozef P.; Bjornberg, Alicia; Pour, Maayan; Rao, Anjali; Patel, Ayushi S.; Misirlioglu, Selim; Barkley, Dalia; Tang, Kwan Ho; Dolgalev, Igor; Liberman, Deborah A.; Avital, Gal; Kuperwaser, Felicia; Chiodin, Marta; Levine, Douglas A.; Papagiannakopoulos, Thales; Marusyk, Andriy; Lionnet, Timothee; Yanai, Itai
Title=Cellular adaptation to cancer therapy along a resistance continuum, 2024, doi:10.1038/s41586-024-07690-9, ID=29448987
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =ATAC-seq sample preparation and sequencing ATAC-seq samples (C, P10, P320, T5-T320 and T320W) were prepared in duplicates using a modified version of the OMNI-ATAC protocol 49 . Briefly, cells grown in tissue culture under drug treatment with their respective adapted doses were trypsinized, stained for expression of CD44 and CD24 and sorted as previously described (C and T5-T320).

Authors=Hasegawa, Kazuteru; Zhao, Yang; Garbuzov, Alina; Corces, M. Ryan; Neuhofer, Patrick; Gillespie, Victoria M.; Cheung, Peggie; Belk, Julia A.; Huang, Yung-Hsin; Wei, Yuning; Chen, Lu; Chang, Howard Y.; Artandi, Steven E.
Title=Clonal inactivation of TERT impairs stem cell competition, 2024, doi:10.1038/s41586-024-07700-w, ID=30669813
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =ATAC-seq ATAC-seq libraries were made as described previously 52 using the Omni-ATAC protocol. Adjustments to the protocol were made to reflect two main features of the cell types profiled in this work.

Authors=Collinson, Glyn A.; Glocer, Alex; Pfaff, Robert; Barjatya, Aroh; Conway, Rachel; Breneman, Aaron; Clemmons, James; Eparvier, Francis; Michell, Robert; Mitchell, David; Imber, Suzie; Akbari, Hassanali; Davis, Lance; Kavanagh, Andrew; Robertson, Ellen; Swanson, Diana; Xu, Shaosui; Miller, Jacob; Cameron, Timothy; Chornay, Dennis; Uribe, Paulo; Nguyen, Long; Clayton, Robert; Graves, Nathan; Debchoudhury, Shantanab; Valentine, Henry; Ghalib, Ahmed; The Endurance Mission Team; Adkins, S.; Akbari, H.; Albano, R.; Baddeley, L.; Bahr, H.; Bain, G.; Bancroft, C.; Barjatya, A.; Barrie, A.; Binder, M.; Bissett, S.; Blix, K.; Bolton, A.; Bonsteel, B.; Borgen, H.; Bowden, D.; Bowker, D.; Bowlen, E.; Bradshaw, M.; Breneman, A.; Bridges, G.; Cameron, T.; Campbell, M.; Cathell, P.; Chornay, D.; Clayton, R.; Clemmons, J.; Collinson, G.; Conser, L.; Conway, R.; Davis, L.; Debchoudhury, S.; Demaine, P.; Detwiler, D.; Disbrow, M.; Doughty, J.; Eilertsen, L.; Ellis, S.; Eparvier, F.; Ethridge, R.; Fahringer, R.; Farrell, J.; Francheshini, M.; Frost, C.; Gass, T.; Ghalib, A.; Glocer, A.; Grabusky, C.; Graves, N.; Haggstrom, I.; Hanssen, P.; Harlan, G.; Harper, T.; Haugh, H.; Helgesen, E.; Henderson, J.; Henderson, D.; Herseth, K.; Imber, S.; Jensen, K.; Jester, T.; Jillard, R.; Johnson, E.; Johnson, H.; Jones, G.; Jones, T.; Kavanagh, A.; King, M.; Knight, D.; Laman, R.; Lankford, T.; Lien, R.; Lotz, P.; Maimone, M.; Marsh, G.; Marshall, R.; Martin, S.; McFaden, T.; Michell, R.; Mitchell, D.; Moffett, M.; Morris, N.; Mueseler, A.; Nelson, C.; Nguyen, L.; Ogundere, W.; Osbakk, K.; Page, D.; Paschalidis, N.; Pfaff, R.; Pirner, C.; Pittman, E.; Polidan, J.; Puopolo, D.; Raley, D.; Rawlings, Z.; Ribbens, P.; Robertson, E.; Rodriguez, S.; Rosanova, G.; Rose, B.; Rosnack, T.; Russell, T.; Samara, M.; Serabian, B.; Sherman, T.; Simonsen, R.; Snyder, T.; Soreng, J.; Sutton, V.; Sveen, J.; Swanson, D.; Swift, R.; Taylor, W.; Terwiliger, R.; Tiede, S.; Tucker, C.; Uribe, P.; Valentine, H.; Wallace, M.; Waters, F.; West, L.; West, B.; Wilson, T.; Wroblewski, N.; Xu, S.; Zarro, D.; Zesta, E.
Title=Earth's ambipolar electrostatic field and its role in ion escape to space, 2024, doi:10.1038/s41586-024-07480-3, ID=30744082
journal=Nature
Keywords found:iri, international reference ionosphere
Sample usage ( BODY ) =The black dotted lines show a prediction by the IRI empirical model. Dashed red lines show how the ionosphere of Earth should fall off according to a classical hydrostatic equilibrium in which gravity is the only controlling force.
Sample usage ( BODY ) =The latter (Fig. 3c,d , solid blue line) matches closely with the density profile from (1) in situ measurement by the SLP instrument (orange region), (2) simultaneous remote sensing by EISCAT radar (green region) (Extended Data Fig. 6 ) and is in good agreement with (3) the prediction by the International Reference Ionosphere (IRI) model (black dotted line). This close agreement gives an additional cross-check on the interpretation of the photoelectron peak shift as resulting from an ambipolar electric field.

Authors=Cornish, Alex J.; Gruber, Andreas J.; Kinnersley, Ben; Chubb, Daniel; Frangou, Anna; Caravagna, Giulio; Noyvert, Boris; Lakatos, Eszter; Wood, Henry M.; Thorn, Steve; Culliford, Richard; Arnedo-Pac, Claudia; Househam, Jacob; Cross, William; Sud, Amit; Law, Philip; Leathlobhair, Maire Ni; Hawari, Aliah; Woolley, Connor; Sherwood, Kitty; Feeley, Nathalie; Gul, Guler; Fernandez-Tajes, Juan; Zapata, Luis; Alexandrov, Ludmil B.; Murugaesu, Nirupa; Sosinsky, Alona; Mitchell, Jonathan; Lopez-Bigas, Nuria; Quirke, Philip; Church, David N.; Tomlinson, Ian P. M.; Sottoriva, Andrea; Graham, Trevor A.; Wedge, David C.; Houlston, Richard S.
Title=The genomic landscape of 2,023 colorectal cancers, 2024, doi:10.1038/s41586-024-07747-9, ID=30821870
journal=Nature
Keywords found:hdp
Sample usage ( BODY ) =Signatures were extracted using a hierarchical Dirichlet process (HDP) implemented in the R package hdp (v.0.1.5) 91 . The hierarchical Dirichlet process structure was initialized with one common grandparent node, a parent node for each of the MSS, MSI and POL tumour subtypes, and a child node for each of the 1,765 tumour samples in which SVs were called.

Authors=Yang, Haojun; Zingaro, Vincenzo Andrea; Lincoff, James; Tom, Harrison; Oikawa, Satoshi; Oses-Prieto, Juan A.; Edmondson, Quinn; Seiple, Ian; Shah, Hardik; Kajimura, Shingo; Burlingame, Alma L.; Grabe, Michael; Ruggero, Davide
Title=Remodelling of the translatome controls diet and its impact on tumorigenesis, 2024, doi:10.1038/s41586-024-07781-7, ID=30821877
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =The metabolites were extracted using the ice-cold 4:4:2 acetonitrile:methanol:water (20 ml of solvent per mg of tissue, liquid chromatography with mass spectrometry (LC-MS) grade solvents), homogenized (Omni International, TH115-PCR5H, stainless steel probe), vortexed and subjected twice to sonication for 4 min in an ice-cold water bath, frozen in liquid nitrogen for 1 min, thawed on ice and subsequently vortexed for 5 min at 2,000 rpm and 4 degC using a Thermomixer.

Authors=Soula, Mariluz; Unlu, Gokhan; Welch, Rachel; Chudnovskiy, Aleksey; Uygur, Beste; Shah, Vyom; Alwaseem, Hanan; Bunk, Paul; Subramanyam, Vishvak; Yeh, Hsi-Wen; Khan, Artem; Heissel, Soren; Goodarzi, Hani; Victora, Gabriel D.; Beyaz, Semir; Birsoy, Kivanc
Title=Glycosphingolipid synthesis mediates immune evasion in KRAS-driven cancer, 2024, doi:10.1038/s41586-024-07787-1, ID=30892311
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =For tumour samples, 10 mg of tissue were homogenized in 667 ml of methanol using a Bead Ruptor (Omni). Ice-cold chloroform (333 ml) was added to the cell lysate and tissue homogenate followed by incubation on a heat block (2,000 rpm) at 48 degC for 30 min.

Authors=Berube, Benjamin; Ernst, Evan; Cahn, Jonathan; Roche, Benjamin; de Santis Alves, Cristiane; Lynn, Jason; Scheben, Armin; Grimanelli, Daniel; Siepel, Adam; Ross-Ibarra, Jeffrey; Kermicle, Jerry; Martienssen, Robert A.
Title=Teosinte Pollen Drive guides maize diversification and domestication by RNAi, 2024, doi:10.1038/s41586-024-07788-0, ID=30892675
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =Two biological replicate samples of BC 8 S 3 leaf tissue were used to prepare Dovetail Omni-C Kit libraries following the manufacturer's protocol, and sequenced as a PE150 run on a NextSeq500.

Authors=Cavalet-Giorsa, Emile; Gonzalez-Munoz, Andrea; Athiyannan, Naveenkumar; Holden, Samuel; Salhi, Adil; Gardener, Catherine; Quiroz-Chavez, Jesus; Rustamova, Samira M.; Elkot, Ahmed Fawzy; Patpour, Mehran; Rasheed, Awais; Mao, Long; Lagudah, Evans S.; Periyannan, Sambasivam K.; Sharon, Amir; Himmelbach, Axel; Reif, Jochen C.; Knauft, Manuela; Mascher, Martin; Stein, Nils; Chayut, Noam; Ghosh, Sreya; Perovic, Dragan; Putra, Alexander; Perera, Ana B.; Hu, Chia-Yi; Yu, Guotai; Ahmed, Hanin Ibrahim; Laquai, Konstanze D.; Rivera, Luis F.; Chen, Renjie; Wang, Yajun; Gao, Xin; Liu, Sanzhen; Raupp, W. John; Olson, Eric L.; Lee, Jong-Yeol; Chhuneja, Parveen; Kaur, Satinder; Zhang, Peng; Park, Robert F.; Ding, Yi; Liu, Deng-Cai; Li, Wanlong; Nasyrova, Firuza Y.; Dvorak, Jan; Abbasi, Mehrdad; Li, Meng; Kumar, Naveen; Meyer, Wilku B.; Boshoff, Willem H. P.; Steffenson, Brian J.; Matny, Oadi; Sharma, Parva K.; Tiwari, Vijay K.; Grewal, Surbhi; Pozniak, Curtis J.; Chawla, Harmeet Singh; Ens, Jennifer; Dunning, Luke T.; Kolmer, James A.; Lazo, Gerard R.; Xu, Steven S.; Gu, Yong Q.; Xu, Xianyang; Uauy, Cristobal; Abrouk, Michael; Bougouffa, Salim; Brar, Gurcharn S.; Wulff, Brande B. H.; Krattinger, Simon G.
Title=Origin and evolution of the bread wheat D genome, 2024, doi:10.1038/s41586-024-07808-z, ID=31261145
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =For TA2576, two-week-old, dark-treated leaf tissue samples were harvested and cross-linked with formaldehyde for library preparation and Hi-C sequencing by Phase Genomics, yielding 543 million paired-end reads (150 bp). For CWI 86942, two Omni-C libraries were generated and sequenced from two-week-old, dark-treated leaf tissue samples as a service by Dovetail Genomics.

Authors=Khilkevich, Andrei; Lohse, Michael; Low, Ryan; Orsolic, Ivana; Bozic, Tadej; Windmill, Paige; Mrsic-Flogel, Thomas D.
Title=Brain-wide dynamics linking sensation to action during decision-making, 2024, doi:10.1038/s41586-024-07908-w, ID=31589252
journal=Nature
Keywords found:iri
Sample usage ( BODY ) =Fig. 4 Representation and integration of visual evidence in association and premotor areas emerges with learning. a , Schematic of stimulus presentation with random reward delivery used for recordings in untrained mice ( Methods ). b , Brain maps of unit counts recorded from untrained mice. IRI, inter-reward interval. c , Examples of top two (lowest P value) fast TF-responsive neurons in trained mice (solid lines) or untrained mice (dashed lines) in SCs, VISp, MOs, CP, SIM, DG, MRN and in the orofacial motor nucleus.

Authors=Wang, Xiongjun; Liu, Ruilong; Zhu, Wencheng; Chu, Huiying; Yu, Hua; Wei, Ping; Wu, Xueyuan; Zhu, Hongwen; Gao, Hong; Liang, Ji; Li, Guohui; Yang, Weiwei
Title=Author Correction: UDP-glucose accelerates SNAI1 mRNA decay and impairs lung cancer metastasis, 2024, doi:10.1038/s41586-024-08142-0, ID=31623746
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =Dissected tumour tissues (50 mg) were incubated with 500 ml ice-cold methanol (80%) and then ground with a tissue grinder (OMNI) on dry ice. The sample was vortexed for 1 min at 4 degC and then incubated at -80 degC for 2 h, followed by centrifugation at 14,000 g for 20 min at 4 degC.

Authors=Hou, Yu; Sun, Linyu; LaFleur, Martin W.; Huang, Linglin; Lambden, Conner; Thakore, Pratiksha I.; Geiger-Schuller, Kathryn; Kimura, Kimitoshi; Yan, Longjun; Zang, Yue; Tang, Ruihan; Shi, Jingwen; Barilla, Rocky; Deng, Liwen; Subramanian, Ayshwarya; Wallrapp, Antonia; Choi, Hee Sun; Kye, Yoon-Chul; Ashenberg, Orr; Schiebinger, Geoffrey; Doench, John G.; Chiu, Isaac M.; Regev, Aviv; Sharpe, Arlene H.; Kuchroo, Vijay K.
Title=Neuropeptide signalling orchestrates T cell differentiation, 2024, doi:10.1038/s41586-024-08049-w, ID=31949028
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =ATAC-seq ATAC-seq was performed according to the Omni-ATAC protocol 68 . In total, 10,000 cells were sorted for each ATAC-seq sample preparation.

Authors=Spencer Chapman, Michael; Wilk, C. Matthias; Boettcher, Steffen; Mitchell, Emily; Dawson, Kevin; Williams, Nicholas; Muller, Jan; Kovtonyuk, Larisa; Jung, Hyunchul; Caiado, Francisco; Roberts, Kirsty; O'Neill, Laura; Kent, David G.; Green, Anthony R.; Nangalia, Jyoti; Manz, Markus G.; Campbell, Peter J.
Title=Clonal dynamics after allogeneic haematopoietic cell transplantation, 2024, doi:10.1038/s41586-024-08128-y, ID=32090454
journal=Nature
Keywords found:hdp
Sample usage ( BODY ) =Mutational signature extraction Mutational signatures were extracted de novo using a hierarchical Dirichlet process 51 as implemented in R package HDP ( https://github.com/nicolaroberts/hdp ). These reflect the signatures of underlying mutational processes that have been active in the HSPC colonies.

Authors=Liu, Peng; Huang, Mei-Ling; Guo, Hua; McCallum, Matthew; Si, Jun-Yu; Chen, Yuan-Mei; Wang, Chun-Li; Yu, Xiao; Shi, Lu-Lu; Xiong, Qing; Ma, Cheng-Bao; Bowen, John E.; Tong, Fei; Liu, Chen; Sun, Ye-hui; Yang, Xiao; Chen, Jing; Guo, Ming; Li, Jing; Corti, Davide; Veesler, David; Shi, Zheng-Li; Yan, Huan
Title=Design of customized coronavirus receptors, 2024, doi:10.1038/s41586-024-08121-5, ID=32090460
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =Protein concentrations were determined using the Omni-Easy Instant BCA Protein Assay Kit (Epizyme, ZJ102). Western blot For detecting the cellular expression of CVRs or other receptors, cells were washed with PBS and lysed using RIPA buffer (50 mM Tris-pH 7.4, 150 mM NaCl, 1% Triton X-100, 0.5% sodium deoxycholate, 0.1% SDS, 25 mM b-glycerophosphate, 1 mM EDTA, and 1 mM PMSF) on ice for 15 min.

Authors=Jayakodi, Murukarthick; Lu, Qiongxian; Pidon, Helene; Rabanus-Wallace, M. Timothy; Bayer, Micha; Lux, Thomas; Guo, Yu; Jaegle, Benjamin; Badea, Ana; Bekele, Wubishet; Brar, Gurcharn S.; Braune, Katarzyna; Bunk, Boyke; Chalmers, Kenneth J.; Chapman, Brett; Jorgensen, Morten Egevang; Feng, Jia-Wu; Feser, Manuel; Fiebig, Anne; Gundlach, Heidrun; Guo, Wenbin; Haberer, Georg; Hansson, Mats; Himmelbach, Axel; Hoffie, Iris; Hoffie, Robert E.; Hu, Haifei; Isobe, Sachiko; Konig, Patrick; Kale, Sandip M.; Kamal, Nadia; Keeble-Gagnere, Gabriel; Keller, Beat; Knauft, Manuela; Koppolu, Ravi; Krattinger, Simon G.; Kumlehn, Jochen; Langridge, Peter; Li, Chengdao; Marone, Marina P.; Maurer, Andreas; Mayer, Klaus F. X.; Melzer, Michael; Muehlbauer, Gary J.; Murozuka, Emiko; Padmarasu, Sudharsan; Perovic, Dragan; Pillen, Klaus; Pin, Pierre A.; Pozniak, Curtis J.; Ramsay, Luke; Pedas, Pai Rosager; Rutten, Twan; Sakuma, Shun; Sato, Kazuhiro; Schuler, Danuta; Schmutzer, Thomas; Scholz, Uwe; Schreiber, Miriam; Shirasawa, Kenta; Simpson, Craig; Skadhauge, Birgitte; Spannagl, Manuel; Steffenson, Brian J.; Thomsen, Hanne C.; Tibbits, Josquin F.; Nielsen, Martin Toft Simmelsgaard; Trautewig, Corinna; Vequaud, Dominique; Voss, Cynthia; Wang, Penghao; Waugh, Robbie; Westcott, Sharon; Rasmussen, Magnus Wohlfahrt; Zhang, Runxuan; Zhang, Xiao-Qi; Wicker, Thomas; Dockter, Christoph; Mascher, Martin; Stein, Nils
Title=Structural variation in the pangenome of wild and domesticated barley, 2024, doi:10.1038/s41586-024-08187-1, ID=32470242
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =Hi-C library preparation and Illumina sequencing In situ Hi-C libraries were prepared from 1-week-old barley seedlings on the basis of the previously published protocol 13 . Dovetail Omni-C data were generated for Bowman, Aizu6, Golden Melon and 10TJ18 as per the manufacturer's instructions ( https://dovetailgenomics.com/products/omni-c-product-page/ ).

Authors=Liao, Yun; Gao, Iris H.; Kusakabe, Takato; Lin, Woan-Yu; Grier, Alexander; Pan, Xiangyu; Morzhanaeva, Olga; Shea, Terrance P.; Yano, Hiroshi; Karo-Atar, Danielle; Olsen, Kaitlin A.; Oh, Ji Hoon; Vandegrift, Kurt J.; King, Irah L.; Cuomo, Christina A.; Artis, David; Rehermann, Barbara; Lipman, Neil; Iliev, Iliyan D.
Title=Fungal symbiont transmitted by free-living mice promotes type 2 immunity, 2024, doi:10.1038/s41586-024-08213-2, ID=32470256
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =Western blot analysis Tissue samples were first immersed in 500 ml RIPA lysis buffer (89900, Thermo Fisher Scientific) supplemented with protease inhibitor cocktail tablet (5892988001, Sigma-Aldrich) and then homogenized with OMNI bead disruptor at high speed for 60 s. The tissue extracts were then spun down at 12,000 rpm for 5 min at 4 degC and the supernatants were denatured in 2x Laemmli buffer (1610737, Bio-Rad) at 95 degC for 10 min.

Authors=Doughty, Benjamin R.; Hinks, Michaela M.; Schaepe, Julia M.; Marinov, Georgi K.; Thurm, Abby R.; Rios-Martinez, Carolina; Parks, Benjamin E.; Tan, Yingxuan; Marklund, Emil; Dubocanin, Danilo; Bintu, Lacramioara; Greenleaf, William J.
Title=Single-molecule states link transcription factor binding to gene expression, 2024, doi:10.1038/s41586-024-08219-w, ID=32470274
journal=Nature
Keywords found:omni
Sample usage ( BODY ) =After spinning cells down (5 min, 300 r.c.f., 4 degC), the supernatant was aspirated using a P200 to avoid cell loss. To lyse cells using the Omni-ATAC protocol, cells were then resuspended in 200 ml of fresh ice-cold lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl 2 , 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin) by pipetting up and down three times.