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31 results for “whole-genome bisulfite sequencing”
List of known SNP positions (based on SNP chip data) for base quality score recalibration of alignments for whole-genome resequencing and whole-genome bisulfite sequencing data from great tits (Parus major)
<p>The profiling of epigenetic marks like DNA methylation has become a central aspect of studies in evolution and ecology. Bisulfite sequencing is commonly used for assessing genome-wide DNA methylation at single nucleotide resolution but these data can also provide information on genetic variants like single nucleotide polymorphisms (SNPs). However, bisulfite conversion causes unmethylated cytosines to appear as thymines, complicating the alignment and subsequent SNP calling. Several tools have been developed to overcome this challenge, but there is no independent evaluation of such tools for non-model species, which often lack genomic references. Here, we used whole-genome bisulfite sequencing (WGBS) data from four female great tits (<i>Parus major</i>) to evaluate the performance of seven tools for SNP calling from bisulfite sequencing data. We used SNPs from whole-genome resequencing data of the same samples as baseline SNPs to assess common performance metrics like sensitivity, precision, and the number of true positive, false positive, and false negative SNPs for the full range of variant and genotype quality values. We found clear differences between the tools in either optimizing precision (Bis-SNP), sensitivity (biscuit), or a compromise between both (all other tools). Overall, the choice of SNP caller strongly depends on which performance parameter should be maximized and whether ascertainment bias should be minimized to optimize downstream analysis, highlighting the need for studies that assess such differences.</p>
List of known SNP positions (based on SNP chip data) for base quality score recalibration of alignments for whole-genome resequencing and whole-genome bisulfite sequencing data from great tits (Parus major)
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A comparative analysis of 5-azacytidine and zebularine induced DNA demethylation using whole-genome bisulfite sequencing
GEO Series GSE80300. Arabidopsis thaliana. 15 samples. Type: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Whole-genome bisulfite sequencing of Mandarin fish ranavirus
GEO Series GSE262554. Mandarin fish ranavirus. 4 samples. Type: Methylation profiling by high throughput sequencing.
Methylated DNA is over-represented in whole-genome bisulfite sequencing data
GEO Series GSE58217. Arabidopsis thaliana. 18 samples. Type: Methylation profiling by high throughput sequencing.
whole-genome bisulfite sequencing (BS-seq) of HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1)
GEO Series GSE51867. Homo sapiens. 3 samples. Type: Methylation profiling by high throughput sequencing.
Single-base resolution DNA methylation profiles of two highly inbred chicken lines, Leghorn and Fayoumi, by whole-genome bisulfite sequencing (MethylC-seq).
GEO Series GSE56975. Gallus gallus. 2 samples. Type: Methylation profiling by high throughput sequencing.
Whole-genome bisulfite sequencing across 27 developmental stages in Sus scrofa skeletal muscle
GEO Series GSE157043. Sus scrofa. 81 samples. Type: Methylation profiling by high throughput sequencing.
Whole-genome bisulfite sequencing of Infectious spleen and kidney necrosis virus
GEO Series GSE241500. Infectious spleen and kidney necrosis virus. 3 samples. Type: Methylation profiling by high throughput sequencing.
Whole-genome bisulfite sequencing analysis of Pten's function in regulating cardiomyocyte differentiation
GEO Series GSE160236. Mus musculus. 4 samples. Type: Methylation profiling by high throughput sequencing.
Whole-genome bisulfite sequencing and histone 3.3 ChIP-seq of microdissected developing mouse lens
GEO Series GSE213901. Mus musculus. 17 samples. Type: Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Single-Cell Whole-Genome Bisulfite Sequencing for Analysis of Epigenetic Heterogeneity
GEO Series GSE56879. Mus musculus. 56 samples. Type: Methylation profiling by high throughput sequencing.
Whole-genome bisulfite sequencing in the whole blood of three dog breeds
GEO Series GSE252908. Canis lupus familiaris. 19 samples. Type: Methylation profiling by high throughput sequencing.
Whole-Genome Bisulfite Sequencing of Nasopharyngeal Carcinoma and Nasopharyngeal Epithelial Tissues [WGBS]
GEO Series GSE173559. Homo sapiens. 20 samples. Type: Methylation profiling by high throughput sequencing.
Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells
GEO Series GSE41923. Mus musculus. 14 samples. Type: Methylation profiling by high throughput sequencing.
Longitudinal study of the human sperm methylome aging through whole-genome bisulfite sequencing
GEO Series GSE222340. Homo sapiens. 20 samples. Type: Methylation profiling by high throughput sequencing.
Whole-genome bisulfite sequencing analysis for intestinal budding organoids derived from induced or tissue-derived intestinal stem cells, and for mouse embryonic fibroblasts
GEO Series GSE222669. Mus musculus. 8 samples. Type: Methylation profiling by high throughput sequencing.
NPC268 whole-genome bisulfite sequencing (WGBS)
GEO Series GSE233426. Homo sapiens. 1 samples. Type: Methylation profiling by high throughput sequencing.
Methylome dataset by Whole-genome bisulfite sequencing (WGBS) using whole blood of dogs
GEO Series GSE309781. Canis lupus familiaris. 39 samples. Type: Methylation profiling by high throughput sequencing.
Whole-Genome Bisulfite Sequencing of Nasopharyngeal Carcinoma and Nasopharyngeal Epithelial Tissues [SeqCapEpi]
GEO Series GSE173551. Homo sapiens. 12 samples. Type: Methylation profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.