Studies
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Kay et al. 2026, DNA Repair 166 (2026) 103955 (DOI: 10.1016/j.dnarep.2026.103955; PMID: 42566817). A study of how sex and the Aag base-excision-repair gene modulate NDMA-induced liver damage, mutagenesis and tumourigenesis in mice. Reach out to Jenny Kay (kay@silentspring.org) with any questions.
**Abstract: ** N-Nitrosodimethylamine (NDMA) is present in food, water, and drugs and is considered a probable human carcinogen by the International Agency for Research on Cancer. The mechanism of ...
Submitter: Juanita Pardo Sanchez
Investigation: MIT SRP
Assays: Chemical Challenge, Cleaved caspase-3 staining and analysis, Flow Cytometry, Flow Cytometry Analysis, GPT Assay, HistoPathology Analysis, Imaging, RaDR Image Machine Learning Analysis, Tissue Collection, Tissue Imaging, Tissue Sectioning, γH2AX staining and analysis
Barathkumar Baskaran, Michelle Wang, Kristen A. Riedinger, Glen Andrew D. de Vera, Elijah E. Martin, Chad D. Vecitis, Desiree L. Plata
DOI: https://doi.org/10.1021/acs.est.6c00610
This work demonstrates formation of N-nitrosodimethylamine during electrochemical treatment of nitrite-impacted waters with mechanistic understanding to inform mitigation. ...
Experimental data for initial rate kinetics of EDA (Sll0107) from Synechocystis for KDPG, OAA, and KHG, with a mathematical model based on MM kinetics to estimate the Vm and Km values.
Submitter: Jacky Snoep
Investigation: The cyanobacterium Synechocystis has a promiscu...
Assays: Experimental data EDA kinetics, Mathematical model for EDA kinetic analysis
Michael C. Chao, Michael R. Chase, Shoko Wakabayashi, Andrew Vickers, Byron Roman, Forrest Hopkins, Peter H. Culviner, Maximillan G. Marin, Pauline Maiello, Collin R. Dietrich, Zandrea Ambrose, Philana Ling Lin, Qingyun Liu, Sarah M. Fortune
DOI: https://doi.org/10.64898/2026.04.03.714442
Abstract: Whole genome sequencing of Mycobacterium tuberculosis (Mtb) populations from clinical samples has increasingly identified genes undergoing selection within and ...
The soluble and membrane protein-enriched fraction of clonal enrichment culture BzS1 were prepared and analyzex by means of nanoLC separation of generated peptides coupled to ESI-iontrap MS/MS.
Submitter: Lars Wöhlbrand
Investigation: Shotgun and geLC MS/MS data of clonal enrichmen...
Assays: Membrane protein-enriched fraction of clonal enrichment culture BzS1 dur..., Membrane protein-enriched fraction of clonal enrichment culture BzS1 dur..., Soluble protein fraction of clonal enrichment culture BzS1 during growth..., Soluble protein fraction of clonal enrichment culture BzS1 during growth...
Nina E Gubina, Lindsay B Volk, Anna F Dormitzer, Emily M Michelsen, Lee J Pribyl, Joshua J Corrigan, Esha D Dalvie, Amanda L Armijo, Monét Norales, Nicolette A Bugher, Kayla M Schonvisky, Desiree L Plata, Bevin P Engelward, Robert G Croy, John M Essigmann, Bogdan I Fedeles
DOI: https://doi.org/10.1093/narmme/ugag035
Abstract: N-Nitrosodimethylamine (NDMA) is classified as an animal and probable human carcinogen. Murine liver DNA adducts, mutations, MGMT and ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: All Metadata, Chemical Challenge - Metadata, DNA Extraction - Metadata, ELISA - Data Linked, GPT Assay - Data Linked, Library Prep - Metadata, Mass Spectrometry - Data Linked, Mass Spectrometry Analysis - Data Linked, Mutational Spectra Analysis - Data Linked, PCR - Data Linked, RNA Extraction - Metadata, RaDR - Data Linked, Short Read Sequencing - Data Linked, Tissue Collection - Metadata
Andrew W Simonson,1,2 Michael C Chao,3,4 E Grace Bothwell,1,2 Mark A Rodgers,1,2 Luke E Hood,1,2 Forrest Hopkins,3,4 Michael R Chase,3,4 Andrew J Vickers,3,4 Alex A Smith,1,2 Ryan J Kelly,1,2 Cassaundra L Ameel,1,2 Edwin Klein,5 Harris Chishti,1,2 Marshall Malin,1,2 H Jake Borish,1,2 Pauline Maiello,1,2 Charles A Scanga,1,2 Philana Ling Lin,2,6 Sarah M Fortune,3,4,7 JoAnne L Flynn1,2*
Mycobacterium tuberculosis (Mtb) remains endemic in much of the world, resulting in frequent exposures to the ...
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Hibberd Victoria
Assays: cca1 lhy Long #1 CAB2 marker, cca1 lhy Long #1 CCA1 marker, cca1 lhy Long #1 CCR2 marker
Unpublished
DOI: none
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Kim, W.Y.
Assays: Kim et al. (2005); CO, FT; 16L:8D; WT, elf3, Kim2007 ZTL in blue light
Unpublished
DOI: none
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Ito, S.
Assays: Ito 2007 wt LD PRR9 protein, Ito et al. (2008); GI, FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, toc1, pr...
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Niwa Y.
Assays: Niwa et al. (2007); GI, FKF1, CDF1, CO, FT mRNA; 10L:14D; WT, cca1;lhy, ...
Unpublished
DOI: none
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Nakamichi Norihito
Assays: Nakamichi et al. (2007); FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, prr7;5..., Nakamichi_2010_draft: PRR9,PRR7,PRR5
Unpublished
DOI: none
Unpublished
DOI: none
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Hall A
Assays: The TIME FOR COFFEE Gene Maintains the Amplitude and Timing of Arabidops...
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Kieron D Edwards
Assays: FLOWERING LOCUS C Controls Temperature Response of the Arabidopsis Clock
Unpublished
DOI: none
Unpublished
DOI: none
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Gould Peter
Assays: 12C BL-cryptochrome paper-rep1, 12C BL-cryptochrome paper-rep2, 12C BL-cryptochrome paper-rep3, 12C RBL-cryptochrome paper-rep1, 12C RBL-cryptochrome paper-rep2, 12C RBL-cryptochrome paper-rep3, 12C RL-cryptochrome paper-rep1, 12C RL-cryptochrome paper-rep2, 12C RL-cryptochrome paper-rep3, 12C RL-cryptochrome paper-rep4, 17C BL-cryptochrome paper-rep1, 17C BL-cryptochrome paper-rep2, 17C BL-cryptochrome paper-rep3, 17C RBL-cryptochrome paper-rep1, 17C RBL-cryptochrome paper-rep2, 17C RBL-cryptochrome paper-rep3, 17C RL-cryptochrome paper-rep1, 17C RL-cryptochrome paper-rep2, 17C RL-cryptochrome paper-rep3, 17C RL-cryptochrome paper-rep4, 27C BL-cryptochrome paper-rep1, 27C BL-cryptochrome paper-rep2, 27C BL-cryptochrome paper-rep3, 27C RBL-cryptochrome paper-rep1, 27C RBL-cryptochrome paper-rep2, 27C RBL-cryptochrome paper-rep3, 27C RL-cryptochrome paper-rep1, 27C RL-cryptochrome paper-rep2, 27C RL-cryptochrome paper-rep3, 27C RL-cryptochrome paper-rep4, LUC CAB CCR2 MUT BL30 2LD to 5LL 17C 05/10/11
Unpublished
DOI: none
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Thomson Adrian
Assays: AT0005 4x SD-3xLL, AT0006 4x LD-3xLL, AT0007 4x 03:21-LL, AT0009 4x 9:15-LL, AT0010 4x 15:9-LL, AT0011 4x 12:12-LL, AT0028: 4x 3:21-LL, AT0030: 4x 9:15-LL, AT0032: 4x15:9-LL, AT0033: 4x18:6-LL, AT0039: 6:18 then DD, AT0040: 4x 9:15-DD, AT0045: 4x15:9-DD, AT0046: 4x18:6-DD, AT0053: 4x3:21-LL, AT0055: 4x9:15-LL, AT0057: 4x12:12-LL, AT0059: 4x15:09-LL, AT0061: 4x18:6-LL, AT0062: 4x6:18-LL, AT0064: 4x3:21-LL, AT0066: 4x6:18-LL, AT0068: 4x3:21-DD, AT0070: 4x6:18-DD, AT0072: 4x9:15-DD, AT0073: 4x12:12-DD, AT0074: 4x15:9-DD, AT0075: 4x18:6-DD, AT0077: 4x3:21-DD, AT0079: 4x12:12-DD, AT0091: 4x12:12-LL
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Wenden Benedicte
Assays: CCA1 and CCR2 markers in elf4 mutant under Far Red light, Clock genes under Far Red light - 3, Clock genes under Far Red light - 5, Clock genes under Far Red light - 6, Wenden_qPCR_clock_cFR, WT and elf4, Wenden_qPCR_clock_cFR, WT and phyA
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Munoz Felipe
Assays: Analysis of Control Strains Neurospora crassa, Carbon Source, Controls, Entrainment Control Analysis
Changing planetary rotation rescues the biological clock mutant lhy cca1 of Arabidopsis thaliana
Millar et al. (2015)
DOI: 10.1101/034629
Submitter: Daniel Thedie
Investigation: Millar Andrew
Assays: 030413H3: 12B-12Dx4 BB3, 060213H3: 12B-12Dx4 BBx3, 060313H1: 5L15Dx4 LLx3 (T-20), 060313H2: 12F-12Dx4 FFx3, 130212H1: 5L15Dx4 LLx3 (T-20), 130213H3: 12R-12Dx4 RRx3, 130313H1: 14L14D x 4 LL x 3 (T-28), 130313H2: 12F-12Dx4 FFx3, 200213H1: 15L5D x4 LL x3 (T-20), 200213H3: 12B-12Dx4 BB3, 200313H2: 7L 21Dx4 LLx3 (T-28), 200313H3: 12L-12Dx4 LLx3, 270213H1: 10L10Dx4 LLx3 (T-20), 270213H3: 12R-12Dx4 RRx3, 270313H1: 21L 7Dx4 LLx3 (T-28), 270313H3: 12L-12Dx4 LLx3, 290313H2: 15L 5Dx4 LLx3, AT0043: 4x 12:12-DD, AT0048 4x 18:6-DD, AT0078: 4x6:18-DD, AT0080: 4x18:6-DD
Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf
Wenden et al. (2012)
DOI: 10.1073/pnas.1118814109
Submitter: Daniel Thedie
Investigation: Wenden Benedicte
Assays: BW-detached_LD-LL_#03, BW-detached_LD-LL_#06, BW-detached_LL-LL_#14, BW-detached_LL-LL_#16, BW-detached_LL-LL_#20, BW-intact_LD-LL_#23, BW-intact_LL-LD_#31, BW-intact_LL-LL_#37, BW-intact_LL-LL_#46, BW-intact_LL-LL_#56, BW-intact_LL-LL_#58
