cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25550/vvw
title: Micro-CT images of adult mouse skulls, Collaborative Cross C57BL6 x PWK

description: The dataset consists of a set of images for 4 mice with one parent from the C57BL6 strain and the other from the PWK 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/vwa
title: Micro-CT images of adult mouse skulls, Collaborative Cross 129S1 x WSB

description: The dataset consists of a set of images for 11 mice with one parent from the 129S1 strain, and the other from the WSB 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: 10.25550/1-4xs2
title: Single cell RNA-sequencing of E11.5 C57BL/6J mouse fusing upper lip and primary palate

description: Wild-type C57BL/6J embryos were isolated at E11.5 and staged between 45-46 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 and RNA sequenced using the 10X Genomics platform. Approximately 8000 cells were sequenced to a depth of 100,000 reads per cell.
DOI: 10.25550/1-4zs2
title: FB0121_Trio WES of 36 yo female and 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. Catherine Nowak of Boston Children's Hospital. Phenotype - Agenesis of corpus callosum - Midline facial defects - Cleft palate - Wide nasal root - Bifid tongue - Maxilala
DOI: 10.25550/1-4zs4
title: FB0139_Trio WES_Female Proband & 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. Joan Stoler of Boston Children's Hospital. Phenotype - Bilateral iris coloboma
DOI: 10.25550/2b8t
title: FB0070_12yo girl w/ micrognathia (progressive, she did not have as a child) & contracture of fingers

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: 10.25550/2b92
title: FB0094_Trio WES_ Male proband with unilateral cleft lip and palate, complete situs inversus

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: 10.25550/2b96
title: FB0099 Female proband with Robin sequence, cleft palate and micrognathia. Additional five family members sequenced.

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. Additional information: Mother has micrognathia and heart valve deficiency. Maternal aunt 1 has multiple sclerosis, maternal aunt 2 has Ehlers Danlos syndrome. Maternal grandmother has artificial heart valve.
DOI: 10.25550/2b9p
title: FB0105_Trio WES_ Female with Microform cleft lip, 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. Phenotype - tongue nodules - accessory gingival frenulae - agenesis of corpus callosum
DOI: 10.25550/2baa
title: FB0110_9yo female fraternal twins with cleft lip and palate, alveolar cleft

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 Lost Angeles.
DOI: 10.25550/tny
title: microCT - Soft Tissue of Smad4flfl Control mouse at E16.5

description: This dataset includes 1 microCT scan of the skull of a Smad4flfl 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/twe
title: microCT - Head soft tissue of CTGF -/- knockout mouse at P0

description: This dataset includes microCT scans of the head tissue of two CTGF -/- knockout mice at stage P0. The scans are in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/tyt
title: Skull vault formation in individual WT AB Fish

description: An individual fish was imaged successively from 19-21 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/vb8
title: microCT - Soft Tissue of an Msx1-/- mouse at E14.5

description: Mouse ID: AH286 This dataset includes microCT scans of the skull of an Msx1-/- 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/vbg
title: microCT - Soft Tissue of a Wnt1-Cre;Tgfbr2fl/fl;Alk5fl/+ mouse at E14.5

description: Mouse ID: JI319 This dataset includes microCT scans of the skull of a Wnt1-Cre;Tgfbr2fl/fl;Alk5fl/+ 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/vc6
title: Transgenic Mouse Enhancer OPT Assays - mm1217

description: ChIP-seq, RNA-seq and transgenic assays to identify non-coding regulatory elements (enhancers) active during craniofacial development
DOI: 10.25550/ve8
title: What MiRNAs Are Expressed In The E14.5 Mouse Midfacial Tissue?

description: Researching what miRNAs are expressed in the E14.5 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/vep
title: microCT - Soft Tissue of ctgf-/- mouse at P0

description: Mouse ID: CP062 This dataset includes microCT scans of the skull of a ctgf-/- 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/vmj
title: microCT - Bone Tissue of C57BL6J mouse at E18.5

description: 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/vrj
title: microCT - Soft Tissue of a Wnt1-Cre;Tgfbr2fl/fl mouse at E14.5

description: Mouse ID: JI314 This dataset includes microCT scans of the skull of a Wnt1-Cre;Tgfbr2fl/fl 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: 10.5519/qd.9zyqim51
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (17347 records)
DOI: 10.25550/tky
title: microCT - Bone Tissue of Msx1 Control Mouse at E18.5

description: Mouse ID: AH228 This dataset includes microCT scans of the skull of an Msx1 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/tqa
title: microCT - Soft Tissue of Fgfr2 Control Mouse at P0

description: Mouse ID: ZZ263 This dataset includes 1 microCT scan of the skull of an Fgfr2 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/tqp
title: ChIP seq analysis of p300 bound regions in E15.5 mouse palates

description: This dataset includes the results of ChIP-Seq analysis of p300 bound regions in E15.5 mouse palates. The results are also presented as tracks on the Genome Browser (see links in the Additional Information section) . The data include the following information for each peak called: * ranking. Called peaks are ranked by maximum coverage, those with equal maximum coverage are then ranked by local p-value. * the location of the peak, shown as chromosome start and end positions (mouse genome build mm9) * peak length * position of the peak summit * tags: the number of reads in peaks (# reads in region, not maximum read coverage depth) * score: -(log(pvalue)) * fold enrichment: enrichment in peak vs input sample * FDR: false-discovery rate annotation based on post-peak calling filtering of peaks based on genome annotation To download the data, log in and click on the "Download dataset" button.
DOI: 10.25550/tr0
title: Micro-CT images of adult mouse skulls, Collaborative Cross NOD x WSB

description: The dataset consists of a set of images for 11 mice with one parent from the NOD strain, and the other parent from the WSB 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/tvj
title: microCT - Soft Tissue of a C57BL6J mouse at E16.5

description: Mouse ID: JI205 This dataset includes a microCT scan of the skull of a C57BL6J 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/tzg
title: What MiRNAs Are Expressed In The E12.5 Mouse Midfacial Tissue?

description: Researching what miRNAs are expressed in the E12.5 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/v0e
title: What MiRNAs Are Expressed In The E10.5 Mouse Midfacial Tissue?

description: Researching what miRNAs are expressed in the E10.5 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/v2g
title: microCT - Soft Tissue of an Msx1-/- mouse at E13.5

description: Mouse ID: AH277 This dataset includes microCT scans of the skull of an Msx1-/- 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/v50
title: microCT - Bone Tissue of Msx1 Control mouse at P0

description: Mouse ID: AH349 This dataset includes microCT scans of the skull of an Msx1 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/v5p
title: microCT - Bone Tissue of K14-Cre;Tgfbr2flfl mice at E17.5

description: This dataset includes microCT scans of the skulls of K14-Cre; Tgfbr2flfl mice 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/vdj
title: Sample to subject mapping file for the 3D Facial Images-Tanzania dataset

description: This dataset contains a sample-to-subject mapping file for the 3D Facial Images-Tanzania dataset (accession number FB00000667.01). **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/vea
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm417

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, chr14:24339368-24340818 **Name:** mCF103 **Vista Enhancer ID:** mm417 **Nearest craniofacial gene or locus:** ZFP503 **Enhancer expression:** positive **Tissues where active:** branchial arch **Comment on OPT files:** signal lost? 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 mCF103metadata.txt from the External Reference section .
DOI: 10.25550/vhy
title: Micro-CT images of adult mouse skulls, Collaborative Cross A/J x 129S1

description: The dataset consists of a set of images for 1 mouse with one parent from the A/J strain, and the other from the 129S1 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/vkc
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm448

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, chr19:59497704-59500058 **Name:** mCF134 **Vista Enhancer ID:** mm448 **Nearest craniofacial gene or locus:** VAX1 **Enhancer expression:** positive **Tissues where active:** facial mesenchyme, nose, limbs **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 * 3 movie (.avi) files: 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: Coronal plane movie, Sagittal plane movie, Transverse plane movie * 3 files in .tgz (or.tar) 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 (or .tar) 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 mCF134metadata.txt from the External Reference section .
DOI: 10.25550/vsa
title: microMRI images of skulls of Smad4ff mice at E18.5

description: microMRI images of skulls of Smad4ff mice at E18.5. The dataset contains 3-D images in niftii format for 1 mouse.
DOI: 10.25550/vve
title: microCT - Soft Tissue of a K14-Cre;Tgfbr2fl/fl mouse at E18.5

description: Mouse ID: JI328 This dataset includes microCT scans of the skull of a K14-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/vxt
title: Interesting mouse HCR images

description: A collection of numerous TIFF images displaying mouse HCR data.
DOI: 10.25550/2a8y
title: Whole-genome transcriptome profiling of E14.5 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: 10.25550/2b8e
title: FB0045_2yo male with prenatal suspicion of hand/food syndactyly and coronal suture synostosis_Candidate Gene: FGFR2

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 - hearing loss - appearance of Apert syndrome
DOI: 10.25550/3qej
title: Activity of human neural crest enhancer near COL13A1 in E11.5 transgenic mouse embryo - Tg(hg38_chr10:69710540-69711365::LacZ).

description: Tg(hg38_chr10:69710540-69711365::LacZ) human neural crest enhancer with biased activity in the frontonasal process, periocular mesenchyme/optic cup, maxillary and mandibular 1st branchial arch, 2nd branchial arch, 3rd branchial arch, heart field, forelimb and hindlimb buds, and somites in comparison to the activity of the equivalent chimp enhancer. LacZ signal was also consistently observed in the forebrain, midbrain, hindbrain, trigeminal (V) ganglion, and midgut.
DOI: 10.25550/3qm6
title: Activity of human neural crest enhancer near NARS2 in E11.5 transgenic mouse embryo – Tg(hg38_chr11:78595308-78596197::LacZ).

description: Tg(hg38_chr11:78595308- 78596197::LacZ) human neural crest enhancer with biased activity in the forebrain, midbrain, maxillary prominence of the 1st branchial arch, forelimb and hindlimb buds, midgut, somites, and tail mesenchyme in comparison to the activity of the equivalent chimp enhancer. LacZ signal was also consistently observed in the periocular mesenchyme, mandibular prominence of the 1st branchial arch, and 2nd branchial arch.