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1,574
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1,574 results for “genome sequencing”
Whole genome methylation profiling in HepG2 cells using WGBS (Whole Genome Bisulfite Sequencing)
GEO Series GSE104245. Homo sapiens. 2 samples. Type: Methylation profiling by high throughput sequencing.
Whole genome bisulfite sequencing of apple fruits
GEO Series GSE109188. Malus domestica. 8 samples. Type: Methylation profiling by high throughput sequencing.
Whole Genome Bisulfite Sequencing of Botrytis cinerea
GEO Series GSE114821. Botrytis cinerea. 4 samples. Type: Methylation profiling by high throughput sequencing.
Whole genome bisulfite sequencing of peach fruits
GEO Series GSE165094. Prunus persica. 12 samples. Type: Methylation profiling by high throughput sequencing.
Whole genome bisulfite sequencing of mouse DC subsets
GEO Series GSE190440. Mus musculus. 3 samples. Type: Methylation profiling by high throughput sequencing.
Synodos LGG Whole Genome Sequencing (bam)
RNA sequencing data (bam files) from tumor specimens of individuals with Neurofibromatosis Type 1-associated Low-Grade Glioma (LGG). Includes various glioma subtypes.
Whole genome sequencing of core-binding factor leukemia
Pediatric de novo acute myeloid leukemia (AML) is a heterogeneous disease that can be divided into clinically distinct subtypes based on the presence of specific chromosomal abnormalities or gene alterations. One of the best characterized subtypes of AML involves leukemias with alterations of the core-binding factor (CBF)-complex, which comprises the FAB subtypes M2 and M4Eo and associates with a favorable outcome. Patients with the AML M2 subtype harbor a translocation between chromosomes 8 and 21 [t(8;21)] that yields the chimeric fusion gene RUNX1(AML1)-RUNX1T1(ETO), while patients with AML M4Eo express the chimeric fusion gene CBFB-SMMHC(MYH11) as a result of an inversion/translocation event of chromosome 16 [inv(16)/t(16;16)]. In an effort to define the total complement of genetic changes in CBF-leukemia, we performed paired-end whole genome sequencing (WGS) on diagnostic leukemia blasts and matched germ line samples from 17 pediatric CBF-leukemia patients using the Illumina platform. Somatic alterations, including single nucleotide variations (SNVs) and structural variations (SVs), including insertions, deletions, inversions, and inter- and intra-chromosomal rearrangements, were detected using complementary analysis pipelines (Bambino, CREST and CONSERTING). Recurrent screening of identified mutations will be performed in a cohort of approximately 94 cases of CBF-leukemias.
Whole Exome Sequencing of Craniopharyngioma Tumors at Human Genome Sequencing Center, Baylor College of Medicine
Craniopharyngioma is rare dysontogenic tumor that occurs at the base of the brain, above the pituitary gland. It is one of the most commonly diagnosed brain tumors in children aged 5-10 years old. In the United States, there are an estimated 350 new cases of craniopharyngioma diagnosed each year. Craniopharyngioma is thought to be derived from remnants of the developmental (embryonic) tissue from which the pituitary gland is derived. Although craniopharyngioma is a histologically benign tumor, it has a malignant behavior. They occur most commonly in the sellar and suprasellar regions, posing great challenges to clinical management. Activating mutations in the beta-catenin gene, CTNNB1 were identified in the majority of adamantinomatous craniopharyngiomas whereas the contribution of other genetic factors has yet to be explored. With the collaboration of Texas Children's Cancer and Hematology Centers at Baylor College of Medicine, the Human Genome Sequencing Center had access to 29 tumor specimens and matched normal blood samples from Craniopharyngioma patients. Whole-exome sequencing was performed to characterize the profile of somatic mutations. The deposited BAM files record the sequence alignments used to generate the mutation data.
Enabling Whole Genome Sequencing Analysis from FFPE Specimens in Clinical Oncology
This study includes whole genome sequencing from 44 pediatric patients at Memorial Sloan Kettering derived from formalin-fixed paraffin-embedded (FFPE) tissue. This dataset was used to train and validate a classification strategy called FFPErase for detecting artifact mutations from FFPE damage.
Genomic sequencing of Pediatric Rhabdomyosarcoma
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood accounting for approximately 350 newly diagnosed cases yearly in the United States. With the development of multimodal chemotherapy regimens, relapse-free survival rates have improved to 70-80% in patients with localized disease albeit with significant toxicity. Unfortunately, despite aggressive treatment, patients with metastatic or recurrent disease continue to suffer from high mortality. Further characterization of the genetic events underlying this tumor type is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. In a collaborative effort between the National Cancer Institute, the Children's Oncology Group, and the Broad Institute, we use a combination of whole-genome and whole-exome sequencing to characterize the landscape of somatic alterations in 147 tumor/normal pairs. This study also uses spatial transcriptome technology to investigate the tumor biology and their microenvironment surrounding cells.
Comprehensive Genomic Sequencing of Pediatric Cancer Cases (CMRI/KUCC)
This study provides paired tumor normal genomic sequencing data from ~ 200 children with cancer, including both solid tumors and leukemias, done by the Children's Mercy Research Institute (CMRI) and University of Kansas Cancer Center (KUCC). These data include whole genome sequencing (generally, ~20x), whole exome sequencing (generally, ~300x), bulk RNA sequencing (generally, ~80 million reads), and single-cell RNA and ATAC sequencing (>50,000 reads/cell). Additional phenotypic, pathologic, and genetic data, gathered clinically for these samples, are also provided.
Genomic sequencing of Pediatric Rhabdomyosarcoma
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Comprehensive Genomic Sequencing of Pediatric Cancer Cases (CMRI/KUCC)
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Whole-genome bisulfite sequencing anaysis of PSCs
GEO Series GSE195691. Homo sapiens. 2 samples. Type: Methylation profiling by high throughput sequencing.
Mitochondrial Genome of Kadsura coccinea Constructed from Oxford Nanopore Sequencing
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The non-reference sequence data and the gene annotation information of chicken linear pan-genome
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Multiple sequence alignments of Treponema pallidum complete genomes using three different references for mapping NGS reads
<p>Each file corresponds to the multiple sequence alignment of 75 complete Treponema pallidum genome sequences using the genomes of strains Nichols, SS14, and CDC-2 as references for mapping. This is supplemental data to the manuscript "Evolutionary processes in the emergence and recent spread of <em>Treponema pallidum</em>, the causative agent of syphilis" by Marta Pla-Díaz, Leonor Sánchez-Busó, Lorenzo Giacani, David Šmajs, Philipp P. Bosshard, Homayoun C. Bagheri, Verena J. Schuenemann, Kay Nieselt, Natasha Arora and Fernando González-Candelas</p>
Deciphering Complex Antibiotic Resistance Patterns in Helicobacter pylori Through Whole Genome Sequencing and Machine Learning
<p>Helicobacter pylori affects billions of people worldwide. Despite the availability of different antibiotics, emerging resistance of H. pylori renders antibiotic treatment ineffective. Next generation sequencing provides a powerful technology to investigate the genotype-phenotype connection for H. pylori. However, the prediction of antibiotic resistance using whole genome sequencing data remains a formidable challenge. Here we conducted a comprehensive investigation into the antibiotic resistance profiles of H. pylori strains against five distinct antibiotics, alongside assessing clinical treatment outcomes for Amoxicillin and Clarithromycin combination therapy. Concurrently, we performed whole-genome sequencing on a collection of H. pylori isolates. We rigorously evaluated the potential for predicting antibiotic resistance through univariate statistical tests, multivariate unsupervised and supervised machine learning. Our study contributes valuable insights towards enhancing precision and effectiveness in antibiotic treatment strategies for H. pylori infections with the application of whole-genome sequencing for H. pylori.</p>
Whole genome bisulfite sequencing of sstr2 knockout mice
GEO Series GSE165022. Mus musculus. 6 samples. Type: Methylation profiling by high throughput sequencing.
Epigenetic regulation of gene expression is instructed by promoter sequence and refined by developmental progression [genomic]
GEO Series GSE41447. Mus musculus. 16 samples. Type: Methylation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array.
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.