This my collection of annotated metadata
Alzheimer’s disease is a neurodegenerative disorder accounting for more than 50% of cases of dementia. Diagnosis of Alzheimer’s disease relies on cognitive tests and analysis of amyloid beta, protein tau, and hyperphosphorylated tau in cerebrospinal fluid. Although these markers provide relatively high sensitivity and specificity for early disease detection, they are not suitable for monitor of disease progression. In the present study, authors used label-free shotgun mass spectrometry to analyse the cerebrospinal fluid proteome of Alzheimer’s disease patients and non-demented controls to identify potential biomarkers for Alzheimer’s disease. Authors processed the data using five programs (DecyderMS, Maxquant, OpenMS, PEAKS, and Sieve) and compared their results by means of reproducibility and peptide identification, including three different normalization methods. After depletion of high abundant proteins we found that Alzheimer’s disease patients had lower fraction of low-abundance proteins in cerebrospinal fluid compared to healthy controls (p<0.05). Consequently, global normalization was found to be less accurate compared to using spiked-in chicken ovalbumin for normalization. In addition, we determined that Sieve and OpenMS resulted in the highest reproducibility and PEAKS was the programs with the highest identification performance. Finally, authors successfully verified significantly lower levels (p<0.05) of eight proteins (A2GL, APOM, C1QB, C1QC, C1S, FBLN3, PTPRZ, and SEZ6) in Alzheimer’s disease compared to controls using an antibody-based detection method. These proteins are involved in different biological roles spanning from cell adhesion and migration, to regulation of the synapse and the immune system.
Enhancer location: Mouse genome mm9, chr14:47230349-47231452; Name: mCF73 Vista Enhancer ID: mm387 Nearest craniofacial gene or locus: BMP4; Enhancer expression: positive Tissues where active: branchial arch, facial mesenchyme, nose, limbs, neural tube; Comment on OPT files: slightly damaged embryo;
Enhancer location: Mouse genome mm9, chr14:22932439-22935173; Name: mCF100; Nearest craniofacial gene or locus: ZFP503; Enhancer expression: positive; Tissues where active: branchial arch, eye, forebrain, limbs,midbrain
Enhancer location: Mouse genome mm9, chr14:24339368-24340818; Name: mCF103; Nearest craniofacial gene or locus: ZFP503; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files: signal lost?;
Enhancer location: Mouse genome mm9, chr2:4282958-4283735; Name: mCF106; Nearest craniofacial gene or locus: None; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files: damaged embryo / the signal is internal, see y sections for example
Enhancer location: Mouse genome mm9, chr2:4508633-4509808; Name: mCF109; Nearest craniofacial gene or locus: None; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, nose, limbs; Comment on OPT files: no clip file
Enhancer location: Mouse genome mm9, chr5:38216912-38220459; Name: mCF112; Nearest craniofacial gene or locus: Msx1; Enhancer expression: positive; Tissues where active: branchial arch, ear, eye, facial mesenchyme, genital tubercle, hindbrain, limb, midbrain, nose, somite
Enhancer location: Mouse genome mm9, chr5:38292345-38293728; Name: mCF113; Nearest craniofacial gene or locus: Msx1; Enhancer expression: positive; Tissues where active: facial mesenchyme, nose; Comment on OPT files: no clip file
Enhancer location: Mouse genome mm9, chr5:38308981-38309832; Name: mCF114; Nearest craniofacial gene or locus: Msx1; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, genital tubercle, limb; Comment on OPT files: slightly damaged embryo
Enhancer location: Mouse genome mm9, chr15:63025492-63026341; Name: mCF144; Nearest craniofacial gene or locus: NOG; Enhancer expression: positive; Tissues where active: branchial arch, limbs, other; Comment on OPT files: no clip file
Enhancer location: Mouse genome mm9, chr13:119304649-119305832; Name: mCF149; Nearest craniofacial gene or locus: FGF10; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files: embryo damaged during OPT. Has to be re-sent.
Enhancer location: Mouse genome mm9, chr14:46563519-46564802; Name: mCF70; Nearest craniofacial gene or locus: BMP4; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, nose, limbs, neural tube; Comment on OPT files: slightly damaged embryo
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr14:24305238-24305824; Name: mCF101; Vista Enhancer ID: mm415; Nearest craniofacial gene or locus: ZFP503; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr14:24313049-24314033; Name: mCF102; Vista Enhancer ID: mm416; Nearest craniofacial gene or locus: ZFP503 This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track 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: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr2:4477194-4478921; Name: mCF108; Vista Enhancer ID: mm422; Nearest craniofacial gene or locus: None; Enhancer Status: Other; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr1:194615789-194617278; Name: mCF116; Vista Enhancer ID: mm430; Nearest craniofacial gene or locus: IRF6 This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track 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: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr3:121656460-121657306; Name: mCF120; Vista Enhancer ID: mm433; Nearest craniofacial gene or locus: ABCA4; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr11:87994053-87995154; Name: mCF124; Vista Enhancer ID: mm438; Nearest craniofacial gene or locus: NOG; Enhancer Status: Other; This data set includes the following: – Apdf 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. o see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr11:88087585-88089577; Name: mCF125; Vista Enhancer ID: mm439; Nearest craniofacial gene or locus: NOG; Enhancer status: Other;This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track 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: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr19:59341620-59342768; Name: mCF133; Vista Enhancer ID: mm447; Nearest craniofacial gene or locus: VAX1; Enhancer expression: Other; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr19:60091349-60092721; Name: mCF135; Vista Enhancer ID: mm449; Nearest craniofacial gene or locus: VAX1; Enhancer expression: other; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:143245796-143246980; Name: mCF136; Vista Enhancer ID: mm450; Nearest craniofacial gene or locus: NOG; Enhancer expression: negative; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:143385863-143387546; Name: mCF137; Vista Enhancer ID: mm451; Nearest craniofacial gene or locus: Sox4; Enhancer expression: Other; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:144893166-144894534; Name: mCF142; Vista Enhancer ID: mm456; Nearest craniofacial gene or locus: Sox5; Enhancer expression: Other; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track>; Enhancer location: Mouse genome mm9, chr15:62734249-62735453; Name: mCF143; Vista Enhancer ID: mm457; Nearest craniofacial gene or locus: 8q24; Enhancer expression: Negative; This data set includes the following: – Apdf 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.To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr14:46843672-46844634; Name: mCF71; Vista Enhancer ID: mm385; Nearest craniofacial gene or locus: BMP4; Enhancer expression: negative; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr14:46867125-46868800; Name: mCF72; Vista Enhancer ID: mm386; Nearest craniofacial gene or locus: BMP4; Enhancer expression: negative; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr5:19999596-20000707; Name: mCF75; Vista Enhancer ID: mm389; Nearest craniofacial gene or locus: None; Enhancer expression: other; This data set includes the following: – Apdf 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, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here See Genome Browser Track Enhancer location: Mouse genome mm9, chr5:20455843-20456804; Name: mCF76; Vista Enhancer ID: mm390; Nearest craniofacial gene or locus: none; Enhancer expression: negative; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here See Genome Browser Track Enhancer location: Mouse genome mm9, chr5:21001721-21003173; Name: mCF77; Vista Enhancer ID: mm391; Nearest craniofacial gene or locus: none; Enhancer expression: negative; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6: 4433466-4435322; Name: mCF84; Vista Enhancer ID: mm398; Nearest craniofacial gene or locus: Col1A2; Enhancer expression: other; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6: 4438997-4440635; Name: mCF85; Vista Enhancer ID: mm399; Nearest craniofacial gene or locus: Col1A2; Enhancer expression: negative; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:50760703-50761820; Name: mCF87; Vista Enhancer ID: mm401; Nearest craniofacial gene or locus: none; Enhancer expression: negative; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
Enhancer location: Mouse genome mm9, chr6:50771120-50773588; Name: mCF88; Vista Enhancer ID: mm402; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: branchial arch, forebrain, hindbrain, midbrain, neural tube, other
The data preparation protocols for this study are described here The results are also presented as tracks on the FaceBase Genome Browser mirror. Enhancer location: Mouse genome mm9, chr6:50771120-50773588; Name: mCF88; Vista Enhancer ID: mm402; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: branchial arch, forebrain, hindbrain, midbrain, neural tube, other; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
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
The data preparation protocols for this study are described here. The results are also presented as tracks on the FaceBase Genome Browser mirror. 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: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:51001775-51003272; Name: mCF93; Vista Enhancer ID: mm407; Nearest craniofacial gene or locus: none; Enhancer expression: other; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:51054237-51055194; Name: mCF94; Vista Enhancer ID: mm408; Nearest craniofacial gene or locus: none; Enhancer expression: negative; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:51122426-51123469; Name: mCF95; Vista Enhancer ID: mm409; Nearest craniofacial gene or locus: none; Enhancer expression: negative; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:51283777-51284475; Name: mCF96; Vista Enhancer ID: mm410; Nearest craniofacial gene or locus: none; Enhancer expression: negative; This data set includes the following: – Apdf 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. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
Enhancer location: Mouse genome mm9, chr5:38358865-38360435; Name: mCF115; Nearest craniofacial gene or locus: Msx1; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, genital tubercle, limb
Enhancer location: Mouse genome mm9, chr6:50933970-50934809; Name: mCF92; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: facial mesenchyme, limbs
Enhancer location: Mouse genome mm9, chr19:58446412-58447549; Name: mCF131; Nearest craniofacial gene or locus: VAX1; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, nose, limbs, neural tube; Comment on OPT files: no clip file
Enhancer location: Mouse genome mm9, chr19:59497704-59500058; Name: mCF134; Nearest craniofacial gene or locus: VAX1; Enhancer expression: positive; Tissues where active: facial mesenchyme, nose, limbs; Comment on OPT files: slightly damaged embryo
Enhancer location: Mouse genome mm9, chr3:121750391-121752165 Name: mCF121; Nearest craniofacial gene or locus: ABCA4; Enhancer expression: positive; Tissues where active: nose, facial mesenchyme, forebrain; Comment on OPT files: damaged embryo
Enhancer location: Mouse genome mm9, chr6: 4503540-4505066; Name: mCF86; Nearest craniofacial gene or locus: Col1A2; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, nose, limbs; Comment on OPT files: signal is internal
Enhancer location: Mouse genome mm9, chr6:50874551-50876236; Name: mCF89; Nearest craniofacial gene or locus: BMP4; Enhancer expression: positive; Tissues where active: branchial arch
Enhancer location: Mouse genome mm9, chr6:50931070-50932326; Name: mCF91; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, other, trigeminal V; Comment on OPT files: signal is internal
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 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.
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 FaceBase Genome Browser mirror
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 Genome Browser
Enhancer location: Mouse genome mm9, chr16:15194506-15196207; Name: mCF69; Vista Enhancer ID: mm383; Nearest craniofacial gene or locus: Snai2; Enhancer expression: positive; Tissues where active: branchial arch, nose, facial mesenchyme, other; Comment on OPT files: none
Enhancer location: Mouse genome mm9, chr16: 15084685-15085804; Name: mCF152; Vista Enhancer ID: mm466; Nearest craniofacial gene or locus: Snai2; Enhancer expression: positive; Tissues where active: branchial arch, nose, tail, hindbrain, limb; Comment on OPT files: none
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
Enhancer location: Mouse genome mm9, chr8: 26550663-26552575; Name: mCF160; Vista Enhancer ID: mm919; Nearest craniofacial gene or locus: Fgfr1; Enhancer expression: positive; Tissues where active: facial mesenchyme, limb; Comment on OPT files: none
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
Enhancer location: Mouse genome mm9, chr8:26653487-26656234; Name: mCF161; Vista Enhancer ID: mm612; Nearest craniofacial gene or locus: Fgfr1; Enhancer expression: positive; Tissues where active: branchial arch, eye, nose, hindbrain, forebrain, limb, midbrain; Comment on OPT files: none
Enhancer location: Mouse genome mm9, chr5:112006329-112007316; Name: mCF170; Vista Enhancer ID: mm621; Nearest craniofacial gene or locus: Mn1; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr5:112030286-112031759; Name: mCF171; Vista Enhancer ID: mm622; Nearest craniofacial gene or locus: Mn1; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files:
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:
Enhancer location: Mouse genome mm9, chr13: 48874997-48876671; Name: mCF175; Vista Enhancer ID: mm922; Nearest craniofacial gene or locus: Barx1; Enhancer expression: positive; Tissues where active: branchial arch, hindbrain, midbrain; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr15: 60684551-60685838; Name: mCF191; Vista Enhancer ID: mm642; Nearest craniofacial gene or locus: 8q24; Enhancer expression: positive; Tissues where active: branchial arch, ear, eye, heart, nose, facial mesenchyme, dorsal root ganglion, forebrain, limb, midbrain; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr1: 194624291-194626894; Name: mCF195; Vista Enhancer ID: mm646; Nearest craniofacial gene or locus: Irf6; Enhancer expression: positive; Tissues where active: branchial arch, nose, facial mesenchyme, forebrain, limb, somite; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr17: 44754669-44756591; Name: mCF205; Vista Enhancer ID: mm924; Nearest craniofacial gene or locus: Runx2; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr17: 44859063-44860738; Name: mCF206; Vista Enhancer ID: mm657; Nearest craniofacial gene or locus: Runx2; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files:
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:
Enhancer location: Mouse genome mm9, chr13: 116476829-116478253; Name: mCF219; Vista Enhancer ID: mm933; Nearest craniofacial gene or locus: Isl1; Enhancer expression: positive; Tissues where active: nose, cranial nerve, dorsal root ganglion; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr7: 137569281-137570835; Name: mCF224; Vista Enhancer ID: mm938; Nearest craniofacial gene or locus: Fgfr2; Enhancer expression: positive; Tissues where active: eye, tail, other, limb; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr5: 12505539-12509076; Name: mAN261; Vista Enhancer ID: mm832; Nearest craniofacial gene or locus: Sema3d; Enhancer expression: positive; Tissues where active: branchial arch, ear, nose; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr1: 93859505-93862537; Name: mAN330; Vista Enhancer ID: mm901; Nearest craniofacial gene or locus: Twist2; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr10: 36203387-36205893; Name: mAN32; Vista Enhancer ID: mm693; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: nose, forebrain, limb, midbrain; Comment on OPT files:
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:
Enhancer location: Human genome hg19, chr4: 4522867-4524050; Name: UL198; Vista Enhancer ID: hs746; Nearest craniofacial gene or locus: Msx1; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files:
Enhancer location: Human genome hg19, chr5: 174160174-174161818; Name: CF6; Vista Enhancer ID: hs1256; Nearest craniofacial gene or locus: Msx2; Enhancer expression: positive; Tissues where active: nose, hindbrain, forebrain, limb; Comment on OPT files: no 3D movie available
This dataset includes the results of ChIP-Seq analysis of p300 bound regions in E14.5 mouse palates. The results are also presented as tracks on the Genome Browser 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.
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 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.