cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25550/vxy
title: Skull vault formation in individual WT AB Fish

description: An individual fish was imaged successively from 11-21 dpf by confocal microscopy, during the period of induction and growth of the frontal and parietal bones. The fish was transgenic for col1a1a:gfp, marking chondrocytes, and for sp7:mcherry, marking osteoblasts.
DOI: 10.25550/3qq6
title: Activity of chimp neural crest enhancer near NARS2 in E11.5 transgenic mouse embryo – Tg(panTro4_chr11:76409267-76410157::LacZ).

description: Tg(panTro4_chr11:76409267-76410157::LacZ) chimp neural crest enhancer with activity in the periocular mesenchyme, mandibular prominence of the 1st branchial arch, 2nd branchial arch, proximal forelimb bud, and tail mesenchyme. This enhancer lacks the expression in the forebrain, midbrain, maxillary prominence of the 1st branchial arch, hindlimb bud and midgut, as well as decreased expression in the forelimb bud, somites, and 2nd branchial arch when compared with the equivalent human enhancer; this demonstrates a human species-specific bias when comparing these two species.
DOI: 10.25550/tmm
title: Gene expression profiling of the tongue in mice with a conditional inactivation of Tgfbr2 at embryonic day E14.5

description: We performed global gene expression analyses of the tongue in Wnt1-Cre;Tgfbr2^fl/fl and Tgfbr2^fl/fl control mice at embryonic day E14.5. Total RNA samples (1 ug per sample) were converted into biotin-labeled cRNA using the Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP and standard protocols recommended by Affymetrix (Santa Clara, CA). Fragmented cDNA was applied to GeneChip, Mouse Genome 430 2.0 Arrays (Affymetrix) that contain probe sets designed to detect over 39000 transcripts. Microarrays were hybridized, processed and scanned, as previously described using manufacturers recommended conditions.
DOI: 10.25550/tn2
title: RNA-Seq analysis in E13.5 mouse palates

description: This dataset includes the results of RNA-Seq analysis in E13.5 mouse palates. The downloadable Excel file includes for each gene: * gene: official mouse gene symbol * gene length (bp, exons only) * RPKM (Reads per kb / million reads) in two replicate samples To download the data, log in and click on the "Download dataset" button. In addition to the tabulated Excel format, the same data can also be viewed as genome-wide coverage maps on the links to Genome Browser in the Additional Information section .
DOI: 10.25550/tp0
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm938

description: See link to the data preparation protocols for this study in the Additional Information section **Enhancer location:** Mouse genome mm9, chr7: 137569281-137570835 **Name:** mCF224 **Vista Enhancer ID:** mm938 **Nearest craniofacial gene or locus:** Fgfr2 **Enhancer expression:** positive **Tissues where active:** eye, tail, other, limb **Comment on OPT files:** This data set includes the following: * 4 movie (.avi) files: A CLIP file that provides an overview of the 3-D model generated by Optical Projection Tomography (OPT)Thresholding-based false-color representation shows unstained regions of the embryo in green, LacZ signal in red. In addition, 3 movies representing a pass-through view of the OPT model in the coronal, sagittal, or transverse plane. * 4 files in .tgz format. Each of these corresponds to one of the .avi files and unzips to a set of .png files, each of which represents the individual frames of the movie (and, in case of the transverse/sagittal/coronal movies, can be used to retrieve individual virtual sections through features of interest in .png image format). [.tgz files can be unzipped with WinZip or Stuffit on a PC or Mac. On linux, treat the file as a gzipped .tar file: gunzip &lt; file.tgz | tar xvf - ]
DOI: 10.25550/tv6
title: microCT - Soft Tissue of Wnt1-Cre;Tgfbr2flf;Alk5fl+ mouse at E15.5

description: Mouse ID: JI246 This dataset includes 1 microCT scan of the skull of an Wnt1-Cre; Tgfbr2flfl; Alk5fl+ mouse mouse at E15.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/v68
title: Gene expression profiling of the mandible in mice with a conditional inactivation of Erk2 at embryonic day E12.5

description: We performed global gene expression analyses of the mandible in Wnt1-Cre;Erk2^fl/fl and Erk2^fl/fl control mice at embryonic day E12.5. Total RNA samples (1 ug per sample) were converted into biotin-labeled cRNA using the Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP and standard protocols recommended by Affymetrix (Santa Clara, CA). Fragmented cDNA was applied to GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix) that contain probe sets designed to detect over 39000 transcripts. Microarrays were hybridized, processed and scanned as previously described using manufacturers recommended conditions.
DOI: 10.25550/v8t
title: microCT - Bone Tissue of C57BL6J Mouse at E18.5

description: Mouse ID: JI234 This dataset includes 1 microCT scan of the skull of a C57BL6J mouse at E18.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/vae
title: microCT - Soft Tissue of Wnt1-Cre;Tgbr2fl/fl;Tgfb2+ mouse at E18.5

description: Mouse ID: JI217 This dataset includes 1 microCT scan of the skull of a Wnt1-Cre; Tgfbr2fl/fl; Tgfb2+ mouse at E18.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/vcm
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm657

description: See link to the data preparation protocols for this study in the Additional Information section **Enhancer location:** Mouse genome mm9, chr17: 44859063-44860738 **Name:** mCF206 **Vista Enhancer ID:** mm657 **Nearest craniofacial gene or locus:** Runx2 **Enhancer expression:** positive **Tissues where active:** branchial arch **Comment on OPT files:** This data set includes the following: * 4 movie (.avi) files: A CLIP file that provides an overview of the 3-D model generated by Optical Projection Tomography (OPT)Thresholding-based false-color representation shows unstained regions of the embryo in green, LacZ signal in red. In addition, 3 movies representing a pass-through view of the OPT model in the coronal, sagittal, or transverse plane. * 4 files in .tgz format. Each of these corresponds to one of the .avi files and unzips to a set of .png files, each of which represents the individual frames of the movie (and, in case of the transverse/sagittal/coronal movies, can be used to retrieve individual virtual sections through features of interest in .png image format). [.tgz files can be unzipped with WinZip or Stuffit on a PC or Mac. On linux, treat the file as a gzipped .tar file: gunzip &lt; file.tgz | tar xvf - ]
DOI: 10.25550/vne
title: microCT - Soft Tissue of K14-Cre;Tgfbr2flfl mouse at E15.5

description: This dataset includes 1 microCT scan of the skull of a K14-Cre;Tgfbr2fl/fl mouse at E15.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/vra
title: microCT - Soft Tissue of C57BL6J mouse at E13.5

description: This dataset includes 1 microCT scan of the skull of a C57BL6J mouse at E13.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/vwt
title: microCT - Bone Tissue of Fgfr2flfl control at P0

description: This dataset includes 1 microCT scan of the skull of a Fgfr2flfl mouse at P0. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.5281/zenodo.3437653
title: Injectable, Scalable 3D Tissue-Engineered Model of Marrow Hematopoiesis

description: Raw data associated with the publication "<strong>Injectable, Scalable 3D Tissue-Engineered Model of Marrow Hematopoiesis"</strong> <strong>DOI: 10.1016/j.biomaterials.2019.119665</strong>
DOI: 10.5281/zenodo.3437654
title: Injectable, Scalable 3D Tissue-Engineered Model of Marrow Hematopoiesis

description: Raw data associated with the publication "<strong>Injectable, Scalable 3D Tissue-Engineered Model of Marrow Hematopoiesis"</strong> <strong>DOI: 10.1016/j.biomaterials.2019.119665</strong>
DOI: 10.17632/gncknw3g7h.10
title: Data for: Ethnomedicine of Tetun ethnic people in West Timor Indonesia; Philosophy and practice in the treatment of malaria

description: Supplementary data PLANTS USED FOR THE TREATMENT OF MALARIA BY TETUN ETHNIC PEOPLE IN WEST TIMOR (INDONESIA) Note: 1. Data collected in April 20017 to December 2017 in Belu and Malaka Districts (West Timor, Indonesia). 2. Data collected by interview on 94 informants of Tetun ethnic people.
DOI: 10.18739/a2599z20q
title: North Greenland Eemian Ice Drilling (NEEM) 2008 S3 Firn Core Impurity Data

description: This dataset was used to create a depth-age scale of the NEEM (North Greenland Eemian Ice Drilling) 2008 S3 firn core using annual layer counting of multiple seasonally-varying chemical parameters (McConnell et al., 2007). This depth-age scale was used to date the layers of other NEEM firn cores, in an effort to date the layers of interesting physical property and chemical impurities layers. The 2008 S3 chronology is consistent with the independently layer-counted 2011 S1 (Sigl et al., 2015) and D4 core chronologies (McConnell et al., 2007) at &gt;10 volcanic tie points between 1750 and 2008. Mean 1850 to 2008, water-equivalent accumulation rates in the 2008 S3 and 2011 S1 cores were 202 and 206 kilograms per square meter per year (kg/m2/y) (0.220 and 0.224 meters ice eq. per annum (m/a)), respectively, suggesting relatively uniform net snowfall rates at NEEM. Estimated uncertainty in the 2008 S3 and 2011 S1 chronologies are &lt;1 year, suggesting an estimated uncertainty in the 2009 S2 chronology used in this study of &lt;2 years. This data set includes measurements of S (nanograms per gram (ng/g)), Sr (nanograms per gram (ng/g)), and Ca (nanograms per gram (ng/g)) concentrations by Year (A.D.) and depth from surface (m) from the NEEM 2008 S3 firn core.
DOI: 10.18739/a2930nv40
title: Microbial community composition of lake sediment in Thule, Greenland during the summer of 2014

description: Microbes have survived, and thrived, on our planet for at least 3.5 billion years, and yet we know surprisingly little about these organisms, in large part due to the phenomenon of uncultivability. The phenomenon of uncultivability was first noted in 1898, and it has continuously been observed that the number of microbial cells in samples are inconsistent with the number of colonies formed on nutrient media, now known as “The Great Plate Count Anomoly.” To this day, much of what we know about microbes is from culture-independent approaches, and the majority of microbial species in nature remain uncultivated. It has been shown previously that growing microorganisms in their natural environment (in situ) can greatly increase recovery, likely due to the availability of critical growth factors present in their native habitat, but absent within the lab. Here, we compare standard cultivation approaches with a variety of in situ based cultivation techniques to grow microorganisms in an extreme environment of the High Arctic (lake sediment in Thule, Greenland). Cultivation experiments were performed on 3 occasions throughout the summer of 2014 using either standard cultivation, five in situ devices, or under anaerobic conditions. The resulting culture collections were compared. A total of 1173 isolates were cultivated and, utilizing PCR-aided amplification of the 16S rRNA gene, taxonomically identified using the Silva v.117 database. Our isolates grouped into 183 OTUs, across 89 generas and 24 Orders, representing 4 bacterial phyla, 1 eukaryotic phylum. We observed minimal overlap among culture collections obtained by different approaches: only 21 of 183 OTUs were common among all three techniques (standard, in situ, anaerobic), with both standard and in situ methods resulting in large, byt unique collections. Representatives from the orders Xanthomonadales, Streptomycetales, and Cytophagales were isolated exclusively by traditional cultivation, while isolates belonging to the orders Solirubrobacterales, Chromatiales, and Bacillales were cultivated exclusively by the in situ approaches. Overall, our results show that multiple methods of cultivation should be employed in conjunction to generate a thorough collection of isolates from a given environment.
DOI: 10.25550/tpc
title: microCT - Soft Tissue of K14-Cre;Tgfbr2fl/fl mouse at P0

description: Mouse ID: JI210 This dataset includes 1 microCT scan of the skull of a K14-Cre;Tgfbr2fl/fl mouse at P0. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/trw
title: microCT - Soft Tissue of a K14-Cre;Fgfr2fl/fl mouse at E18.5

description: Mouse ID: ZZ274 This dataset includes microCT scans of the skull of a K14-Cre;Fgfr2fl/fl mouse at E18.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/tse
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm933

description: See link to the data preparation protocols for this study in the Additional Information section **Enhancer location:** Mouse genome mm9, chr13: 116476829-116478253 **Name:** mCF219 **Vista Enhancer ID:** mm933 **Nearest craniofacial gene or locus:** Isl1 **Enhancer expression:** positive **Tissues where active:** nose, cranial nerve, dorsal root ganglion **Comment on OPT files:** This data set includes the following: * 4 movie (.avi) files: A CLIP file that provides an overview of the 3-D model generated by Optical Projection Tomography (OPT)Thresholding-based false-color representation shows unstained regions of the embryo in green, LacZ signal in red. In addition, 3 movies representing a pass-through view of the OPT model in the coronal, sagittal, or transverse plane. * 4 files in .tgz format. Each of these corresponds to one of the .avi files and unzips to a set of .png files, each of which represents the individual frames of the movie (and, in case of the transverse/sagittal/coronal movies, can be used to retrieve individual virtual sections through features of interest in .png image format). [.tgz files can be unzipped with WinZip or Stuffit on a PC or Mac. On linux, treat the file as a gzipped .tar file: gunzip &lt; file.tgz | tar xvf - ]
DOI: 10.25550/tt2
title: microCT - Soft Tissue of C57BL6J at P0

description: This dataset includes 1 microCT scan of the skull of a C57BL6J mouse at P0. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/tt8
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm403

description: See link to the data preparation protocols for this study in the Additional Information section See links to Genome Browser in the Additional Information section. **Enhancer location:** Mouse genome mm9, chr6:50874551-50876236 **Name:** mCF89 **Vista Enhancer ID:** mm403 **Nearest craniofacial gene or locus:** BMP4 **Enhancer expression:** positive **Tissues where active:** branchial arch This data set includes the following: * A .pdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. Follow corresponding link in the Additional Information section to see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory * 4 movie (.avi) files: A CLIP file that provides an overview of the 3-D model generated by Optical Projection Tomography (OPT). Thresholding-based false-color representation shows unstained regions of the embryo in green, LacZ signal in red. In addition, 3 movies representing a pass-through view of the OPT model in the coronal, sagittal, or transverse plane. See links in External Referece section to download the following movie files: Overview movie, Coronal plane movie, Sagittal plane movie, Transverse plane movie * 4 files in .tgz format. Each of these corresponds to one of the .avi files and unzips to a set of .png files, each of which represents the individual frames of the movie (and, in case of the transverse/sagittal/coronal movies, can be used to retrieve individual virtual sections through features of interest in .png image format). [.tgz files can be unzipped with WinZip or Stuffit on a PC or Mac.On linux, treat the file as a gzipped .tar file: gunzip &lt; file.tgz | tar xvf - ] * Tested element.txt: Download the text file mCF89metadata.txt from the External Reference section
DOI: 10.25550/tvm
title: microCT - Bone Tissue of a Fgfr2fl/fl Control mouse at E16.5

description: Mouse ID: ZZ353 This dataset includes microCT scans of the skull of a Fgfr2fl/fl Control mouse at E16.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/twm
title: microCT - Soft Tissue of a Wnt1-Cre; Tgfbr2fl/fl mouse at E15.5

description: Mouse ID: AS351 This dataset includes microCT scans of the head of a Wnt1-Cre; Tgfbr2fl/fl mouse at E15.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/v3m
title: Transgenic Mouse Enhancer OPT Assays - hs1629

description: ChIP-seq, RNA-seq and transgenic assays to identify non-coding regulatory elements (enhancers) active during craniofacial development. Follow this [link](http://enhancer.lbl.gov/cgi-bin/imagedb3.pl?form=presentation&show=1&experiment_id=1629&organism_id=1) to see associated data in the VISTA browser. (Note that the VISTA Browser data from this link corresponds to E11.5 while the data shown in here is for E14.5)
DOI: 10.25550/v76
title: Gene expression RNA-Seq - mouse E14.5 Wild Type Anterior Oral Palate

description: This data set contains BAM RNA-Seq data for the Anterior Oral region of the palatal shelves at the E14.5 time-point in the developing mouse. Wild-type CD-1 outbred mice were used in this experiment. For each different region: Anterior Medial Palate - From the anterior region of the palatal shelf (closer to the front of the face). Also closer to the center of the palatal shelves (closer to the Medial-Edge Epithelia). Posterior Medial Palate - From the posterior region of the palatal shelf (closer to the hind-brain). Also located closer to the center of the palatal shelves (closer to the MEE). Anterior Lateral Palate - From the anterior region of the palatal shelf (closer to the front of the face). The lateral region located further from the MEE. Posterior Lateral Palate - From the posterior region of the palatal shelf (closer to the hind-brain). The lateral region located further from the MEE. Anterior Nasal Palate - From the anterior region of the palatal shelf (closer to the front of the face). The nasal half of the palate located closer to the nose. Posterior Nasal Palate - From the posterior region of the palatal shelf (closer to the hind-brain). The nasal half of the palate located closer to the nose. Anterior Oral Palate - From the anterior region of the palatal shelf (closer to the front of the face). The oral half of the palate located closer to the tongue. Posterior Oral Palate - From the posterior region of the palatal shelf (closer to the hind-brain). The oral half of the palate located closer to the tongue. There are 3 replicates for each region collected (four for the ant. nasal region). Regions were isolated using Laser Capture Microdissection with the Arcturus Veritas instrument, then RNA-purified and processed for RNA Seq. The RNA-Seq was performed using 50 bp single-end reads (at least 20 million reads). Sequencing was performed on the Illumina HiSeq 2500.
DOI: 10.25550/vdg
title: microCT - Bone Tissue of a Wnt1-Cre;Tgfbr2fl/fl mouse at E18.5

description: Mouse ID: JI119 This dataset includes 1 microCT scan of the skull of a Wnt1-Cre;Tgfbr2fl/fl mouse at E18.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/vew
title: microCT - Soft Tissue of Smad4flfl Control mouse at E18.5

description: Mouse ID: DH214 This dataset includes 1 microCT scan of the skull of a Smad4fl/fl control mouse at E18.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/vmy
title: microCT - Soft Tissue of an Msx1+/- Control mouse at E13.5

description: Mouse ID: AH279 This dataset includes microCT scans of the skull of an Msx1+/- Control mouse at E13.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/vt8
title: microCT - Soft Tissue of K14Cre;Tgfbr2flfl at E16.5

description: This dataset includes 1 microCT scan of the skull of a K14-Cre;Tgfbr2fl/fl mouse at E16.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.18739/a21j9776b
title: Chronologies, vegetation, and physical/geochemical data from peat cores, Nejanilini Lake region, Manitoba, Canada, 2008-2009

description: Small peat-forming ecosystems in arctic landscapes may play a significant role in the regional biogeochemistry of high-latitude systems, yet they are understudied compared to arctic uplands and other major peat-forming regions of the North. We present a new data set of 25 radiocarbon-dated permafrost peat cores sampled around eight low arctic lake sites in northern Manitoba (Canada) to examine the timing of peat initiation and controls on peat accumulation throughout the Holocene. We used macrofossils and charcoal to characterize changes in the plant community and fire, and we explored potential impacts of these local factors, as well as regional climatic change, on rates of carbon (C) accumulation and C stocks. Peat initiation was variable across and within sites, suggesting the influence of local topography, but 56% of the cores initiated after 3000 B.P. Most cores initiated and remained as drier bog hummock communities, with few vegetation transitions in this landscape. C accumulation was relatively slow and did not appear to be correlated with Holocene-scale climatic variability, but C stocks in this landscape were substantial (mean = 45.4 kg C per square meter), potentially accounting for 13.2 Pg C in the Taiga Shield ecozone. To the extent that small peat-forming systems are underrepresented in peatland mapping, soil organic carbon (SOC) stocks may be underestimated in arctic regions. Mean fire severity appeared to be negatively correlated with C accumulation rates. Initiation and accumulation of soil C may respond to both regional and local factors, and substantial lowland soil C stocks have the potential for biogeochemical impacts on adjacent aquatic ecosystems. More information can be found at doi.org/10.1002/2016JG003662
DOI: 10.18739/a2ws8hm1z
title: Greenland Icebergs: WorldView Digital Elevation Model derived Melt Data, 2011-2016

description: Observations of iceberg location, surface elevation, surface area, submerged area, change in surface elevation over time, change in volume over time (i.e. meltwater flux), and area-averaged submarine melt rates were compiled for 637 icebergs discharged from seven large glaciers draining the Greenland Ice Sheet from 2011-2016. The data were extracted from 2 m-resolution digital elevation models that were constructed from stereo panchromatic WorldView satellite images. Iceberg surface area and surface elevation estimates were extracted from repeat digital elevation models and converted to estimates of ice volume change, then divided by the estimated submerged iceberg area to yield area-averaged melt rates. The purpose of the iceberg meltwater flux and melt rate data was to determine whether remote sensing methods could be used to quantify spatial and temporal variations in iceberg melt rates as a potential means to infer changes in ocean forcing in iceberg-congested fjords.