cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25550/1-5004
title: Single cell RNA-sequencing of E11.5 Crect; ROSA26-lacZ mouse fusing upper lip and primary palate

description: Only mouse embryos that were positive for both Crect, an ectoderm specific Cre recombinase transgene, and the ROSA26 LacZ reporter allele were used for this study. Not that these mice are on a mixed genetic background. After isolation of E11.5 embryos with 45 somites, the face was isolated from the head using published procedures. Subsequently, the region of the upper face where the nasal and maxillary prominences are juxtaposed was microdissected out using forceps so that the region containing the lambdoid junction, the nasolacrimal groove, and the nasal fin were obtained. This tissue contained ectoderm and mesenchyme, as well as cells associated with blood vessels. Following dispersion into single cells by enzymatic and mechanical methods, cells were processed for single cell RNA sequencing using the 10X Genomics platform. Approximately 7000 cells were sequenced to a depth of 100,000 reads per cell.
DOI: 10.25550/1-50jc
title: Activity of human neural crest enhancer intronic in CACNA1C in E11.5 transgenic mouse embryos – Tg(hg38_ chr12:2284416-2285167::LacZ).

description: Tg(hg38_ chr12:2284416-2285167::LacZ) human neural crest enhancer with biased activity in the midbrain-hindbrain junction, frontonasal process, and maxillary process of BA1 when compared to the orthologous chimp enhancer. Transgenic embryos also show reproducible activity in the forebrain, midbrain, hindbrain, optic cup, mandibular 1st branchial arch, 2nd branchial arch, heart field, anterior forelimb and hindlimb buds, midgut, and dorsal root ganglia.
DOI: 10.25550/1-70m6
title: Activity of predicted mouse neural crest enhancer near Zfhx4 in E13.5 transgenic mouse embryos– Tg(mm10_chr3:5427552-5428904::LacZ).

description: Tg(mm10_chr3:5427552-5428904 ::LacZ) demonstrates no reproducible enhancer activity at E13.5, with only weak staining in the neural tube.
DOI: 10.25550/1-70mp
title: Activity of human neural crest enhancer near Zfhx4 in E13.5 transgenic mouse embryos– Tg(hg38_chr8:76883303-76884634::LacZ).

description: Tg(hg38_chr8:76883303-76884634::LacZ) human neural crest enhancer with reproducible activity in the periocular mesenchyme, posterior forelimb, and ventral limbs.
DOI: 10.25550/vp4
title: Activity of P. troglodyte neural crest enhancer near CNTNAP2 in E11.5 mouse embryo - Tg(panTro3_chr7:147450637-147451061::LacZ)

description: Tg(panTro3_chr7:147450637-147451061::LacZ) activity in rostral medial and lateral nasal prominences, olfactory placode and projections, and olfactory epithelium and projections.
DOI: 10.25550/vp8
title: Gene expression RNA-Seq - mouse E8.5

description: Gene expression RNA-Seq of mouse embryos at E8.5.
DOI: 10.25550/1-3sm2
title: Activity of human neural crest enhancer near FAM222A in E11.5 transgenic mouse embryo – Tg(hg38_chr12:109709145-109709901::LacZ).

description: Tg(hg38_chr12:109709145-109709901::LacZ) human neural crest enhancer with biased activity in the frontonasal prominence, facial (VII)/vestibulocochlear (VIII) ganglia, heart field, and medial forelimb buds when compared to the orthologous chimp enhancer. Transgenic embryos also show reproducible activity In the midbrain, periocular mesenchyme/optic cup, and floor plate of the neural tube that overlaps with the chimp enhancer-driven LacZ expression.
DOI: 10.25550/1-43f6
title: The Effect of Automated Landmark Identification on Morphometric Analyses Using the Collaborative Cross

description: Morphometric analysis of anatomical landmarks allows researchers to identify specific differences in craniofacial shape between natural populations or experimental groups, but manually identifying landmarks is time-consuming. Previous studies have shown that image registration based automated landmark identification may adequately replace manual landmarking in certain situations. We compare manually and automatically generated adult mouse skull landmarks and subsequent morphometric analyses to elucidate how switching from manual to automated landmarking will impact the morphometric analysis results for large mouse (Mus musculus) samples (n=1206) that represent wide “normal” phenotypic variation (54 genotypes). This large sample size allowed us to investigate how landmarking method impacts estimated differences in genotype mean shape, estimates of shape variance, and whether there were any genotype-specific biases in landmark identification. In addition, we tested whether an initial registration of specimen images to genotype specific averages improves automatic landmark identification accuracy. Our results indicated that automated landmark placement was significantly different than manual landmark placement, but that all methods identified similar patterns of skull shape covariation across our large sample. The addition of a preliminary genotype-specific registration step as part of a two-level procedure did not improve on the accuracy of one-level automatic landmark placement. The landmarks with the lowest automatic landmark accuracy are found in locations with poor image registration alignment. The most serious outliers within morphometric analysis of automated landmarks displayed instances of stochastic image registration error that are likely representative of errors common when applying image registration methods to µCT datasets that were initially collected with manual landmarking in mind. Additional efforts during specimen preparation and image acquisition can help reduce the number of registration errors and improve registration results. Previously identified tendencies of atlas-based registration methods to underestimate variation may reduce statistical power for tests designed to identify differences in variation or covariation patterns. For appropriate samples and research questions, our image registration based automated landmarking method can eliminate the time required for manual landmarking and identify similar general patterns of mean skull shape differences across a large genetically variable mouse sample.
DOI: 10.25550/1-4aa6
title: Activity of human neural crest enhancer near ZNF518B in E11.5 transgenic mouse embryo - Tg(hg38_chr4:10296754-10297578::LacZ).

description: Tg(hg38_chr4:10296754-10297578::LacZ) human neural crest enhancer with biased activity in the forebrain, midbrain, hindbrain, frontonasal process, periocular mesenchyme, cranial ganglia including at least the trigeminal (V) ganglion, maxillary and mandibular prominences of the 1st branchial arch, proximal forelimb bud, distal hindlimb bud, and dorsal root ganglia when compared to the orthologous chimp enhancer. Transgenic embryos also show reproducible activity in the 2nd branchial arch that overlaps with the chimp enhancer-driven lacZ expression, although X-Gal staining is stronger in human.
DOI: 10.25550/1-50dm
title: OFC2: Targeted Sequencing of CL/P GWAS Loci

description: [**Link to project pages of OFC2: Targeted Sequencing of CL/P GWAS Loci**](http://www.facebase.orh/hgai/OFC2.html) [dbGaP Study Accession: phs000625.v1.p1](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000625.v1.p1) Principal Investigators: [Jeffrey C. Murray](https://genetics.grad.uiowa.edu/faculty/jeffrey-c-murray), University of Iowa, Iowa City, IA, USA [Mary L. Marazita](https://www.dental.pitt.edu/person/mary-l-marazita), University of Pittsburgh, Pittsburgh, PA, USA [Richard K. Wilson](https://en.wikipedia.org/wiki/Richard_K._Wilson), Washington University School of Medicine, St. Louis, MO, USA [George Weinstock](https://www.jax.org/research-and-faculty/faculty/george-weinstock) , Jackson Laboratory for Genomic Medicine, Farmington, CT, USA Funding Source: U01-HG005925. Sequencing of Significant Signals from Cleft Lip GWAS. National Institutes of Health, Bethesda, MD, USA. Nonsyndromic cleft lip and palate (NSCL/P) is a complex disorder caused by both genetic and environmental factors and has been the focus of an extensive effort to identify genetic risk factors. A number of candidate gene studies have been performed but have not been widely replicated. To date, four independent genome wide association studies have been performed as well as a meta-analysis. Together these studies have identified many loci associated with NSCL/P. The goal of this project is to use targeted sequencing to further characterize these regions and to progress from the association signals identified by GWAS to the identification of causative genes and/or variants. This study is part of the GWASeq project, a collaboration of five disease studies, which will sequence genomic regions from GWAS to characterize the genetic variation underlying these diseases and to compare study design and methods for the follow-up of GWAS studies by sequencing. The goal of this study is to sequence 1000+ NSCL/P case-parent trios from China and the Philippines and 400 trios of European ancestry. Targeted sequencing was performed on intervals ranging between 60kb to 1Mb surrounding 13 genes/loci previously associated with NSCL/P including: IRF6, MAFB, ARHGAP29, 8q24, PAX7, VAX1, NTN1, NOG, FOXE1, MSX1, BMP4, FGFR2, PTCH1. Sequencing was performed at the Genome Institute at Washington University. Click [here](/hgai/OFC2.html) to access the data and results for this dataset.
DOI: 10.25550/2ahy
title: RNAseq of Wnt1cre;Tgfbr2fl/fl mutants and controls at E10.5
DOI: 10.25550/3typ
title: Single Cell Sequencing - Coronal Suture, Wild Type, E18.5 and P10

description: Single Cell RNA-Seq libraries are from C57BL/6J mice, at development stages TS26/E18.5 (E18) and TS28/P10 (P10), from the coronal suture (C). “scWCE18_S198”, for example, indicates single cell data, WT, coronal suture, E18.5, from sequencing library 198. Single cell libraries are prepared after protease digestion of the sutures on a 10x Chromium instrument model GCG-SR-1 using the Chromium Single Cell Gene Expression (Version 2) kit.
DOI: 10.25550/tng
title: Transgenic Mouse Enhancer OPT Assays - hs1151

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=1151&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/vfp
title: ShapeGUI

description: See link to Craniofacial Analysis tools in the Additional Information section.
DOI: 10.25550/vw6
title: Wild Type E18.5 Frontal Suture Images

description: Wild Type E18.5 Frontal Suture Images
DOI: 10.25550/1-4aet
title: Activity of human neural crest enhancer near HS3ST3A1 in E11.5 transgenic mouse embryo – Tg(hg38_chr17:13395099-13396176::LacZ)

description: Tg(hg38_chr17:13395099-13396176::LacZ) human neural crest enhancer with biased activity in the anterior forebrain, anterior midbrain, hindbrain, frontonasal process, cranial ganglia including at least the trigeminal (V) and innervation of the maxillary prominence of the first branchial arch. Transgenic embryos also show reproducible activity in the periocular mesenchyme/optic cup.
DOI: 10.25550/1-4tdt
title: Whole-genome transcriptome profiling of E13.5 Wnt1-Cre;Alk5flfl by microarray of maxilla and mandible

description: We performed the global gene expression profiling analysis of the proximal (P ) and distal (D) regions of the mandible and proximal (P ) and distal (D) regions of the maxilla using microarray. Total RNA samples (1 ug per sample) were converted into biotin-labeled cRNA using the GeneChip® IVT Labeling Kit and standard protocols recommended by Affymetrix (Santa Clara, CA). Fragmented cRNA was applied to GeneChip, Mouse Genome 430 2.0 Arrays (Affymetrix) that contain probe sets designed to detect over 39,000 transcripts. Microarrays were hybridized, processed and scanned, as previously described using manufacturers recommended conditions.
DOI: 10.25550/1-4tpa
title: Cell Proliferation Heat Map of E10.5 mouse embryo

description: Whole mount staining was used for E10.5 samples. All samples were stained with Ki67 and DAPI. E10.5 whole mount embryos were imaged using Optical Projection Tomography (OPT). Heat maps were generated from images using ImageJ and Amira. Heat maps for E10.5 whole mount embryos showed proliferative cells in specific regions of the embryo.
DOI: 10.25550/1-4tsp
title: Single Cell Sequencing - Frontal Suture, Wild Type, E18.5

description: Single Cell RNA-Seq library is from pooled C57BL/6J mice, at development stage TS26/E18.5 (E18), from the frontal suture (F). “scWFE18_S197”, indicates single cell data, WT, frontal suture, E18.5, from sequencing library 197. Single cell libraries are prepared after protease digestion of the sutures on a 10x Chromium instrument model GCG-SR-1 using the Chromium Single Cell Gene Expression (Version 2) kit.
DOI: 10.25550/26v8
title: FB0055_6yo male with sagittal craniosynostosis, robin sequence, autism, brain glioma_Candidate Gene: NFIX

description: The purpose of this study is to collect, process, and study samples from individuals with known or possible genetic disease, and their family members. The study’s broad goals are to better understand the genetic causes of disease in order to improve the ability to diagnose, treat, and even prevent illness. Our goal is to obtain a genetic diagnosis for health problem(s) the proband has, so the information can be used, when appropriate, to guide medical decisions made by the affected individuals doctor. **This is restricted-access human data.** To gain access to this data, you must first go through the [process outlined here](/odocs/data-guidelines/). This case was brought to the attention of FaceBase from Dr. Pedro Sanchez of Children's Hospital Los Angeles. Phenotype: - Proptosis - Pierre-Robin Sequence - Bilateral chryptorchidism - Brain glioma - Autism - Global Developmental Delay - Excessive wrinkling of palmar skin - Abnormality of the optic nerve - Hypoplasia of the optic nerve - Generalized hirsutism - Prominent fingertip pads - Abnormality of the midface Candidate Gene: _NFIX_
DOI: 10.25550/v7r
title: Wnt GFP Msx1 Snail1 Dapi HCR Images - Medium Stitching (with errors)

description: HCR images of a mouse at E9.5 - Medium Stitching, including errors.
DOI: 10.25550/vk0
title: microMRI images of skulls of Myf5Cre * Smad4FF mice at E16.5

description: microMRI images of skulls of Myf5Cre * Smad4FF mice at E16.5. The dataset contains 3-D images in niftii format for each of 2 mice.
DOI: 10.25550/vke
title: Wnt1 GFPT wist 1BF Wnt1 Dapi HCR Stack Stiched

description: HCR images of a mouse at E9.5 - Stach Stitched
DOI: 10.25550/1-4adm
title: Activity of chimp neural crest enhancer near ZNF518B in E11.5 transgenic mouse embryo – Tg(panTro4_chr4:9996809-9997635::LacZ).

description: Tg(panTro4_chr4:9996809-9997635::LacZ) chimp neural crest enhancer with reproducible activity in the 2nd branchial arch and floor plate of the neural tube. This enhancer lacks many of the expression domains associated with the orthologous human enhancers, demonstrating human biased activity when comparing these two species.
DOI: 10.25550/1-4tgt
title: Whole-genome transcriptome profiling of E12.5 Wnt1-Cre;Alk5flfl by microarray of maxilla and mandible
DOI: 10.25550/1-4tqc
title: Cell Proliferation Heat Map of E10.5 Wnt1-Cre;Alk5flfl mouse embryo

description: Whole mount staining was used for E10.5 samples. All samples were stained with Ki67 and DAPI. E10.5 whole mount embryos were imaged using Optical Projection Tomography (OPT). Heat maps were generated from images using ImageJ and Amira. Heat maps for E10.5 whole mount embryos showed proliferative cells in specific regions of the embryo.
DOI: 10.25550/1-4xec
title: Activity of a human consensus recurrent motif from neural crest enhancers in E11.5 transgenic mouse embryos.

description: Human neural crest enhancer motif with reproducible activity in the telencephalon, optic cup, olfactory placode, cranial nerves (III, IV, V, VII, VIII, X, and XII), dorsal root ganglia, neural tube, notochord, and medial forelimb and hindlimb buds.
DOI: 10.25550/1-4xfj
title: Activity of predicted human neural crest enhancer 1.25Mb upstream of SOX9 in E11.5 transgenic mouse embryo

description: Sox9-E1.25Mb shows no replicable enhancer activity at either E9.5 or E11.5.
DOI: 10.25550/1-4xmc
title: Activity of human neural crest enhancer near STX2 in E11.5 transgenic mouse embryo – Tg(hg38_chr12:130776454-130777125::LacZ).

description: Tg(hg38_chr12:130776454-130777125::LacZ) human neural crest enhancer with reproducible activity in the periocular mesenchyme, outflow tract of the heart, midgut, and dorsal root ganglia.
DOI: 10.25550/1-4xna
title: Activity of chimp neural crest enhancer near STX2 in E11.5 transgenic mouse embryo – Tg(panTro4_chr12:131731289-131731964::LacZ).

description: Tg(panTro4_chr12:131731289-131731964::LacZ) chimp enhancer with reproducible activity in the midbrain, hindbrain, and neural tube.
DOI: 10.25550/3v0e
title: Single Cell Sequencing - Lambdoid Suture, Wild Type, E18.5 and P10

description: Single Cell RNA-Seq libraries are from C57BL/6J mice, at development stages TS26/E18.5 (E18) and TS28/P10 (P10), from the lambdoid suture (L). “scWLE18_S199”, for example, indicates single cell data, WT, lambdoid suture, E18.5, from sequencing library 199. Single cell libraries are prepared after protease digestion of the sutures on a 10x Chromium instrument model GCG-SR-1 using the Chromium Single Cell Gene Expression (Version 2) kit.
DOI: 10.34725/dvn/yral4o
title: SL Calculated Household Indicators combined data

description: Combined data of all indicators and a subset with the main indicators computed from various sections of the SL Household module
DOI: 10.34725/dvn/yral4o/lb9ved
title: 0.Disclaimer.pdf

description: Data disclaimer
DOI: 10.34725/dvn/yral4o/qnmuwo
title: SL_Computed_All_Indicators_Complete_Data.tab

description: Data of all the computed indicators from various sections of the SL Household Module in a STATA format.
DOI: 10.5281/zenodo.3441764
title: Changes in emm types and superantigen gene content of Streptococcus pyogenes causing invasive infections in Portugal - Dataset

description: Properties of <em>Streptococcus</em> <em>pyogenes</em> isolated from invasive infections in Portugal between 2000 and 2015.
DOI: 10.5281/zenodo.3441765
title: Changes in emm types and superantigen gene content of Streptococcus pyogenes causing invasive infections in Portugal - Dataset

description: Properties of <em>Streptococcus</em> <em>pyogenes</em> isolated from invasive infections in Portugal between 2000 and 2015.
DOI: 10.25550/1-415t
title: FB0057_13yo female with Robin sequence, microglossia, microstomia structure of the oropharynx

description: The purpose of this study is to collect, process, and study samples from individuals with known or possible genetic disease, and their family members. The study’s broad goals are to better understand the genetic causes of disease in order to improve the ability to diagnose, treat, and even prevent illness. Our goal is to obtain a genetic diagnosis for health problem(s) the proband has, so the information can be used, when appropriate, to guide medical decisions made by the affected individuals doctor. **This is restricted-access human data.** To gain access to this data, you must first go through the [process outlined here](/odocs/data-guidelines/). This case was brought to the attention of FaceBase from Dr. Pedro Sanchez of Children’s Hospital Los Angeles. Phenotype: - Robin Sequence - Microstomia - Trismus Chiari I - Lambdoid craniosynostosis
DOI: 10.25550/1-4x9p
title: RNAseq of in vitro derived cranial neural crest cells

description: 20 RNAseq samples of in vitro derived human and chimpanzee cranial neural crest cells. **This is restricted-access human data.** To gain access to this data, you must first go through the [process outlined here](/odocs/data-guidelines/).
DOI: 10.25550/1-4xga
title: Activity of human neural crest enhancer near SOX9 in transgenic mouse embryos – Tg(hg38_chr17:70869447-70870220::LacZ).

description: Tg(hg38_chr17:70869447-70870220::LacZ) human neural crest enhancer at two stages stages. At E9.5, the enhancer is active in the frontonasal process, branchial arches 1 and 2, otic vesicle, intermediate mesoderm/urogenital ridge and somites. At E11.5, reproducible activity is observed in the cranial nerves including the trigeminal (V), facial (VII)/vestibulocochlear (VIII), glossopharyngeal (IX), and vagus (X), medial forelimb buds, midgut, and dorsal root ganglia.
DOI: 10.25550/1-4xjp
title: Activity of human neural crest enhancer 1.45Mb upstream of SOX9 in transgenic mouse embryos – Tg(hg19_chr17:68668081-68671159::LacZ).

description: Tg(hg19_chr17:68668081-68671159::LacZ) human neural crest enhancer at two stages stages. At E9.5, the enhancer is active in frontonasal process. At E11.5, reproducible activity is observed in the anterior forebrain, frontonasal process, periocular mesenchyme, maxillary and mandibular prominences of the 1st branchial arch, and anterior limb buds.
DOI: 10.25550/1-4xqr
title: Activity of chimp neural crest enhancer near TLN2 in E11.5 transgenic mouse embryo – Tg(panTro4_chr15:60014674-60015559::LacZ).

description: Tg(panTro4_chr15:60014674-60015559::LacZ) chimp neural crest enhancer with reproducible activity in the posterior forebrain, midbrain, periocular mesenchyme, trigeminal (V) ganglia, maxillary and mandibular prominences of the 1st branchial arch, 2nd branchial arch, heart field, and dorsal root ganglia.
DOI: 10.25550/1-4zw4
title: ChIP-Seq of mouse E15.5 Face (Mandibular Process)

description: We have generated histone ChIP-Seq libraries for dissected mouse mandibular tissue. We performed ChIP-Seq with markers of active chromatin (H3K27ac, H3K4me1) and repressive chromatin (H3K27me3). We also generated a ChIP input library.
DOI: 10.25550/1-4zw6
title: ChIP-Seq of mouse E15.5 Face (Nose)

description: We have generated histone ChIP-Seq libraries for dissected mouse nose tissue. We performed ChIP-Seq with markers of active chromatin (H3K27ac, H3K4me1). We also generated a ChIP input library.
DOI: 10.25550/thy
title: Activity of human neural crest enhancer near CNTNAP2 in E11.5 mouse embryo - Tg(hg19_chr7:145843942-145844366::LacZ)

description: Tg(hg19_chr7:145843942-145844366::LacZ) activity in telencephalic vesicles, midbrain and hindbrain domains, midbrain/hinbrain junction, medial and lateral nasal processes, olfactory placode, eye pit, periocular mesenchyme, trigeminus nerve, maxillary and mandibular processes of Branchial Arches 1 and 2.
DOI: 10.25550/vpw
title: 3D facial surface models of Pseudoachondroplasia in humans

description: 3D facial surface models of Pseudoachondroplasia in humans. **This is restricted-access human data.** To gain access to this data, you must first go through the [process outlined here](/odocs/data-guidelines/).
DOI: 10.25345/c5fh3v
title: MassIVE MSV000084331 - Spatial Protein Expression of Panax Ginseng by In-depth Proteomic Analysis for Ginsenoside Biosynthesis and Transportation
title: Spatial Protein Expression of Panax Ginseng by In-depth Proteomic Analysis for Ginsenoside Biosynthesis and Transportation. 2732 proteins and 3608 proteins were identified from ginseng root and cauline leaf, respectively, which was the largest data set reported so far.