cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5401618.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - overlap integral and R0 values, and A/D ratios

description: This Excel spreadsheet, includes the results of calculation of overlap integral and R0 values for all possible combinations of TA and NTD labeled strands (using the data from steady-state fluorescence spectra of all possible singly-labeled dsDNA constructs. See figure S1 and Table S1 for information for relevant doubly-labeled dsDNA constructs.
DOI: 10.6084/m9.figshare.5401606
title: H2MM analyses of free promoter constructs - control for H2MM statistics

description: This library holds all H2MM input and analysis files for the H2MM analysis of Free promoter,<br>This was performed to identify the values of BIC' at a 2-state model, expected for free DNA with a single conformational state, and another state for acceptor photo-blinking.
DOI: 10.6084/m9.figshare.5401606.v2
title: H2MM analyses of free promoter constructs - control for H2MM statistics

description: This library holds all H2MM input and analysis files for the H2MM analysis of Free promoter,<br>This was performed to identify the values of BIC' at a 2-state model, expected for free DNA with a single conformational state, and another state for acceptor photo-blinking.
DOI: 10.6084/m9.figshare.5401618.v2
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - overlap integral and R0 values, and A/D ratios

description: This Excel spreadsheet, includes the results of calculation of overlap integral and R0 values for all possible combinations of TA and NTD labeled strands (using the data from steady-state fluorescence spectra of all possible singly-labeled dsDNA constructs. See figure S1 and Table S1 for information for relevant doubly-labeled dsDNA constructs.
DOI: 10.6084/m9.figshare.5401606.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - H2MM analyses of free promoter constructs - control for H2MM statistics

description: This library holds all H2MM input and analysis files for the H2MM analysis of Free promoter,<br>This was performed to identify the values of BIC' at a 2-state model, expected for free DNA with a single conformational state, and another state for acceptor photo-blinking.
DOI: 10.6084/m9.figshare.5401618.v3
title: Promoter open complex - overlap integral and R0 values, and A/D ratios

description: This Excel spreadsheet, includes the results of calculation of overlap integral and R0 values for all possible combinations of TA and NTD labeled strands (using the data from steady-state fluorescence spectra of all possible singly-labeled dsDNA constructs. See figure S1 and Table S1 for information for relevant doubly-labeled dsDNA constructs.
DOI: 10.6084/m9.figshare.5401540
title: FPS analysis - output - combined PyMOL file

description: This PyMOL file includes all the layers that are shown in figure 5. <br>1. The original pdb file, 4XLN2. The reconstructed one with the constraints of <i>RPo state</i> distance set3. The reconstructed one with the constraints of <i>scrunched RPo state</i> distance set<br>4. for 1-3, all the available positions of the dye AVs5. pseudoatoms representing the mean positions of the dyes6. lines connecting the relevant mean positions of the relevant dyes
DOI: 10.6084/m9.figshare.5401552
title: Anterior thalamic neuropil responds to blue light

description: The anterior thalamic neuropil shows that it is more responsive to blue rather than red light (Figure 4).
DOI: 10.6084/m9.figshare.5401558.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - H2MM analysis - input files

description: H2MM input files, extracted from analysis of raw data of RPo measurements, using the ALiX software, following the procedure and criteria in the supplementary materials. For each doubly-labeled constructs, these include files with the suffix:<br>1. _H2MM.txt - tables with smFRET bursts and their properties2. _BG.txt - the calculated BG rates per each 2s of measurement3. _H2MM_photonID.txt - a list of identities of burst photons to photon streams (0 - DexDem, 1 - DexAem, 2 - AexDem, 3 - AexAem)4. _H2MM_timestamps.txt - a list of timestamps of burst photons, in units of clocktime (12.5 ns)
DOI: 10.6084/m9.figshare.5401537
title: FPS analysis - output for analysis of scrunched RPo state

description: The fileset include output of FPS analysis applied onto the <i>scrunched RPo state</i> conformation. It includes:<br>1. distances.txt - a table of the best fit D-A distances, and their deviations from the experimental mean D-A distances2. RMSD.txt - the RMSD of the fit3. Rtable_RDAMean.txt - a table that includes the calculated mean D-A distances4. .pml scripts that allow presentation of the outcome of FPS analysis in PyMOL5. .pse file that includes combined_file_scrunchedRPo_dwells6. .xyz files that include the dyes' AVs for the optimized structure
DOI: 10.6084/m9.figshare.5401552.v1
title: Anterior thalamic neuropil responds to blue light

description: The anterior thalamic neuropil shows that it is more responsive to blue rather than red light (Figure 4).
DOI: 10.6084/m9.figshare.5401525
title: FPS analysis - input - input data

description: These files include the following input for the FPS procedure:<br>1. dye_positions.txt - a table that lists the unique name of the dye attachment point, the structure subunit (template or nontemplate strand, pdb files) to which the dye is conjugated, if it is an acceptor or a donor (A/D), the coarse-grained model used to calculate the dye AV, the dye coarse-grained dimensions (Linker length and width and ellipsoidal radii of fluorophore) and the atom ID (in the PDB file of the subunit) to which the dye is conjugated.2. distances_1_dwells.txt - a table that lists the D-A pairs and their distances, for the distance set classified as <i>RPo state</i>: the unique name of the acceptor attachment point, the unique name of the donor attachment point, the experimental mean D-A distance, the experimental D-A distance error lower boundary and the experimental D-A distance error upper boundary3. distances_2_dwells.txt - a table that lists the D-A pairs and their distances, for the distance set classified as <i>scrunched RPo state</i>The experimental mean D-A distances are shown in Fig. 4
DOI: 10.6084/m9.figshare.5401534
title: FPS analysis - output for analysis of RPo state

description: The fileset include output of FPS analysis applied onto the <i>RPo state</i> conformation. It includes:<br>1. distances.txt - a table of the best fit D-A distances, and their deviations from the experimental mean D-A distances2. RMSD.txt - the RMSD of the fit3. Rtable_RDAMean.txt - a table that includes the calculated mean D-A distances4. .pml scripts that allow presentation of the outcome of FPS analysis in PyMOL5. .pse file that includes combined_file_RPo_dwells6. .xyz files that include the dyes' AVs for the optimized structure
DOI: 10.6084/m9.figshare.5401540.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - FPS analysis - output - combined PyMOL file

description: This PyMOL file includes all the layers that are shown in figure 5. <br>1. The original pdb file, 4XLN2. The reconstructed one with the constraints of <i>RPo state</i> distance set3. The reconstructed one with the constraints of <i>scrunched RPo state</i> distance set<br>4. for 1-3, all the available positions of the dye AVs5. pseudoatoms representing the mean positions of the dyes6. lines connecting the relevant mean positions of the relevant dyes
DOI: 10.6084/m9.figshare.5401522.v2
title: FPS analysis - input - structure to compare against reconstructed structure

description: This is the pdb:4XLN file of the monomeric unit of bacterial RPo, including the full transcription bubble.The FPS reconstructed complex is compared against this pdb file.
DOI: 10.6084/m9.figshare.5401537.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - FPS analysis - output for analysis of scrunched RPo state

description: The fileset include output of FPS analysis applied onto the <i>scrunched RPo state</i> conformation. It includes:<br>1. distances.txt - a table of the best fit D-A distances, and their deviations from the experimental mean D-A distances2. RMSD.txt - the RMSD of the fit3. Rtable_RDAMean.txt - a table that includes the calculated mean D-A distances4. .pml scripts that allow presentation of the outcome of FPS analysis in PyMOL5. .pse file that includes combined_file_scrunchedRPo_dwells6. .xyz files that include the dyes' AVs for the optimized structure
DOI: 10.6084/m9.figshare.5401519
title: FPS analysis - input - structure subunits

description: These pdb files include the atomic coordinates of the template strand (first file), the nontemplate strand (second file) and the RNAP holoenzyme (third file).These files are used for the docking on top of the 4XLN pdb file using the FRET-derived D-A distance constraints.
DOI: 10.6084/m9.figshare.5401525.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - FPS analysis - input - input data

description: These files include the following input for the FPS procedure:<br>1. dye_positions.txt - a table that lists the unique name of the dye attachment point, the structure subunit (template or nontemplate strand, pdb files) to which the dye is conjugated, if it is an acceptor or a donor (A/D), the coarse-grained model used to calculate the dye AV, the dye coarse-grained dimensions (Linker length and width and ellipsoidal radii of fluorophore) and the atom ID (in the PDB file of the subunit) to which the dye is conjugated.2. distances_1_dwells.txt - a table that lists the D-A pairs and their distances, for the distance set classified as <i>RPo state</i>: the unique name of the acceptor attachment point, the unique name of the donor attachment point, the experimental mean D-A distance, the experimental D-A distance error lower boundary and the experimental D-A distance error upper boundary3. distances_2_dwells.txt - a table that lists the D-A pairs and their distances, for the distance set classified as <i>scrunched RPo state</i>The experimental mean D-A distances are shown in Fig. 4
DOI: 10.6084/m9.figshare.5401522.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - FPS analysis - input - structure to compare against reconstructed structure

description: This is the pdb:4XLN file of the monomeric unit of bacterial RPo, including the full transcription bubble.The FPS reconstructed complex is compared against this pdb file.
DOI: 10.6084/m9.figshare.5401534.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - FPS analysis - output for analysis of RPo state

description: The fileset include output of FPS analysis applied onto the <i>RPo state</i> conformation. It includes:<br>1. distances.txt - a table of the best fit D-A distances, and their deviations from the experimental mean D-A distances2. RMSD.txt - the RMSD of the fit3. Rtable_RDAMean.txt - a table that includes the calculated mean D-A distances4. .pml scripts that allow presentation of the outcome of FPS analysis in PyMOL5. .pse file that includes combined_file_RPo_dwells6. .xyz files that include the dyes' AVs for the optimized structure
DOI: 10.6084/m9.figshare.5401537.v2
title: FPS analysis - output for analysis of scrunched RPo state

description: The fileset include output of FPS analysis applied onto the <i>scrunched RPo state</i> conformation. It includes:<br>1. distances.txt - a table of the best fit D-A distances, and their deviations from the experimental mean D-A distances2. RMSD.txt - the RMSD of the fit3. Rtable_RDAMean.txt - a table that includes the calculated mean D-A distances4. .pml scripts that allow presentation of the outcome of FPS analysis in PyMOL5. .pse file that includes combined_file_scrunchedRPo_dwells6. .xyz files that include the dyes' AVs for the optimized structure
DOI: 10.6084/m9.figshare.5401534.v2
title: FPS analysis - output for analysis of RPo state

description: The fileset include output of FPS analysis applied onto the <i>RPo state</i> conformation. It includes:<br>1. distances.txt - a table of the best fit D-A distances, and their deviations from the experimental mean D-A distances2. RMSD.txt - the RMSD of the fit3. Rtable_RDAMean.txt - a table that includes the calculated mean D-A distances4. .pml scripts that allow presentation of the outcome of FPS analysis in PyMOL5. .pse file that includes combined_file_RPo_dwells6. .xyz files that include the dyes' AVs for the optimized structure
DOI: 10.6084/m9.figshare.5401525.v2
title: FPS analysis - input - input data

description: These files include the following input for the FPS procedure:<br>1. dye_positions.txt - a table that lists the unique name of the dye attachment point, the structure subunit (template or nontemplate strand, pdb files) to which the dye is conjugated, if it is an acceptor or a donor (A/D), the coarse-grained model used to calculate the dye AV, the dye coarse-grained dimensions (Linker length and width and ellipsoidal radii of fluorophore) and the atom ID (in the PDB file of the subunit) to which the dye is conjugated.2. distances_1_dwells.txt - a table that lists the D-A pairs and their distances, for the distance set classified as <i>RPo state</i>: the unique name of the acceptor attachment point, the unique name of the donor attachment point, the experimental mean D-A distance, the experimental D-A distance error lower boundary and the experimental D-A distance error upper boundary3. distances_2_dwells.txt - a table that lists the D-A pairs and their distances, for the distance set classified as <i>scrunched RPo state</i>The experimental mean D-A distances are shown in Fig. 4
DOI: 10.6084/m9.figshare.5401519.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - FPS analysis - input - structure subunits

description: These pdb files include the atomic coordinates of the template strand (first file), the nontemplate strand (second file) and the RNAP holoenzyme (third file).These files are used for the docking on top of the 4XLN pdb file using the FRET-derived D-A distance constraints.
DOI: 10.6084/m9.figshare.5401525.v3
title: FPS analysis - input - input data

description: These files include the following input for the FPS procedure:<br>1. dye_positions.txt - a table that lists the unique name of the dye attachment point, the structure subunit (template or nontemplate strand, pdb files) to which the dye is conjugated, if it is an acceptor or a donor (A/D), the coarse-grained model used to calculate the dye AV, the dye coarse-grained dimensions (Linker length and width and ellipsoidal radii of fluorophore) and the atom ID (in the PDB file of the subunit) to which the dye is conjugated.2. distances_1_dwells.txt - a table that lists the D-A pairs and their distances, for the distance set classified as <i>RPo state</i>: the unique name of the acceptor attachment point, the unique name of the donor attachment point, the experimental mean D-A distance, the experimental D-A distance error lower boundary and the experimental D-A distance error upper boundary3. distances_2_dwells.txt - a table that lists the D-A pairs and their distances, for the distance set classified as <i>scrunched RPo state</i>The experimental mean D-A distances are shown in Fig. 4
DOI: 10.6084/m9.figshare.5400901.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - usALEX-smFRET raw data for figure S3

description: The dataset includes the raw data of usALEX-smFRET measurements (stored in photon-HDF5 file format) of 6 different doubly-labeled lacCONS promoter dsDNA constructs. This raw data is the basis for figure S3.
DOI: 10.6084/m9.figshare.5400901.v3
title: usALEX-smFRET raw data for figure S4

description: The dataset includes the raw data of usALEX-smFRET measurements (stored in photon-HDF5 file format) of 6 different doubly-labeled lacCONS promoter dsDNA constructs. This raw data is the basis for figure S3.
DOI: 10.6084/m9.figshare.5400916.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - a python notebook summarizing the analysis of usALEX-smFRET for the formation of figure S3

description: The following Python notebook summarizes the analysis performed by the FRETBursts software to form figure S3
DOI: 10.6084/m9.figshare.5400901.v2
title: usALEX-smFRET raw data for figure S3

description: The dataset includes the raw data of usALEX-smFRET measurements (stored in photon-HDF5 file format) of 6 different doubly-labeled lacCONS promoter dsDNA constructs. This raw data is the basis for figure S3.
DOI: 10.6084/m9.figshare.5400796
title: Data from: Interannual bumble bee abundance is driven by indirect climate effects on floral resource phenology.

description: This is an archive of the data used in the publication: Ogilvie JE, Griffin SR, Gezon ZJ, Inouye BD, Underwood N, Inouye DW, Irwin RE. 2017. Interannual bumble bee abundance is driven by indirect climate effects on floral resource phenology. Ecology Letters, doi: 10.1111/ele.12854<br>DATA DESCRIPTION<br><br><b>Bombus_floral_climate_data_for_SEMs.csv</b><br><b><br></b>This file has the 2009-2016 data used in the structural equation models. <i><b>peak.bee.count</b></i> is the annual peak number of bumble bees netted from flowers on a sampling day. <i><b>sampling.time.hr</b></i> is the amount of time in hours that a site was sampled on the peak abundance sampling day. <i><b>floral.sum</b></i> is the sum of flowers from first flower accumulated to 80% of the season's total flower count. <b><i>number.floral.days</i></b> is the number of days above a low flower threshold of 0.75 flowers/m<sup>2</sup> (or 3 flowers per 2 x 2 m plot). Flowers were counted within 30 2 x 2 m plots (120 m<sup>2</sup>) every two days. <b><i>may.to.july.precip.cm</i></b> is the amount of precipitation (snow and rain) from May 1 through to the end of July in cm water content (measured at the Rocky Mountain Biological Laboratory, RMBL). <i><b>snowmelt.doy</b></i> is the day of year that a 5 x 5 m plot was bare of snow.<br><b>Longterm_climate_floral_data.csv</b><br><br>This file has the data used to examine long-term trends in the climate and floral variables, 1974-2016. <i><b>snowmelt.doy</b></i> is the day of year that a 5 x 5 m plot was bare of snow. <b><i>may.to.july.precip.cm</i></b> is the amount of precipitation (snow and rain) from May 1 through to the end of July in cm water content (measured at Crested Butte). <i><b>floral.sum</b></i> is the sum of flowers from first flower accumulated to 80% of the season's total flower count. <b><i>number.floral.days</i></b> is the number of days above a low flower threshold of 0.75 flowers/m<sup>2</sup> (or 3 flowers per 2 x 2 m plot). Flowers were counted within 23 2 x 2 m plots (92 m<sup>2</sup>) every two days. There are separate floral variables for the three bumble bee species.<br>Please see the original paper for additional details.
DOI: 10.6084/m9.figshare.5400916.v3
title: A python notebook summarizing the analysis of usALEX-smFRET for the formation of figure S4

description: The following Python notebook summarizes the analysis performed by the FRETBursts software to form figure S3
DOI: 10.6084/m9.figshare.5400802.v2
title: A python notebook summarizing the analysis of usALEX-smFRET for the formation of figure S2

description: The following Python notebook summarizes the analysis performed by the FRETBursts software to form figure S2
DOI: 10.6084/m9.figshare.5400916.v2
title: A python notebook summarizing the analysis of usALEX-smFRET for the formation of figure S3

description: The following Python notebook summarizes the analysis performed by the FRETBursts software to form figure S3
DOI: 10.6084/m9.figshare.5400784
title: Activity to light and dark is spatially segregated in thalamic neuropil

description: The anterior thalamus neuropil of <i>elavl3:GCaMP6f </i>fish responds dorso-caudally to light ON and rostro-ventrally to light OFF (Figure 5)
DOI: 10.6084/m9.figshare.5400784.v1
title: Activity to light and dark is spatially segregated in thalamic neuropil

description: The anterior thalamus neuropil of <i>elavl3:GCaMP6f </i>fish responds dorso-caudally to light ON and rostro-ventrally to light OFF (Figure 5)
DOI: 10.6084/m9.figshare.5400781
title: Optogenetic inhibition of thalamic neurons using ACRs

description: Habenula activity to light ON and OFF in fish with GtACR1 expressed in the thalamus (Figure 8)
DOI: 10.6084/m9.figshare.5400793.v2
title: usALEX-smFRET raw data for figure S2

description: The dataset includes the raw data of usALEX-smFRET measurements (stored in photon-HDF5 file format) of 6 different doubly-labeled lacCONS promoter dsDNA constructs. This raw data is the basis for figure S2.
DOI: 10.6084/m9.figshare.5400781.v1
title: Optogenetic inhibition of thalamic neurons using ACRs

description: Habenula activity to light ON and OFF in fish with GtACR1 expressed in the thalamus (Figure 8)
DOI: 10.6084/m9.figshare.5400793.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - usALEX-smFRET raw data for figure S2

description: The dataset includes the raw data of usALEX-smFRET measurements (stored in photon-HDF5 file format) of 6 different doubly-labeled lacCONS promoter dsDNA constructs. This raw data is the basis for figure S2.
DOI: 10.6084/m9.figshare.5400742
title: UVMeltData.zip

description: UV Melt Data for GAAA tetraloops and d(GNA) triloops<br>
DOI: 10.6084/m9.figshare.5400778.v2
title: A python notebook summarizing the analysis of usALEX-smFRET for the formation of figure 2

description: The following Python notebook summarizes the analysis performed by the FRETBursts software to form figure 2
DOI: 10.6084/m9.figshare.5400778.v1
title: conformational dynamics of the transcription bubble in RNAP-promoter open complex - a python notebook summarizing the analysis of usALEX-smFRET for the formation of figure 2

description: The following Python notebook summarizes the analysis performed by the FRETBursts software to form figure 2
DOI: 10.6084/m9.figshare.5400742.v1
title: UVMeltData.zip

description: UV Melt Data for GAAA tetraloops and d(GNA) triloops<br>
DOI: 10.6084/m9.figshare.5400739
title: OPEN RESEARCH: Keio University - September 12, 2017

description: Event poster, information and photos of speakers from the Keio University event about Open Research: The Future of Scholarly Communication.September 12, 2017Tokyo, Japan<br>Speakers:- Jiro Kokuryo - Vice President for International Collaboration and Information Infrastructure; Professor of Policy Management, Keio University- Ed Gerstner - Regional Scientific Director, Greater China, SpringerNature- Nobuko Miyairi - Regional Director, Asia Pacific, ORCiD- Mark Hahnel - Founder and CEO, figshare (part of the Digital Science portfolio)- Yasuhiro Murayama - Research Executive Director of the Strategic Program Office, National Institute of Information and Communications Technology (NICT)
DOI: 10.6084/m9.figshare.5400769.v2
title: usALEX-smFRET raw data for figure 2

description: The dataset includes the raw data of usALEX-smFRET measurements (stored in photon-HDF5 file format) of 3 different doubly-labeled lacCONS promoter dsDNA constructs. This raw data is the basis for figure 2.