cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3421006.v1
title: Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish <i>Alatina alata</i> (Cnidaria: Medusozoa: Cubozoa)

description: Background: In most animals, the mitochondrial genome is characterized by its small size, organization into a single circular molecule, and a relative conservation of the number of encoded genes. In box jellyfish (Cubozoa, Cnidaria), the mitochondrial genome is organized into 8 linear mito-chromosomes harboring between one and 4 genes each, including 2 extra protein-coding genes: <i>mt-polB</i> and <i>orf314</i>. Such an organization challenges the traditional view of mitochondrial DNA (mtDNA) expression in animals. In this study, we investigate the pattern of mitochondrial gene expression in the box jellyfish <i>Alatina alata</i>, as well as several key nuclear-encoded molecular pathways involved in the processing of mitochondrial gene transcription. Results: Read coverage of DNA-seq data is relatively uniform for all 8 mito-chromosomes, suggesting that each mito-chromosome is present in equimolar proportion in the mitochondrion. Comparison of DNA and RNA-seq based assemblies indicates that mito-chromosomes are transcribed into individual transcripts in which the beginning and ending are highly conserved. Expression levels for <i>mt-polB</i> and <i>orf314</i> are similar to those of other mitochondrial-encoded genes, which provides further evidence for them having functional roles in the mitochondrion. Survey of the transcriptome suggests recognition of the mitochondrial tRNA-Met by the cytoplasmic aminoacyl-tRNA synthetase counterpart and C-to-U editing of the cytoplasmic tRNA-Trp after import into the mitochondrion. Moreover, several mitochondrial ribosomal proteins appear to be lost. Conclusions: This study represents the first survey of mitochondrial gene expression of the linear multi-chromosomal mtDNA in box jellyfish (Cubozoa). Future exploration of small RNAs and the proteome of the mitochondrion will test the hypotheses presented herein.
DOI: 10.6084/m9.figshare.3420982
title: SeqSIMLA2 reference files

description: These are the reference sequence files accepted by SeqSIMLA2 (http://seqsimla.sourceforge.net) for different populations, including European, African, and Asian populations.
DOI: 10.6084/m9.figshare.3420982.v1
title: SeqSIMLA2 reference files

description: These are the reference sequence files accepted by SeqSIMLA2 (http://seqsimla.sourceforge.net) for different populations, including European, African, and Asian populations.
DOI: 10.6084/m9.figshare.3420979
title: SeqSIMLA2 legend files

description: These are the legend files for the reference sequences we generated for SeqSIMLA2 (http://seqsimla.sourceforge.net/download.html).
DOI: 10.6084/m9.figshare.3420979.v1
title: SeqSIMLA2 legend files

description: These are the legend files for the reference sequences we generated for SeqSIMLA2 (http://seqsimla.sourceforge.net/download.html).
DOI: 10.6084/m9.figshare.3420967.v1
title: Proyectos Pedagógicos Productivos

description: Este documento corresponde al listado de autores que han definido el concepto proyecto pedagógicos productivos y el código de referencias que se utilizó para la minería de texto
DOI: 10.6084/m9.figshare.3420967.v2
title: Proyectos Pedagógicos Productivos

description: Este documento corresponde al listado de autores que han definido el concepto proyecto pedagógicos productivos y el código de referencias que se utilizó para la minería de texto
DOI: 10.6084/m9.figshare.3420961
title: BTZR001_10.1371:journal.pone.0157682_Source DataSets.xlsx

description: Source DataSets for manuscript: "Quantitative imaging of cholinergic interneurons reveals a distinctive spatial organization and a functional gradient across the mouse striatum" by Miriam Matamales, Jürgen Götz and Jesus Bertran-Gonzalez published in PLOS ONEDOI: 10.1371/journal.pone.0157682<br><br>
DOI: 10.6084/m9.figshare.3420952
title: FamPipe external files

description: The external allele and haplotype frequencies for genetic variants that can be used by FamPipe (http://fampipe.sourceforge.net)
DOI: 10.6084/m9.figshare.3420952.v1
title: FREQ.tar.gz

description: The external allele frequencies for genetic variants required by FamPipe (http://fampipe.sourceforge.net)
DOI: 10.6084/m9.figshare.3420952.v2
title: FamPipe external files

description: The external allele frequencies for genetic variants required by FamPipe (http://fampipe.sourceforge.net)
DOI: 10.6084/m9.figshare.3420943
title: DO, DOLite, Entrez Gene database, hg19, BLAT

description: Disease Ontology
DOI: 10.6084/m9.figshare.3420943.v1
title: DO, DOLite, Entrez Gene database, hg19, BLAT

description: Disease Ontology
DOI: 10.6084/m9.figshare.3420943.v3
title: DO, DOLite, Entrez Gene database, hg19, BLAT

description: Disease Ontology
DOI: 10.6084/m9.figshare.3420943.v2
title: DO, DOLite, Entrez Gene database, hg19, BLAT

description: Disease Ontology
DOI: 10.6084/m9.figshare.3420910
title: urinary incontinence by demircan_özmen et al

description: urinary incontinence, survey, questionnaires; iciq-sf, wagner's quality of life questionnaire applied in a study population recruited in Zonguldak City-Region of Western Black Sea Costal Rim of Turkey
DOI: 10.6084/m9.figshare.3420910.v1
title: urinary incontinence by demircan_özmen et al

description: urinary incontinence, survey, questionnaires; iciq-sf, wagner's quality of life questionnaire applied in a study population recruited in Zonguldak City-Region of Western Black Sea Costal Rim of Turkey
DOI: 10.6084/m9.figshare.3420907.v1
title: Achilles_v3.3.7_README.txt

description: GeCKOv2 Achilles dataset33 cell lines<br>Achilles_v3.3.7_lognorm.gct contains the replicate-level read counts per million<br>Achilles_v3.3.7a.gct is the guide-level log2FC data used for analyses in the publication. It is not normalized across cell lines, but the median of the negative control sgRNAs are subtracted in each sample (i.e. a score of 0 represents median of the negative controls).<br>Achilles_v3.3.7_gene-soln.gct is the version of the data used for gene-level analyses across cell lines in the publication. Samples are z-score normalized and sgRNAs with &gt;1 perfect match are removed.<br>Achilles_v3.3.7_ABSOLUTE_CN_segtab.txt contains the ABSOLUTE copy number segments for each of the 33 samples.<br>Achilles_v3.3.7_sgRNA_mappings.txt contains the mapped genomic locus (loci) for each sgRNA.<br><br><br>Analysis steps v3.3.7a:<br> 1. QC and identify reps with reproducibility &lt;0.8 or are outliers on PCA or fail FP 2. remove sgRNAs(guides) with low counts in DNA samples: completely remove shRNAs with median &lt;=1 3. remove replicates that fail QC measures 4. fold change(FC) with DNA pool samples 5. zero-center median of negative controls 6. collapse replicates per line 7. sgRNAs are mapped to genes using(Achilles_v3.3.7a.gct)<br>Analysis steps v3.3.7:<br> 1. QC and identify reps with reproducibility &lt;0.8 or are outliers on PCA or fail FP 2. remove sgRNAs(guides) with low counts in DNA samples: completely remove shRNAs with median &lt;=1 3. remove sgRNAs(guides) that have &gt;1 perfect match anywhere in the reference genome 4. remove replicates that fail QC measures 5. fold change(FC) with DNA pool samples 6. Z score normalize each cell line 7. collapse replicates per line 8. sgRNAs are mapped to genes (Achilles_v3.3.7.gct) 9. ATARiS (pval=0.05) was run on guide-level data (Achilles_v3.3.7_gene-soln.gct)<br><br>
DOI: 10.6084/m9.figshare.3420907.v2
title: Achilles_v3.3.7

description: Data deposit for the publication:<br>Aguirre & Meyers, et al. Genomic copy number dictates a gene-independent cell response to CRISPR-Cas9 targeting. Cancer Discovery, 2016.<br>ABSTRACT: The CRISPR-Cas9 system enables genome editing and somatic cell genetic screens in mammalian cells. We performed genome scale loss-of-function screens in 33 cancer cell lines to identify genes essential for proliferation/survival and found a strong correlation between increased gene copy number and decreased cell viability after genome editing. Within regions of copy number gain, CRISPR-Cas9 targeting of both expressed and unexpressed genes, as well as intergenic loci, led to significantly decreased cell proliferation through induction of a G2 cell cycle arrest. By examining single guide RNAs that map to multiple genomic sites, we found that this cell response to CRISPR-Cas9 editing correlated strongly with the number of target loci. These observations indicate that genome targeting by CRISPR-Cas9 elicits a geneindependent anti-proliferative cell response. This effect has important practical implications for interpretation of CRISPR-Cas9 screening data and confounds the use of this technology for identification of essential genes in amplified regions.<br><br>GeCKOv2 Achilles dataset33 cell lines<br>Achilles_v3.3.7_lognorm.gct contains the replicate-level read counts per million<br>Achilles_v3.3.7a.gct is the guide-level log2FC data used for analyses in the publication. It is not normalized across cell lines, but the median of the negative control sgRNAs are subtracted in each sample (i.e. a score of 0 represents median of the negative controls).<br>Achilles_v3.3.7_gene-soln.gct is the version of the data used for gene-level analyses across cell lines in the publication. Samples are z-score normalized and sgRNAs with &gt;1 perfect match are removed.<br>Achilles_v3.3.7_ABSOLUTE_CN_segtab.txt contains the ABSOLUTE copy number segments for each of the 33 samples.<br>Achilles_v3.3.7_sgRNA_mappings.txt contains the mapped genomic locus (loci) for each sgRNA.<br><br><br>Analysis steps v3.3.7a:<br> 1. QC and identify reps with reproducibility &lt;0.8 or are outliers on PCA or fail FP 2. remove sgRNAs(guides) with low counts in DNA samples: completely remove shRNAs with median &lt;=1 3. remove replicates that fail QC measures 4. fold change(FC) with DNA pool samples 5. zero-center median of negative controls 6. collapse replicates per line 7. sgRNAs are mapped to genes using(Achilles_v3.3.7a.gct)<br>Analysis steps v3.3.7:<br> 1. QC and identify reps with reproducibility &lt;0.8 or are outliers on PCA or fail FP 2. remove sgRNAs(guides) with low counts in DNA samples: completely remove shRNAs with median &lt;=1 3. remove sgRNAs(guides) that have &gt;1 perfect match anywhere in the reference genome 4. remove replicates that fail QC measures 5. fold change(FC) with DNA pool samples 6. Z score normalize each cell line 7. collapse replicates per line 8. sgRNAs are mapped to genes (Achilles_v3.3.7.gct) 9. ATARiS (pval=0.05) was run on guide-level data (Achilles_v3.3.7_gene-soln.gct)<br><br>
DOI: 10.6084/m9.figshare.3420907.v3
title: Achilles_v3.3.7

description: Data deposit for the publication:<br>Aguirre & Meyers, et al. Genomic copy number dictates a gene-independent cell response to CRISPR-Cas9 targeting. Cancer Discovery, 2016.<br>ABSTRACT: The CRISPR-Cas9 system enables genome editing and somatic cell genetic screens in mammalian cells. We performed genome scale loss-of-function screens in 33 cancer cell lines to identify genes essential for proliferation/survival and found a strong correlation between increased gene copy number and decreased cell viability after genome editing. Within regions of copy number gain, CRISPR-Cas9 targeting of both expressed and unexpressed genes, as well as intergenic loci, led to significantly decreased cell proliferation through induction of a G2 cell cycle arrest. By examining single guide RNAs that map to multiple genomic sites, we found that this cell response to CRISPR-Cas9 editing correlated strongly with the number of target loci. These observations indicate that genome targeting by CRISPR-Cas9 elicits a geneindependent anti-proliferative cell response. This effect has important practical implications for interpretation of CRISPR-Cas9 screening data and confounds the use of this technology for identification of essential genes in amplified regions.<br><br>GeCKOv2 Achilles dataset33 cell lines<br>Achilles_v3.3.7_lognorm.gct contains the replicate-level read counts per million<br>Achilles_v3.3.7a.gct is the guide-level log2FC data used for analyses in the publication. It is not normalized across cell lines, but the median of the negative control sgRNAs are subtracted in each sample (i.e. a score of 0 represents median of the negative controls).<br>Achilles_v3.3.7_gene-soln.gct is the version of the data used for gene-level analyses across cell lines in the publication. Samples are z-score normalized and sgRNAs with &gt;1 perfect match are removed.<br>Achilles_v3.3.7_ABSOLUTE_CN_segtab.txt contains the ABSOLUTE copy number segments for each of the 33 samples.<br>Achilles_v3.3.7_sgRNA_mappings.txt contains the mapped genomic locus (loci) for each sgRNA.<br><br><br>Analysis steps v3.3.7a:<br> 1. QC and identify reps with reproducibility &lt;0.8 or are outliers on PCA or fail FP 2. remove sgRNAs(guides) with low counts in DNA samples: completely remove shRNAs with median &lt;=1 3. remove replicates that fail QC measures 4. fold change(FC) with DNA pool samples 5. zero-center median of negative controls 6. collapse replicates per line 7. sgRNAs are mapped to genes using(Achilles_v3.3.7a.gct)<br>Analysis steps v3.3.7:<br> 1. QC and identify reps with reproducibility &lt;0.8 or are outliers on PCA or fail FP 2. remove sgRNAs(guides) with low counts in DNA samples: completely remove shRNAs with median &lt;=1 3. remove sgRNAs(guides) that have &gt;1 perfect match anywhere in the reference genome 4. remove replicates that fail QC measures 5. fold change(FC) with DNA pool samples 6. Z score normalize each cell line 7. collapse replicates per line 8. sgRNAs are mapped to genes (Achilles_v3.3.7.gct) 9. ATARiS (pval=0.05) was run on guide-level data (Achilles_v3.3.7_gene-soln.gct)<br><br>
DOI: 10.6084/m9.figshare.3420901
title: Delayed administration of TAT.ARC protein attenuates focal ischemic brain injury and fosters recovery in the long-term: behavioral data of neuroscores and rota rod tests, daily temperature and body weight measures

description: Mice were subjected to 30 min MCAo or sham surgery and TAT.b-Gal or TAT.ARC were administered in the contralateral ventricle after 3h after the onset of ischemia and mice were observed over 28 days. DeSimoni Neuroscore was performed at indicated time points (Fig. 8) as described (De Simoni et al., 2003; Orsini et al., 2012) with some modifications. In brief, general health (Table 2) and specific focal assessments (Table 3) were separately scored, analyzed and finally added to form a summation score. Summative scores added up to a maximum of 43 points with more points meaning more deficits. Rota rod was assessed as described recently (Hoffmann et al., 2015) and the best run out of three replicates at a given time point was used for statistical analysis. Body temperature was measured daily as survival was documented. Body temperature was non-invasively assessed at the same time of the day prior to body weight measurements using subcutaneous transponders (IPTT-300, Bio Medic Data Systems), for unambiguous identification of mice in their home cages as described (Kort et al., 1998; Langer and Fietz, 2014).
DOI: 10.6084/m9.figshare.3420901.v1
title: Fig_8_behavior_temperature_bodyweight

description: Mice were subjected to 30 min MCAo or sham surgery and TAT.b-Gal or TAT.ARC were administered in the contralateral ventricle after 3h after the onset of ischemia and mice were observed over 28 days. DeSimoni Neuroscore was performed at indicated time points (Fig. 8) as described (De Simoni et al., 2003; Orsini et al., 2012) with some modifications. In brief, general health (Table 2) and specific focal assessments (Table 3) were separately scored, analyzed and finally added to form a summation score. Summative scores added up to a maximum of 43 points with more points meaning more deficits. Rota rod was assessed as described recently (Hoffmann et al., 2015) and the best run out of three replicates at a given time point was used for statistical analysis. Body temperature was measured daily as survival was documented. Body temperature was non-invasively assessed at the same time of the day prior to body weight measurements using subcutaneous transponders (IPTT-300, Bio Medic Data Systems), for unambiguous identification of mice in their home cages as described (Kort et al., 1998; Langer and Fietz, 2014).
DOI: 10.6084/m9.figshare.3420898
title: Frequency responses of rat retinal ganglion cells

description: This repository contains the data associated with the manuscript, "Frequency responses of rat retinal ganglion cells", by Alex E. Hadjinicolaou et al., published in PLOS ONE. There are three components:<br>* recordings: whole-cell recordings from retinal ganglion cells (RGCs) [recordings.7z];* reconstructions: morphological reconstructions from a subset of the recorded RGCs [ANU.7z | NVRI, part 1-3.7z]; and* figures: MATLAB code used to generate the manuscript figures.<br>Note that there is not always a 1-1 relationship between the recording name (e.g. 050211r1c3) and the Cell ID associated with the reconstruction (in this case, 20110502_c2). The Excel sheet "recordings" within the file "data summary.xlsx" lists these associations. The "morphology" sheet within the same file contains the soma/dendritic field data obtained from measurements made using FIJI, an ImageJ-based analysis program. Morphological classification was guided by Sun W, Li N, He S. Large-scale morophological survey of rat retinal ganglion cells. Vis Neurosci. 2002;19: 483–493.
DOI: 10.6084/m9.figshare.3420898.v1
title: Frequency responses of rat retinal ganglion cells

description: This repository contains the data associated with the manuscript, "Frequency responses of rat retinal ganglion cells", by Alex E. Hadjinicolaou et al., published in PLOS ONE. There are three components:<br>* recordings: whole-cell recordings from retinal ganglion cells (RGCs) [recordings.7z];* reconstructions: morphological reconstructions from a subset of the recorded RGCs [ANU.7z | NVRI, part 1-3.7z]; and* figures: MATLAB code used to generate the manuscript figures.<br>Note that there is not always a 1-1 relationship between the recording name (e.g. 050211r1c3) and the Cell ID associated with the reconstruction (in this case, 20110502_c2). The Excel sheet "recordings" within the file "data summary.xlsx" lists these associations. The "morphology" sheet within the same file contains the soma/dendritic field data obtained from measurements made using FIJI, an ImageJ-based analysis program. Morphological classification was guided by Sun W, Li N, He S. Large-scale morophological survey of rat retinal ganglion cells. Vis Neurosci. 2002;19: 483–493.
DOI: 10.6084/m9.figshare.3420883
title: TAT.ARC protein administration in the contralateral ventricle decreased lesion volume in subregions of the ischemic territory after 24 h and 72 h after 60 min middle cerebral artery occlusion

description: Stroke volume and regional stroke volume in 2 mm sagital slices used for the biochemical assays were analyzed using Analyze 5.0 and Image J software. For stroke volumetry hyperintense areas of ischemic tissue in T2-weighted images were assigned with a region of interest tool (ROI). This enabled a threshold-based segmentation which was performed by connecting all pixels within a specified threshold range around the selected seed pixel and resulted in a 3D object map of the whole stroke region. The total volume of the whole object map was calculated automatically. To calculate the regional ischemic lesion volumes that would correspond to slices prepared for immunoblots, axial MRI images were divided with ImageJ into 3 equal slices from medial to lateral. The volumes of hyperintense areas in each brain section were calculated by Analyze 5.0 as described above. Brain parenchyma were cropped for presentation purposes. after 60 min MCAo and quantified
DOI: 10.6084/m9.figshare.3420883.v1
title: TAT.ARC protein administration in the contralateral ventricle decreased lesion volume in subregions of the ischemic territory after 24 h and 72 h after 60 min middle cerebral artery occlusion

description: Stroke volume and regional stroke volume in 2 mm sagital slices used for the biochemical assays were analyzed using Analyze 5.0 and Image J software. For stroke volumetry hyperintense areas of ischemic tissue in T2-weighted images were assigned with a region of interest tool (ROI). This enabled a threshold-based segmentation which was performed by connecting all pixels within a specified threshold range around the selected seed pixel and resulted in a 3D object map of the whole stroke region. The total volume of the whole object map was calculated automatically. To calculate the regional ischemic lesion volumes that would correspond to slices prepared for immunoblots, axial MRI images were divided with ImageJ into 3 equal slices from medial to lateral. The volumes of hyperintense areas in each brain section were calculated by Analyze 5.0 as described above. Brain parenchyma were cropped for presentation purposes. after 60 min MCAo and quantified
DOI: 10.6084/m9.figshare.3420880
title: Data Sharing in Political Science: DA-RT, JETS, and Beyond

description: Presentation on DA-RT and data sharing in political science for the workshop Connecting Journals to Data Repositories, June 7, 2016, Harvard Medical School, Boston, MA <br>
DOI: 10.6084/m9.figshare.3420880.v1
title: Data Sharing in Political Science: DA-RT, JETS, and Beyond

description: Presentation on DA-RT and data sharing in political science for the workshop Connecting Journals to Data Repositories, June 7, 2016, Harvard Medical School, Boston, MA <br>
DOI: 10.6084/m9.figshare.3420880.v3
title: Data Sharing in Political Science: DA-RT, JETS, and Beyond

description: Presentation on DA-RT and data sharing in political science for the workshop Connecting Journals to Data Repositories, June 7, 2016, Harvard Medical School, Boston, MA <br>
DOI: 10.6084/m9.figshare.3420880.v2
title: Data Sharing in Political Science: DA-RT, JETS, and Beyond

description: Presentation on DA-RT and data sharing in political science for the workshop Connecting Journals to Data Repositories, June 7, 2016, Harvard Medical School, Boston, MA <br>
DOI: 10.6084/m9.figshare.3420868
title: Delayed administration of TAT.ARC protein attenuates focal ischemic brain injury: Mice were subjected to 60 min MCAo and 5 µg TAT.ARC or control protein was injected 3 h after the onset of ischemia and indirect lesion volume was assessed after 3 days.

description: Mice were treated 3h after the onset 60 min middle cerebral artery occlusion (MCAo) with TAT.b-Gal or TAT.ARC [5µg] in the contralateral ventricle of the brain and were perfused after 72 h. Infarkt volume assessment using haematoxylin staining and the following brain coordinates to select coronal slices. Mouse brains were cut in coronal sections using a mouse brain atlas (Franklin and Paxinos, 2007) to analyze direct and indirect infarct volumes, striatal area in a3 (area 3) and neuronal densities within the striatum in a3: a1 = interaural 6.6 mm/ Bregma = 2.80; a2 = interaural 5.34 mm/ Bregma = 1.54; a3 = interaural 3.94 mm/ Bregma = 0.14; a4 = interaural 1.86 mm/ Bregma = -1.94; a5 = interaural -0.08 mm/ Bregma = -3.88.