cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/ztb04-qec28
title: Coxiella_ Verocells_28dpi

description: Coxiella burnetii Nine Mile phase II clone 4 (NMIIC4) strain. Coxiella cells purified from infected Vero cells.
description: <strong>Tilt Series Date:</strong> 2017-10-19</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Coxiella burnetii</p>
<strong>Strain:</strong> Nine Mile phase II clone 4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Robert Heinzen. Data collected and processed by Debnath Ghosal and Mohammed Kaplan using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Refer to Heinzen lab.</p>
<strong>Sample Preparation:</strong> Freezing: 100% humidity, 4µl sample, Blot force 6, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-19-34/rawdata/</p>Cb_vero_201710190032.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-19-34/rawdata/Cb_vero_201710190032.mrc"
        > <i class="download icon"></i> Download </a></p>

        Cb_vero_201710190032_full.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-19-34/3dimage_89520/Cb_vero_201710190032_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/n8ha6-1t012
title: Lp02 ΔlspDE

description: Raw data files of Lp02 ΔlspDE
description: <strong>Tilt Series Date:</strong> 2017-03-02</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Nicholas Cianciotto at Northwestern University Medical School Data collected and processed by Debnath Ghosal</p>
<strong>Sample Preparation:</strong> 4 grids were frozen for this strain at OD= 3 Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-02-54/rawdata/</p>Lg_DeltaDE_201703020015.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-02-54/rawdata/Lg_DeltaDE_201703020015.mrc"
        > <i class="download icon"></i> Download </a></p>

        Lg_DeltaDE_201703020015_full.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-02-54/3dimage_82829/Lg_DeltaDE_201703020015_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/z6g5c-jv523
title: V. cholerae RT4236 (stationary)

description: Classical strain with ctxA deletionCell harbors pMT5 plasmid (inducible toxT)
description: <strong>Tilt Series Date:</strong> 2015-07-27</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> SIRT</p>
<strong>Collaborators and Roles:</strong> Strain from Ronald K. Taylor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Overnight cultures of Vibrio cholerae O395 NI pMT5 grown in LB pH 6.5, 1 mM IPTG and 100 ug/mL ampicilin. Take the sedimented cell clumps.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-07-27-1/3dimage_73226/</p>20150727_AK16_10001_SIRT_2K.rec,  Reconstruction (Pixel Size 0.0 nm), 12.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-07-27-1/3dimage_73226/20150727_AK16_10001_SIRT_2K.rec"
        > <i class="download icon"></i> Download </a></p>

        20150727_AK16_10001.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-07-27-1/rawdata/20150727_AK16_10001.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/dge9r-b0z32
title: Dividing Caulobacter

description: Dividing Caulobacter, low-quality tomograms
description: <strong>Tilt Series Date:</strong> 2016-02-28</p>
<strong>Data Taken By:</strong> Qing Yao</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -11.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Glow discharged Quantifoil R2/R holey carbon film. 4 ul concentrated gold suspension was added to 16 ul bacteria and mix before plunge freezing. Plunge freezing condition: 6(force)-2(duration time)-1(dry time). Tilt Series Setting: single tilt. constant angular increment, step: 1. tilt range: (-60, 60). dosage: 180/A2. defocus: -10 um. magnification: 27500.</p>
<strong>Sample Preparation:</strong> single tilt. constant angular increment, step: 1.0. tilt range: (-60, 60). dosage: 180/A2. defocus: -10um. magnification: 27500.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2016-02-28-14/3dimage_73449/</p>view80014_full.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2016-02-28-14/3dimage_73449/view80014_full.rec"
        > <i class="download icon"></i> Download </a></p>

        view80014.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2016-02-28-14/rawdata/view80014.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/20t4r-53r83
title: V. cholerae CK2188 delta-tcpR

description: Classical strain with ctxA deletionStrain name CK2188 (tcpR gene knonkout)Cell harbors pMT5 plasmid (inducible toxT)
description: <strong>Tilt Series Date:</strong> 2016-08-06</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain from Gabriela Kovacikova</p>
<strong>Purification / Growth Conditions / Treatment:</strong> O/N cultures of Vibrio cholerae O395 N1 pMT5 grown in LB, 1 mM IPTG and 100 ug/mL ampicillin.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3.5µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2016-08-06-20/rawdata/</p>20160806_YWC218_10020.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2016-08-06-20/rawdata/20160806_YWC218_10020.mrc"
        > <i class="download icon"></i> Download </a></p>

        20160806_YWC218_10020_full.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2016-08-06-20/3dimage_76422/20160806_YWC218_10020_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/whpfn-xe792
title: Oil well Actinobacterium

description: Grid box YWC208
description: <strong>Tilt Series Date:</strong> 2016-04-12</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Unspecified</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 2.0°, constant angular increment, dosage: 125.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Fixed cells received from Meng Wang/ Xiao-Lei Wu Lab at Peking University, China</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Firstly wash cells using PBS for 3 times, then add proper volum of 2.5% glutaraldehyde followed 1 hour room temp incubation (done in Peking), then send to Caltech for freezing.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
  ycw2016-04-12-4_slicer16842.jpg: inhomogeneous tubes
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2016-04-12-4/rawdata/</p>20160410_YWC210_20005.mrc,  Tilt Series (Pixel Size 0.48 nm), 1.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2016-04-12-4/rawdata/20160410_YWC210_20005.mrc"
        > <i class="download icon"></i> Download </a></p>

        20160410_YWC210_20005_full.rec,  Reconstruction (Pixel Size 1.92 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2016-04-12-4/3dimage_74246/20160410_YWC210_20005_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/2z61v-r3r46
title: V. cholerae RT4236 (stationary)

description: Classical strain with ctxA deletion.Cell harbors pMT5 plasmid (inducible toxT).
description: <strong>Tilt Series Date:</strong> 2015-05-11</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain from Ronald K. Taylor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Overnight cultures of Vibrio cholerae O395 NI pMT5 grown in LB pH 6.5, 1 mM IPTG and 100 ug/mL ampicilin</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 finder.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-05-11-53/rawdata/</p>20150511_AK07_10053.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-05-11-53/rawdata/20150511_AK07_10053.mrc"
        > <i class="download icon"></i> Download </a></p>

        20150511_AK07_10053_full.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-05-11-53/3dimage_56463/20150511_AK07_10053_full.rec"
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DOI: 10.22002/ysyav-w4j44
title: V. cholerae CK2188 delta-tcpR

description: Classical strain with ctxA deletionStrain name CK2188 (tcpR gene knonkout)Cell harbors pMT5 plasmid (inducible toxT)
description: <strong>Tilt Series Date:</strong> 2016-08-06</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain from Gabriela Kovacikova</p>
<strong>Purification / Growth Conditions / Treatment:</strong> O/N cultures of Vibrio cholerae O395 N1 pMT5 grown in LB, 1 mM IPTG and 100 ug/mL ampicillin.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3.5µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2016-08-06-5/rawdata/</p>20160806_YWC218_10005.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2016-08-06-5/rawdata/20160806_YWC218_10005.mrc"
        > <i class="download icon"></i> Download </a></p>

        20160806_YWC218_10005_part121_12.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.5hu29g
title: Occurrence Download

description: A dataset containing 796 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is one of (North America, South America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Blechnum gracile"
 ]
}

 The dataset includes 796 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007958-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26036/cnphis0001687
title: Mouse sperm cells Hi-C data

description: The 3D organization of the genome is tightly connected to its biological function. The Hi-C was introduced recently as a method for identifying higher order chromatin interactions genome wide. Aim of this study is determination of genome-wide chromatin interaction frequencies by the Hi-C approach in mouse mature sperm cells and embryonic fibroblasts. The obtained results demonstrated that 3D genome organization of mouse sperm and fibroblast cells show a high degree of similarity with each other and previously described mouse embryonic stem (ES) cells. Both A/B compartments and topological domains described earlier for other cell types are present in sperm cells. However, sperm cells and fibroblasts exhibited statistically significant differences in contact probabilities of defined loci. Tight packaging of sperm cells genome resulted in enrichment of long-range contacts in comparison to fibroblasts. Also, only 30% of differences in the number of contacts are based on differences in densities of their genome package, whereas the main source of differences is gain or loss of contacts specific for defined genome regions. Analysis of interchromosomal contacts in spermatozoa and fibroblasts revealed that large chromosomes have tendency to be co-localized within a nuclei, as well as small chromosomes. We found that the dependence of the contact probability P(s) on genomic distance for sperm is in agreement with fractal globule folding of chromatin. The similarity of the spatial DNA organization in sperm and somatic cell can serves the base for stability of 3D structure of genome through generations.
DOI: 10.26036/cnphis0001688
title: Frankliniella occidentalis isolate:FOCC.00 Genome sequencing

description: Whole genome assembly of Western flower thrips (Frankliniella occidentalis) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001689
title: FDA-CFSAN: microbial foodborne pathogen research

description: Draft and complete genome sequences of foodborne bacterial pathogens collected for research purposes at the FDA''s Center for Food Safety and Applied Nutrition.
DOI: 10.26036/cnphis0001690
title: Transcriptome analysis during seed development provides insights into co-regulated and altered gene expression between a seeded wine grape variety and it seedless somatic variant.

description: We report the application of Illumina mRNA sequencing technology for high-throughput profiling of the transcriptome of a seeded wine cultivar (wild-type) and its seedless somatic variant (mutant), sampled at three key growth stages of grapevine: E-L 15 (single flowers in compact groups), E-L 27 (young berries enlarging) and E-L 38 (berries harvest-ripe). By obtaining over 126 to 143 million and 102 to 127 million reads of 100-bp in length for the wild-type and mutant respectively, we have for the first time provided a holistic view of the transcriptional landscape during seed development in both phenotypes. We found that comparison of differentially expressed (DE) genes, gene patterns and gene enrichment between the wild-type and mutant distinguished transcriptional events in the two lines. For example, differential expression analysis in the pairwise comparison between developmental stages identified DE genes specific to the wild-type background, DE genes specific to the mutant background and DE genes commonly shared in both backgrounds. The analysis of differential expression patterns and functional category enrichment of DE genes highlighted specific and common significant coordination and enrichment of various biological processes during seed development which have lead to the identification of candidate genes for seedlessness that have altered expression in wild-type and mutant. In conclusion, we have shown here a logical approach to identify possible regulators and processes required for normal seed development that may be altered in the seedless phenotype, and highlighted the importance of somatic variants as a resources. Overall design: Examination of absolute expression count for every gene at three key time-points in a seeded grapevine variety and its seedless somatic variant.
DOI: 10.26036/cnphis0001692
title: Genome sequencing of the Anopheles punctulatus group

description: Whole genome sequencing of four species of the Anopheles punctulatus group.
DOI: 10.26036/cnphis0001693
title: Hymenopteran UCE sequences

description: Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci collected across the genome. Among insects, a primary approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g. exons). However, molecular techniques requiring RNA as a template, including transcriptome sequencing, are limited to using very high quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n=1,510) of ultraconserved elements (UCE) shared among the insect order Hymenoptera. We use in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled Hymenoptera, and we design a set of baits for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We use our UCE bait set to enrich an average of 720 UCE loci from 30 hymenopteran taxa, and we use these UCE loci to reconstruct phylogenetic relationships spanning very old (=220 MYA) to very young (=1 MYA) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support. We discuss this approach and our results in the context of elucidating the evolutionary history of one of the most diverse and speciose animal orders.
DOI: 10.26036/cnphis0001694
title: Genome-wide analysis of genome-editing specificity in human iPSCs by the CRISPR/Cas9 gene targeting system

description: Precise genome editing is crucial for realizing the full potential of human induced pluripotent stem cells (hiPSCs). Using six hiPSC lines including those with point mutations, we evaluated Cas9-mediated gene targeting with guide RNAs (gRNAs) targeting three disease-linked mutations and the AAVS1 locus.
DOI: 10.26036/cnphis0001695
title: Bos taurus Gene expression Atlas

description: RNA sequencing of one bos Taurus lactating cow