cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25550/26v4
title: FB0038_Blepharo-cheilo-dontic (BCD) syndrome aka Elschnig Syndrome_Trio Saliva_Candidate Gene: CDH1

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 porband 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. This trio consisted of treating the affected mother as the proband, and obtaining samples on the proband's affected daughter and the unaffected maternal grandmother. Phenotype: - bilateral cleft lip & palate - imperforate anus - low set ears - Distichiasis (Double row of lashes) - Ectropion lateral canthus - Downslanted palpebral fissures Candidate Gene: _CDH1_
DOI: 10.25550/tpg
title: microCT - Soft Tissue of an Fgfr2fl/fl control mouse at E17.5

description: Mouse ID: ZZ292 This dataset includes microCT scans of the skull of an Fgfr2fl/fl control mouse at E17.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/tqr
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm610

description: See link to the data preparation protocols for this study in the Additional Information section **Enhancer location:** Mouse genome mm9, chr8: 26453164-26454807 **Name:** mCF159 **Vista Enhancer ID:** mm610 **Nearest craniofacial gene or locus:** Fgfr1 **Enhancer expression:** positive **Tissues where active:** branchial arch, facial mesenchyme, limb, other **Comment on OPT files:** none 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/tze
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm433

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, chr1:194677837-194678651 **Name:** mCF119 **Vista Enhancer ID:** mm433 **Nearest craniofacial gene or locus:** IRF6 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 * Tested element.txt: Download the text file mCF119metadata.txt from the External Reference section
DOI: 10.25550/v06
title: microCT - Soft Tissue of an Msx1+/- Control mouse at E14.5

description: Mouse ID: AH283 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/v2y
title: microCT - Soft Tissue of Wnt1-Cre;Tgbr2fl/fl;tgfb2+ mouse at E18.5

description: 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/v3e
title: microCT - Bone Tissue of a K14-Cre;Fgfr2fl/fl mouse at E18.5

description: Mouse ID: ZZ273 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/v46
title: microCT - Soft Tissue of Myf5-Cre;Smad4flfl mouse at E17.5

description: Mouse ID: JF253 This dataset includes 1 microCT scan of the skull of a Myf5-Cre; Smad4flfl mouse at E17.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/v6w
title: Gene expression RNA-Seq - mouse E14.5 Wild Type Anterior Lateral Palate

description: This data set contains FASTQ RNA-Seq data for the Anterior Lateral 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/vdy
title: microCT - Soft Tissue of Fgfr2flfl Control Mouse at P0

description: Mouse ID: ZZ188 This dataset includes 1 microCT scan of the skull of a Fgfr2flfl control 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/vhr
title: Gene expression profiling of palatal and mandibular tissue in Msx1-/- mice

description: We performed global gene expression analyses of the palatal and palatal tissue of Msx1-/- and control mice at embryonic day E14.5 Total RNA samples (1 ug per sample) were converted into biotin-labeled cDNA 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 39,000 transcripts. Microarrays were hybridized, processed and scanned, as previously described using manufacturers recommended conditions.
DOI: 10.25550/vjj
title: microCT - Bone Tissue of a K14-Cre;Fgfr2fl/fl mouse at E17.5

description: Mouse ID: ZZ289 This dataset includes microCT scans of the skull of a K14-Cre;Fgfr2fl/fl mouse at E17.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/vmg
title: microCT - Bone Tissue of a Wnt1-Cre; Tgfbr2fl/fl; Alk5fl/+ mouse at E16.5

description: Mouse ID: JI330 This dataset includes microCT scans of the skull of a Wnt1-Cre; Tgfbr2fl/fl; Alk5fl/+ 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/vrm
title: microCT - Bone Tissue of a Wnt1-Cre; Tgfbr2fl/fl; Alk5fl/+ mouse at E16.5

description: Mouse ID: AS329 This dataset includes microCT scans of the skull of a K14-Cre; Fgfr2fl/flmouse 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/vwr
title: Gene expression RNA-Seq - mouse E9.5

description: Gene expression RNA-Seq of mouse embryos at E9.5.
DOI: 10.25550/tm6
title: microCT - Bone Tissue of Tgfbr2 control mice at E16.5

description: Mouse ID: JI305 This dataset includes microCT scans of the skulls of Tgfbr2 control mice 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/tp4
title: microCT - Soft Tissue of a Msx1-/- mouse at E17.5

description: Mouse ID: AH243 This dataset includes microCT scans of the skull of an Msx1-/- mouse at E17.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/tpr
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm613

description: See link to the data preparation protocols for this study in the Additional Information section **Enhancer location:** Mouse genome mm9, chr1: 56343177-56344388 **Name:** mCF162 **Vista Enhancer ID:** mm613 **Nearest craniofacial gene or locus:** None **Enhancer expression:** positive **Tissues where active:** branchial arch, ear **Comment on OPT files:** none 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/tvg
title: microCT - Soft Tissue of a Ctgf-/- mouse at E14.5

description: Mouse ID: CP260 This dataset includes microCT scans of the skull of a Ctgf-/- mouse at E14.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/tvw
title: Gene expression RNA-Seq - mouse E14.5 Wild Type Posterior Nasal Palate

description: This data set contains FASTQ RNA-Seq data for the Posterior Nasal 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/tya
title: Micro-CT images of adult mouse skulls, Collaborative Cross CAST x CAST

description: The dataset consists of a set of images for 3 mice with both parents from the CAST strain. For each mouse we provide an image file in .aim format, a .txt file with the image data, and a .hx file. Morphometrics will be added for the data as measurements are completed.
DOI: 10.25550/tz8
title: What MiRNAs Are Expressed In The E11.5 Mouse Midfacial Tissue?

description: Researching what miRNAs are expressed in the E11.5 mouse midfacial tissue. Methods: miRNA extracted using the Norgen miRNA Purification Kit, miRNA libraries were prepared using BiooScientific NEXTflex Small RNA Sequencing Kit by ligation of 3' barcoded adapters and 5' adapters on small-RNA sequences; miRNA-seq Illumina HiSeq 2000.
DOI: 10.25550/v24
title: microCT - Bone Tissue of a Msx1+/+ Control mouse at E16.5

description: Mouse ID: AH254 This dataset includes microCT scans of the skull of a Msx1+/+ 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/v6y
title: microCT - Bone Tissue of a K14-Cre;Tgfbr2fl/fl mouse at E17.5

description: Mouse ID: JI248 This dataset includes microCT scans of the skull of a K14-Cre;Tgfbr2fl/fl mouse at E17.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/v80
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/vdw
title: microCT - Soft Tissue of a Wnt1-Cre; Tgfbr2fl/fl; Alk5fl/+ mouse at E16.5

description: Mouse ID: JI330 This dataset includes microCT scans of the skull of a Wnt1-Cre; Tgfbr2fl/fl; Alk5fl/+ 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/ve0
title: microCT - Bone Tissue of Msx1-/- mouse at E18.5

description: Mouse ID: AH245 This dataset includes 1 microCT scan of the skull of an Msx1 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/vgm
title: microCT - Soft Tissue of Tgfbr2flfl control at E15.5

description: This dataset includes 1 microCT scan of the skull of a Tgfbr2flfl 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/vh4
title: Micro-CT images of adult mouse skulls, Collaborative Cross C57BL6 x C57BL6

description: The dataset consists of a set of images for 1 mouse with both parents from the C57BL6 strain. For each mouse we provide an image file in .aim format, a .txt file with the image data, and a .hx file. Morphometrics will be added for the data as measurements are completed.
DOI: 10.25550/vj4
title: microCT - Soft Tissue of a Tgfbr2fl/fl;Alk5fl/+ mouse at E17.5

description: Mouse ID: AS326 This dataset includes microCT scans of the skull of a Tgfbr2fl/fl;Alk5fl/+ mouse at E17.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/vkm
title: microCT - Bone Tissue of Msx1 mice at E17.5

description: This dataset includes microCT scans of the skulsl of Msx1 mice at E17.5. The scans are in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/vqp
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm605

description: See link to the data preparation protocols for this study in the Additional Information section **Enhancer location:** Mouse genome mm9, chr13: 119639284-119640197 **Name:** mCF208 **Vista Enhancer ID:** mm605 **Nearest craniofacial gene or locus:** Fgf10 **Enhancer expression:** positive **Tissues where active:** facial mesenchyme, trigeminal V (ganglion, cranial) **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/vya
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm898

description: See link to the data preparation protocols for this study in the Additional Information section **Enhancer location:** Mouse genome mm9, chr9: 87943415-87945786 **Name:** mAN327 **Vista Enhancer ID:** mm898 **Nearest craniofacial gene or locus:** none **Enhancer expression:** positive **Tissues where active:** branchial arch, 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/tjt
title: Human and Chimpanzee ChIP-seq assays

description: Human and Chimpanzee ChIP-seq assays
DOI: 10.25550/tma
title: microCT - Bone Tissue of Ctgf Control Mouse at P0

description: Mouse ID: CP048 This dataset includes microCT scans of the skull of a Ctgf Control 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/tqw
title: Transgenic Mouse Enhancer OPT Assays - mm50

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=50&organism_id=2) to see the associated data in the VISTA browser.
DOI: 10.25550/tw0
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm404

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, chr6:50906958-50908237 **Name:** mCF90 **Vista Enhancer ID:** mm404 **Nearest craniofacial gene or locus:** none **Enhancer expression:** positive **Tissues where active:** branchial arch This data set includes the following: * 4 files in .tgz format. Each of these corresponds to one .avi file 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 - ] * 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 * Tested element.txt: Download the text file mCF90metadata.txt from the External Reference section
DOI: 10.25550/txw
title: microCT - Soft Tissue of a Ctgf+/+ Control mouse at E14.5

description: Mouse ID: CP307 This dataset includes microCT scans of the skull of a Ctgf+/+ Control mouse at E14.5. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format