cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25550/3tm6
title: Activity of P. troglodytes neural crest enhancer near BMPER in E11.5 transgenic mouse embryo - Tg(panTro4_chr7:32036816-32038352::LacZ)

description: Tg(panTro4_chr7:32036816-32038352::LacZ) neural crest enhancer biased in the frontonasal prominence of P. troglodytes in comparison to activity of the equivalent human enhancer. 6/11 LacZ positive embryos exhibited moderate to strong expression in this region. LacZ signal was also consistently observed in the branchial arches, forebrain, limb buds, and somites.
DOI: 10.25550/tjc
title: Coronal suture, WT and Twist1+/- (Saethre-Chotzen syndrome mouse model), E16.5

description: RNA-Seq libraries are from laser capture microdissections of C57BL/6J Fgfr2+/+ (W) and C57BL/6J Saethre-Chotzen syndrome Twist1+/- (T) mice, at development stage TS24/E16.5 (6), from the coronal suture ( C ), with 5 biological replicates (1-5), of the suture mesenchyme (SM), frontal bone osteogenic front (FR), and parietal bone osteogenic front (PA). “W6C1SM”, for example, indicates WT, E16.5, coronal suture, replicate 1, suture mesenchyme.
DOI: 10.25550/tkp
title: microCT - Soft Tissue of Myf5-Cre;Smad4flfl Mice at P0

description: This dataset includes microCT scans of the skulls of Myf5-Cre;Smad4flfl mice at 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/tmc
title: microCT - Bone Tissue of Ctgf Control Mouse at P0

description: Mouse ID: CP084 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/tr2
title: microCT - Soft Tissue of a Ctgf-/- mouse at E14.5

description: Mouse ID: CP258 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/ts8
title: Micro-CT images of adult mouse skulls, Collaborative Cross C57BL6 x WSB

description: The dataset consists of a set of images for 3 mice with one parent from the C57BL6 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/ttw
title: microCT - Bone Tissue of Msx1-/- mouse at P0

description: Mouse ID: GL203 This dataset includes a microCT scan of the skull of an Msx1 -/- 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/vaa
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm429

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, chr5:38358865-38360435 **Name:** mCF115 **Vista Enhancer ID:** mm429 **Nearest craniofacial gene or locus:** Msx1 **Enhancer expression:** positive **Tissues where active:** branchial arch, facial mesenchyme, genital tubercle, limb 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 mCF115metadata.txt from the External Reference section
DOI: 10.25550/vcj
title: microCT - Soft Tissue of Smad4 control mouse at E17.5

description: This dataset includes 1 microCT scan of the skull of a Smad4 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/vpc
title: Transgenic Mouse Enhancer OPT Assays - mm745

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=745&organism_id=2) to see associated data in the VISTA browser.
DOI: 10.25550/vr2
title: microCT - Soft Tissue of Msx1-- mouse at E18.5

description: Mouse ID: AH229 This dataset includes microCT scans 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: 10.5281/zenodo.3438218
title: weecology/PortalData 1.130.0

description: Official Repo of the Portal Project Data
DOI: 10.25550/1-4ztg
title: FB0142_Trio WES_20mo & 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 Massachusetts General Hospital. Phenotype - 20 month old girl from Honduras - Born at 34 weeks - Gestation complicated by slow resuscitation after birth with concern for anoxic brain injury. - Pregnancy complicated by Zika infection.
DOI: 10.25550/1-4zw2
title: ChIP-Seq of mouse E15.5 Face (Maxillary Process)

description: We have generated histone ChIP-Seq libraries for dissected mouse maxillary tissue. We performed ChIP-Seq with markers of active chromatin (H3K27ac, H3K4me1) and repressive chromatin (H3K27me3). We also generated a ChIP input library.
DOI: 10.25550/26r8
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: 10.25550/2b9e
title: FB0101_Trio WES_2yo male with Cleft palate, aniridia, bilateral club feet, plagiocephaly, cataracts, hypoxemia

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: - Cleft palate, - aniridia - bilateral club feet - plagiocephaly - cataracts - hypoxemia
DOI: 10.25550/tkm
title: microCT - Bone Tissue of Wnt1-Cre;Tgfbr2fl/fl;Tak1fl/+ mouse at E18.5

description: This dataset includes 1 microCT scan of the skull of a Wnt1-Cre; Tgfbr2 fl/fl; tak1fl/+ 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/tmy
title: microCT - Bone Tissue of a Fgfr2fl/fl mouse at E18.5

description: Mouse ID: ZZ276 This dataset includes microCT scans of the skull of an 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/ts6
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm440

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, chr11:88341352-88342978 **Name:** mCF126 **Vista Enhancer ID:** mm440 **Nearest craniofacial gene or locus:** NOG **Enhancer Status:** Other 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 mCF126metadata.txt from the External Reference section
DOI: 10.25550/tve
title: microCT - Soft 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 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/tzj
title: Gene expression microarray - mouse E10.5 Lateral Eminence Neural Epithelium

description: Gene expression microarray using tissue obtained by laser capture microdissection (LCM) from the Lateral Eminence Neural Epithelium of mouse embryos at E10.5.
DOI: 10.25550/v1w
title: microCT - Soft Tissue of Wnt1-Cre;Tgfbr2fl/fl;Tgfb2+/- Mouse at E16.5

description: Mouse ID: JI191 This dataset includes 1 microCT scan of the skull of a Wnt1-Cre; Tgfbr2fl/fl; Tbfb2+/- 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/v3r
title: Gene expression RNA-Seq - mouse E14.5 Wild Type Posterior Lateral Palate

description: This data set contains BAM RNA-Seq data for the Posterior 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/v6t
title: Wild type zebrafish developmental series – AB strain (Ag stained)

description: MicroCT imaging of skull development in the zebrafish AB strain contrast stained
DOI: 10.25550/vje
title: microCT - Bone Tissue of Ctgf Control Mouse at P0

description: Mouse ID: CP047 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/vjw
title: microCT - Bone Tissue of C57BL6J at P0

description: This dataset includes 1 microCT scan of the skull of a C57BL6J mouse at P0. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/vn2
title: Micro-CT images of adult mouse skulls, Collaborative Cross 129S1 x C57BL6

description: The dataset consists of a set of images for 19 mice with one parent from the 129S1 strain and the other parent from the C57BL/6 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/vpj
title: Gene expression microarray - mouse E8.5 NonFloor Plate Neural Epithelium

description: Gene expression microarray using tissue obtained by laser capture microdissection (LCM) from the Non-Floor Plate Neural Epithelium of mouse embryos at E8.5.
DOI: 10.25550/vry
title: microCT - Bone Tissue of Msx1 control at P0

description: Mouse ID: GL204 This dataset includes a microCT scan 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: 10.5519/qd.wq1zo9js
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (34 records)
DOI: 10.25550/2724
title: Transgenic Mouse Enhancer Assay - mm1096

description: We used ChIP-seq to identify non-coding regulatory elements (enhancers) active during craniofacial development. This assay is Tg(mm9_chr19:37776187-37778925::LacZ). Follow this [link](https://enhancer.lbl.gov/cgi-bin/imagedb3.pl?form=presentation&show=1&experiment_id=1096&organism_id=2) to see the associated data in the VISTA browser.
DOI: 10.25550/2b8p
title: FB0067_Trio WES_5yo female with Pierre Robin Syndrome, cleft palate ASD s/p repair

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 - Pierre Robin Syndrome - cleft palate s/p repair - congenital cardiac defect: ASD s/p repair
DOI: 10.25550/2b9j
title: FB0102_5 WES_Proband: Robin sequence, cleft palate. Cousin: Robin sequence, cleft palate, micrognathia, hydronephrosis, PDA, developmental 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. Pedro Sanchez.
DOI: 10.25550/2ba2
title: FB0108_Right coronal synostosis, anisometropia and aniseikonia, ptosis of left eyelid, hyperopia

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 - esotropia - left upper lid ptosis - anisometropic astigmatism with hyperopia in both eyes - significant astigmatism in left eye
DOI: 10.25550/tjw
title: Gene expression profiling of the palate in compound mutant mice with a conditional inactivation of Tgfbr2 and conditional haploinsufficiency of Alk5 at embryonic day E14.5

description: We performed global gene expression analyses of the palate in Wnt1-Cre;Tgfbr2^fl/fl ;Alk5^fl/+ compound mutant mice at embryonic day E14.5. Total RNA samples (1 ug per sample) were converted into biotin-labeled cRNA using the Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP and standard protocols recommended by Affymetrix (Santa Clara, CA). Fragmented cDNA was applied to GeneChip, Mouse Genome 430 2.0 Arrays (Affymetrix) that contain probe sets designed to detect over 39000 transcripts. Microarrays were hybridized, processed and scanned, as previously described using manufacturers recommended conditions.
DOI: 10.25550/tta
title: microCT - Soft Tissue of Tgfbr2fl/fl mouse at E14.5

description: Mouse ID: JI323 This dataset includes microCT scans of the skull of a mouse at . The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/tx6
title: Micro-CT images of adult mouse skulls, Collaborative Cross NZO x WSB

description: The dataset consists of a set of images for 5 mice with one parent from the NZO 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/v4m
title: microCT - Soft Tissue of Smad4 control mouse at E17.5

description: Mouse ID: JF252 This dataset includes 1 microCT scan of the skull of a Smad4 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/v56
title: microCT - Soft Tissue of C57BL6J mouse at E16.5

description: This dataset includes 1 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/v7w
title: microCT - Bone Tissue of Myf5-Cre; Smad4fl/fl mouse at P0

description: Mouse ID: DH112 This dataset includes microCT scans of the skull of a Myf5-Cre; Smad4fl/fl mouse at P0. The scan is in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/v8y
title: Gene expression RNA-Seq - mouse E14.5 Wild Type Posterior Lateral Palate

description: This data set contains FASTQ RNA-Seq data for the Posterior 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/v9y
title: microCT - Soft Tissue of Msx1 mice at E17.5

description: This dataset includes microCT scans of the soft tissue of the skull 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/var
title: microCT - Soft Tissue of Msx1 Control mouse at E18.5

description: This dataset includes 1 microCT scan of the skull of a 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/vb2
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