cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25550/1-4zqp
title: FB0116_16yo female, Cleft palate, VSD, macrocephaly, speech delay

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. Ophir Klein of UCSF Benioff Children's Hospital. Phenotype: - 16yo female - Cleft palate - VSD - Macrocephaly - Speech delay
DOI: 10.25550/1-4zra
title: FB0117_3yo female with Pierre Robin, hearing loss, heart defect, cleft palate

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. Ophir Klein of UCSF Benioff Children's Hospital. Phenotype - Cleft palate, retrognathia - Cardiac defects: ASD and VSD - Mild hearing impairment
DOI: 10.25550/1-4zv4
title: FB0143_Trio WES_16yo Male & Unaffected Parents

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. Eric Liao of Masachusetts General Hospital. Phenotype - Presented at age 10 - Progressive lower jaw growth with associated soft tissue enlargement - Loose lower teeth
DOI: 10.25550/2854
title: khronos mutant zebrafish

description: micro computed tomography of an adult skull of khronos mutant at 7um voxel resolution. The mutation underlying khronos is not yet available.
DOI: 10.25550/2b9a
title: FB0100 Two affected male siblings, ages 12 and 4, with short stature micrognathia, cleft palate

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.
DOI: 10.25550/2baj
title: FB0114_5mo male with inilateral anophthalma & microtia, preauricular tags, absent left radias, HFM_Candidate Gene: HECTD1

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. Joan Stoler of Boston Children’s Hospital.
DOI: 10.25550/vcr
title: Activity of human neural crest enhancer near PAPPA in E11.5 mouse embryo - Tg(hg19_ chr9:118163085-118163446::LacZ)

description: Tg(hg19_ chr9:118163085-118163446::LacZ) activity in telencephalon, midbrain, hindbrain, midbrain/hindbrain junction, medial and lateral nasal processes, eye pit, periocular mesenchyme, domains of craniofacial nerves V to X, maxillary, mandibular, branchial arch 2, sympathetic ganglia, somites and median limb domains.
DOI: 10.25550/vfa
title: Activity of P. troglodyte neural crest enhancer near PAPPA in E11.5 mouse embryo - Tg(panTro3_chr9:114353941-114354302::LacZ)

description: Tg (panTro3_chr9:114353941-114354302::LacZ) activity in midbrain, periocular mesenchyme, domains of craniofacial nerves VII to X, neural tube and craniofacial ganglia. Lateral view of whole mount embryo and transverse vibratome section.
DOI: 10.25550/vtc
title: Activity of human neural crest enhancer near LRP6 in E11.5 mouse embryo - Tg(hg19_ chr12:12,367,496-12,368,000::LacZ)

description: Tg(hg19_ chr12:12,367,496-12,368,000::LacZ) activity in midbrain (bi-lateral pattern), vagal nerve (X), neural tube and sympathetic ganglia.
DOI: 10.25550/1-50de
title: OFC1: International Consortium to Identify Genes and Interactions Controlling Oral Clefts- Genome Wide Association Study

description: [**Link to project pages of OFC1: International Consortium to Identify Genes and Interactions Controlling Oral Clefts- Genome Wide Association Study**](http://www.facebase.org/hgai/OFC1.html) [dbGap Study Accession: phs000094.v1.p1](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000094.v1.p1) Principal Investigator: Terri H. Beaty, Johns Hopkins School of Public Health, Baltimore, MD, USA Funding Source: U01-DE018993. International Consortium to Identify Genes and Interactions Controlling Oral Clefts. National Institutes of Health, Bethesda, MD, USA Oral clefts represent the most common group of craniofacial birth defects in humans, and include cleft lip with or without cleft palate (CL/P) and cleft palate (CP). Oral clefts have a complex and heterogeneous etiology, with strong evidence for both genetic and environmental causal factors. Candidate gene studies and genome wide linkage studies have yielded compelling but inconsistent evidence that multiple genes control risk, and several studies have shown evidence for interaction between genes and environmental exposures, especially maternal smoking and nutrient intake. This consortium assembled a large collection of cases and their parents from multiple populations for genome wide association studies as part of the Gene Environment Association Studies initiative (GENEVA), which was developed through the trans-NIH Genes, Environment, and Health Initiative (GEI). Genotyping was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR). The study was supported by the National Institute of Dental and Craniofacial Research (NIDCR). Data cleaning and harmonization were done at the GEI-funded GENEVA Coordinating Center at the University of Washington. Information on how to obtain individual level data is available on [dbGap](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000094.v1.p1). Click [here](/hgai/OFC1.html) to access the data and results for this dataset.
DOI: 10.25550/1-50dy
title: FV1: GWAS of Facial Measures in Europeans

description: [**Link to project pages of FV1: GWAS of Facial Measures in Europeans**](http://www.facebase.org/hgai/FV1.html) dbGaP Study Accession: [phs000949.v1.p1](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000949.v1.p1) Principal Investigator: [Seth Weinberg](https://www.dental.pitt.edu/person/seth-weinberg-0), University of Pittsburgh School of Dental Medicine, Pittsburgh, PA, USA Funding Source: U01-DE020078, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA U01-DE020057, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA R01-DE016148, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA U01-DE020054, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA U01-DE024425, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA K99-DE02560, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA Contract #HHSN268201200008I, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA X01-HG007821, National Human Genome Research Institute, Bethesda, MD, USA Although ample evidence exists that facial appearance and structure are highly heritable, there is a dearth of information regarding how variation in specific genes relates to the diversity of facial forms evident in our species. With the advent of affordable, non-invasive 3D surface imaging technology, it is now possible to capture detailed quantitative information about the face in a large number of individuals. By coupling state- of-the-art 3D imaging with advances in high-throughput genotyping, an unparalleled opportunity exists to map the genetic determinants of normal facial variation. The project contains the results of GWAS performed on 3D facial measurements from two cohorts of US Caucasians collected as part of the FaceBase consortium. These results were published in PLoS Genetics by Shaffer et al. (2016). Click [here](/hgai/FV1.html) to access the data and results for this dataset.
DOI: 10.25550/2b8j
title: FB0046_6 yo female with craniofacial abnormalities, vertebral anomalies_Candidate Gene: DYNC1H1

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. Ophir Klein of UCSF Benioff Children's Hospital. Phenotype - Craniofacial microsomia - preauriculartags - speech disturbance - vertebral anomalies - scoliosis - multifocal epilepsy - speech disturbance - vertigo - developmental delay
DOI: 10.25550/2b9y
title: FB0107 Cleft palate, dysplastic ears, short stature, linear hyperpigmented streaks on skin, hearing loss, scoliosis, tetralogy of fallot

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.
DOI: 10.25550/tk4
title: Temporal analysis of ectoderm and mesenchyme expression in the developing mouse facial prominences

description: Temporal analysis of ectoderm and mesenchyme expression in the developing mouse facial prominences
DOI: 10.25550/tsj
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm642

description: See link to the data preparation protocols for this study in the Additional Information section **Enhancer location:** Mouse genome mm9, chr15: 60684551-60685838 **Name:** mCF191 **Vista Enhancer ID:** mm642 **Nearest craniofacial gene or locus:** 8q24 **Enhancer expression:** positive **Tissues where active:** branchial arch, ear, eye, heart, nose, facial mesenchyme, dorsal root ganglion, forebrain, limb, midbrain **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/tte
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm414

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, chr14:22932439-22935173 **Name:** mCF100 **Vista Enhancer ID:** mm414 **Nearest craniofacial gene or locus:** ZFP503 **Enhancer expression:** positive **Tissues where active:** branchial arch, eye, forebrain, limbs,midbrain 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 mCF100metadata.txt from the External Reference section .
DOI: 10.25550/v0c
title: Alk5 Control and Mutant -- E16.5 Bone and Soft Tissue microCT images

description: Alk5 Control and Mutant -- E16.5 Bone and Soft Tissue microCT images
DOI: 10.25550/vww
title: Alk5 Control and Mutant – E18.5 Bone and Soft Tissue microCT images

description: Alk5 Control and Mutant – E18.5 Bone and Soft Tissue microCT images
DOI: 10.25550/vx4
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: 10.5281/zenodo.3424948
title: Data for [Inverse magnetic susceptibility fabrics in pelagic sediment: Implications for magnetofossil abundance and alignment]

description: Data for [Inverse magnetic susceptibility fabrics in pelagic sediment: Implications for magnetofossil abundance and alignment]
DOI: 10.25550/1-3sb2
title: Activity of human neural crest enhancer near GPR158 in E11.5 transgenic mouse embryo – Tg(hg38_chr10:25522061-25522992::LacZ).

description: Tg(hg38_chr10:25522061-25522992::LacZ) human neural crest enhancer with biased activity in the periocular mesenchyme, medial maxillary 1st branchial arch, mandibular 1st branchial arch, 2nd branchial arch, 3rd branchial arch, forelimb and hindlimb buds, and dorsal root ganglia when compared to the orthologous chimp enhancer. Transgenic embryos also show reproducible activity in the frontonasal prominence and midgut that overlaps with the chimp enhancer expression.
DOI: 10.25550/1-3swa
title: FB0122_29yo female with bilateral hearing loss, open anterior fontanel with widened metopic sutures which required surgical repair_Candidate Gene: HECTD4

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. Ophir Klein of UCSF Benioff Children's Hospital. Phenotype -Previous dx of Conradi-Huenermann syndrome - recent genetic testing and biochemical testing was normal - Frontonasal dysplasia, frontal alopecia, orbital hypertelorism - Open anterior fontanel with widened metopic sutures which required surgical repair - Pectus excavatum - Bilateral hearing loss due to fusion of bones
DOI: 10.25550/1-3vke
title: Microcomputed tomography of gpr137b mutant adult skull

description: Microcomputed tomography of an adult skull of homozygous gpr137b mutant fish
DOI: 10.25550/264c
title: MicroCT-Skull Wnt1-Cre;Alk5fl/fl mouse at P0

description: This dataset includes 1 microCT scan of the skull of a Wnt1-Cre;Alk5fl/fl mouse at P0 (YC391CCMB). The scan is in NiFTI format, which can be read by a number of free software applications including those listed below. To receive the scan in DICOM format, please email help@facebase.org. The following programs allow you to load and explore files in NiFTI format: – ImageJ, a java-based program that runs on most operating systems, including MAC OSX – MBAT, from the Laboratory of Neural Imaging at USC – Mango, from Neuroimaging Informatics Tools and Resources Clearinghouse, offers desktop, web, and iPad-compatible versions. – MRIcro, which runs on Windows and Linux systems.
DOI: 10.25550/3v4a
title: E18.5 wildtype mouse microCT
DOI: 10.25550/vjg
title: microMRI images of skulls of Ctgf+/+ mice at E14.5

description: microMRI images of skulls of Ctgf+/+ mice at E14.5. The dataset contains 3-D images in niftii format for each of 4 mice.
DOI: 10.25550/vm0
title: Wild type zebrafish developmental series – WIK strain

description: MicroCT imaging of skull development in the zebrafish WIK strain
DOI: 10.25550/vpy
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm387

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, chr14:47230349-47231452 **Name:** mCF73 **Vista Enhancer ID:** mm387 **Nearest craniofacial gene or locus:** BMP4 **Enhancer expression:** positive **Tissues where active:** branchial arch, facial mesenchyme, nose, limbs, neural tube **Comment on OPT files:** slightly damaged embryo 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 mCF73metadata.txt from the External Reference section .
DOI: 10.25550/vx6
title: Whole-genome transcriptome profiling by microarray of maxilla and mandible

description: To perform global gene expression profiling analysis of mandible and maxilla development and will integrate these datasets with cell lineage and quantitative 3D dynamic imaging analyses.
DOI: 10.5281/zenodo.3424949
title: Data for [Inverse magnetic susceptibility fabrics in pelagic sediment: Implications for magnetofossil abundance and alignment]

description: Data for [Inverse magnetic susceptibility fabrics in pelagic sediment: Implications for magnetofossil abundance and alignment]