cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25550/vg0
title: ChIP seq analysis of p300 bound regions in E13.5 mouse palates

description: This dataset includes the results of ChIP-Seq analysis of p300 bound regions in E13.5 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/vmp
title: microMRI images and video of skulls of unaffected wild type mice at E14.5

description: microMRI images of skulls of unaffected wild type mice at E14.5 The dataset contains 3-D images in niftii format for each of 10 wild type mice. This is an update of dataset FB00000112
DOI: 10.25550/vyc
title: Wild type zebrafish developmental series – AB strain

description: MicroCT imaging of skull development in the zebrafish AB strain
DOI: 10.25550/1-50kp
title: Activity of chimp neural crest enhancer intronic in CACNA1C in E11.5 transgenic mouse embryos – Tg(panTro4 _chr12:2344837-2345607::LacZ).

description: Tg(panTro4 _chr12:2344837-2345607::LacZ) chimp neural crest enhancer with reproducible activity in the forebrain, midbrain, hindbrain, optic cup, maxillary and mandibular 1st branchial arch, 2nd branchial arch, heart field, and dorsal root ganglia. This enhancer lacks the expression in the frontonasal process associated with the orthologous human enhancer, demonstrating human biased activity when comparing these two species.
DOI: 10.25550/tkj
title: Sprouty Background Effect

description: Inbred genetic background significantly influences the expression of phenotypes associated with known genetic perturbations and can underlie variation in disease severity between individuals with the same mutation. However, the effect of epistatic interactions on the development of complex traits, such as craniofacial morphology, is poorly understood. We use the morphometric landmarks associated with a previous FaceBase analysis (Genetic Determinants of Orofacial Shape and Relationship to Cleft Lip/Palate) to 1) quantify the effect of three Sprouty null mutations on craniofacial shape and 2) to quantify how the associated dysmorphology is modulated by three inbred backgrounds. While it is commonly known that a given mutation may have different phenotypic effects across mouse backgrounds, our quantitative results represent an important first step towards elucidating genetic interactions underlying variation in robustness to known genetic perturbations in mice. Taking background effects into account will be necessary to identify genetic and developmental interactions that modulate the severity of craniofacial dysmorphology, because variation in the penetrance or severity of a disease mutation among humans is almost certainly based on similar interactions. In addition, identical micro-CT image and landmarking protocols make this a valuable comparative dataset to the Collaborative Cross mouse dataset of adult mouse morphology already found on FaceBase.
DOI: 10.25550/tsp
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm419

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, chr2:4269384-4270396 **Name:** mCF105 **Vista Enhancer ID:** mm419 **Nearest craniofacial gene or locus:** None **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 mCF105metadata.txt from the External Reference section
DOI: 10.25550/ttc
title: microCT - Soft Tissue of a K14-Cre;Tgfbr2fl/fl mouse at E17.5

description: Mouse ID: JI247 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/ttm
title: microCT - Soft Tissue of Smad4 Control Mice at P0

description: This dataset includes microCT scans of the skulls of Smad4 control 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/ttp
title: Micro-CT images of adult mouse skulls, Collaborative Cross C57BL6 x CAST

description: The dataset consists of a set of images for 7 mice with one parent from the C57BL6 strain and the other 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/ttt
title: microCT - Soft Tissue of a K14-Cre;Fgfr2fl/fl mouse at E15.5

description: Mouse ID: ZZ356 This dataset includes microCT scans of the skull of a K14-Cre;Fgfr2fl/fl 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/tv2
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/tv8
title: microCT - Skull bones of Tgfbr2fl/fl mouse at P0

description: This dataset contains a microCT scan of the skull bones of a TGFBR2 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/tx2
title: microCT - Bone Tissue of Msx1 Control Mice at E16.5

description: This dataset includes microCT scans of the skulls of Msx1 Control mice at E16.5. The scans are in NiFTI format. See Help section for a list of free applications to view files in NiFTI format
DOI: 10.25550/v04
title: Skull vault formation in individual WT AB Fish

description: An individual fish was imaged successively from 19-30 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/v0p
title: microCT - Soft Tissue of Wnt1-Cre;Tgfbr2flfl;Alk5fl+ mouse at E18.5

description: Mouse ID: JI239 This dataset includes 1 microCT scan of the skull of a Wnt1-Cre; Tgfbr2flfl; Alk5fl+ 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/v2a
title: microCT - Bone Tissue of a Wnt1-Cre; Tgfbr2fl/fl; Alk5fl/+ mouse at E16.5

description: Mouse ID: JI329 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/v7m
title: microCT - Soft Tissue of Msx1-- mouse at E15.5

description: Mouse ID: AH282 This dataset includes microCT scans of the skulls of an Msx1-- 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/vj8
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm406

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, chr6:50933970-50934809 **Name:** mCF92 **Vista Enhancer ID:** mm406 **Nearest craniofacial gene or locus:** none **Enhancer expression:** positive **Tissues where active:** facial mesenchyme, limbs 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 mCF92metadata.txt from the External Reference section
DOI: 10.25550/vv4
title: Micro-CT images of adult mouse skulls, Collaborative Cross NOD x PWK

description: The dataset consists of a set of images for 19 mice with one parent from the NOD strain, and the other parent 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: 10.18739/a2dv1cn8t
title: Large scale water manipulation experiment in the Arctic tundra

description: This data set includes data from the Barrow Environmental Observatory (BEO) as part of the National Science Foundation (NSF) Biocomplexity Program. This involved increasing and decreasing the water table over large areas of tundra and observing the effects over the diverse microtopography of the region. It also includes measurements from the drained section (BEC) and flooded section (BEN) of Cake Eater Lake. Note: Files were updated on 04 Jan 12. Most of the data are the same (with same units) but in all years now photosynthetically active radiation (PAR) has been replaced by incoming shortwave global solar radiation in the spectral range from 310 to 2800 nm (unit is Wm-2). This radiation for 2006-2008 is from the BEC tower, while for 2005: from 1 to 29 July the radiation is from ARM-Barrow and after the 29 July until the end of August is again from BEC. Because the ARM site is closer to the coast from the BE sites and it is more cloudy a regression of the data from 1-29 July was performed to match conditions at the BE.
DOI: 10.25550/25rg
title: ChIP-seq and RNA-seq of mouse e13.5 maxillary process

description: We have generated histone ChIP-seq libraries for dissected mouse maxilla tissue. We performed ChIP-seq with markers of active chromatin (H3K27ac, H3K4me1) and repressive chromatin (H3K27me3). For each tissue we also generated a ChIP input library and total RNA-seq library. This is part of a series of experiments including parallel collection of dissected craniofacial tissues including maxilla, mandible and nose, and murine stages including e11.5, e13.5 and e15.5.
DOI: 10.25550/tjy
title: Coronal suture, WT and Twist1+/- (Saethre-Chotzen syndrome mouse model), E18.5

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 TS26/E18.5 (8), 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). “W8C1SM”, for example, indicates WT, E18.5, coronal suture, replicate 1, suture mesenchyme.
DOI: 10.25550/try
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 The results are also presented as tracks on the Genome Browser (see links 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: * 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/twt
title: microCT - Bone Tissue of Smad4fl/fl Control mouse at E16.5

description: Mouse ID: DH215 This dataset includes 1 microCT scan of the skull of a Smad4fl/fl 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/txa
title: microCT - Soft Tissue of CTGF-- mice at E14.5

description: This dataset includes microCT scans of the skulls of CTGF-- mice 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/v20
title: microCT - Soft Tissue of a Tgfbr2fl/fl mouse at E17.5

description: Mouse ID: JI250 This dataset includes microCT scans of the skull of a 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/v7g
title: Transgenic Mouse Enhancer Assay - Vista Enhancer ID: mm921

description: See link to the data preparation protocols for this study in the Additional Information section **Enhancer location:** Mouse genome mm9, chr5: 112104097-112105406 **Name:** mCF172 **Vista Enhancer ID:** mm921 **Nearest craniofacial gene or locus:** Mn1 **Enhancer expression:** positive **Tissues where active:** facial mesenchyme, other **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/v98
title: microCT - Soft Tissue of a C57BL/6J mouse at E14.5

description: Mouse ID: JI340 This dataset includes microCT scans of the skull of a C57BL/6J 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/vbw
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/vd0
title: microCT - Soft Tissue of a K14-Cre;Fgfr2fl/fl mouse at E15.5

description: Mouse ID: ZZ354 This dataset includes microCT scans of the skull of a K14-Cre;Fgfr2fl/fl 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/vdp
title: microCT - Soft Tissue of Wnt1Cre;Tgfbr2flfl;Tgfb2+- at E16.5

description: 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/ver
title: Gene expression RNA-Seq - mouse E14.5 Wild Type Anterior Medial Palate

description: This data set contains FASTQ RNA-Seq data for the Anterior Medial 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/vj6
title: microCT - Soft Tissue of Smad4flfl Control mouse at E18.5

description: This dataset includes 1 microCT scan of the skull of a Smad4flfl 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/vna
title: microMRI images of skulls of wild type mice at E16.5

description: microMRI images of skulls of unaffected wild type mice at E16.5. The dataset contains 3-D images in niftii format for each of 6 mice.
DOI: 10.25550/vpt
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/vxc
title: Transgenic Mouse Enhancer OPT Assays - hs1603

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=1603&organism_id=1) to see associated data in the VISTA browser.
DOI: 10.25550/vxw
title: Gene expression RNA-Seq - mouse E14.5 Wild Type Posterior Medial Palate

description: This data set contains BAM RNA-Seq data for the Posterior Medial 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: 10.25550/1-70ne
title: Activity of predicted human neural crest enhancer near Zfhx4 in E13.5 transgenic mouse embryos– Tg(hg38_chr8:76912494-76913266::LacZ).

description: Tg(hg38_chr8:76912494-76913266::LacZ) demonstrates no reproducible enhancer activity at E13.5.
DOI: 10.25550/2618
title: ChIP-seq and RNA-seq of mouse e13.5 mandibular process

description: We have generated histone ChIP-seq libraries for dissected mouse mandibular process tissue. We performed ChIP-seq with markers of active chromatin (H3K27ac, H3K4me1) and repressive chromatin (H3K27me3). For each tissue we also generated a ChIP input library and total RNA-seq library. This is part of a series of experiments including parallel collection of dissected craniofacial tissues including maxilla, mandible and nose, and murine stages including e11.5, e13.5 and e15.5.
DOI: 10.25550/tk8
title: microCT - Soft Tissue of Msx1-- mouse at E16.5

description: Mouse ID: AH257 This dataset includes microCT scans of the skull of a Msx1-- 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