Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell genome sequencing of murine lymphoma and epidermal cells

ABSTRACT: Single cell genome sequencing of murine lymphoma and epidermal cells to identify copy number variations in individual cells

PROVIDER: PRJEB18546 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Hodgkin lymphoma

Project description:This SuperSeries is composed of the following subset Series: GSE25986: Gene expression profiling of cell lines derived from classical Hodgkin lymphoma GSE25987: Gene expression profiling of Hodgkin lymphoma cell line KMH2: Comparison of CIITA-BX648577 knockdown cultures with non-silencing controls GSE25989: Copy number analysis of Hodgkin lymphoma cell lines KM-H2 and L-428 Refer to individual Series *** This submission represents the microarray gene expression and microarray copy number components of the study

2010-12-11 | E-GEOD-25990 | biostudies-arrayexpress

Copy Number Variations identified in 225 Diffuse Large B-Cell Lymphoma tumors

Project description:Copy Number Variations identified in 225 Diffuse Large B-Cell Lymphoma tumors

| PRJNA564130 | ENA

Single cell genome sequencing of murine and human tumors

Project description:Chromosome instability (CIN) leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes affecting two out of three cancers. Continuous CIN in murine T-cells was previously shown to dramatically accelerate lymphomagenesis in a p53-deficient background. Despite the predicted ongoing CIN in our mouse model, we observed whole chromosome copy number changes that affected all lymphoma cells, suggesting that CIN is somehow suppressed in the aneuploid lymphomas or that selection for frequently lost/gained chromosomes outcompetes the CIN-imposed missegregation. To distinguish between these explanations and to examine karyotype dynamics in CIN lymphoma, we used a newly developed single-cell whole genome-sequencing (scWGS) platform that provides a complete and unbiased overview of copy number variations (CNV) in individual cells. In this study we applied single cell whole genome sequencing (scWGS) to map and quantify karyotype heterogeneity in primary mouse lymphoma and human leukaemia samples. We used cohorts of Mps1f/f; Lck-Cre+, Mps1f/f; p53f/f; Lck-Cre+ and Mps1f/f; p53f/+; Lck-Cre+ mice, and Lck-Cre- mice as controls. Mice were sacrificed when exhibiting signs of lymphoma (10-14 weeks of age, typically dyspnoea due to an enlarged thymus), thymuses were harvested, and primary T-ALL single cell suspensions were frozen for subsequent single cell sequencing analysis.

2016-04-16 | E-MTAB-4183 | biostudies-arrayexpress

Affymetrix SNP array data for follicular lymphoma (FL) and transformed follicular lymphoma (tFL) samples

2013-10-01 | GSE42525 | GEO

Expression data and Copy Number Variations from Diffuse Large B Cell Lymphoma (DLBCL) patients

Project description:Expression data and Copy Number Variations from Diffuse Large B Cell Lymphoma (DLBCL) patients

| PRJNA564132 | ENA

Affymetrix SNP array data for follicular lymphoma (FL) and transformed follicular lymphoma (tFL) samples

Project description:Follicular lymphoma is the most common indolent non-Hodgkin's lymphoma involving germinal centre B cells, with a subset of patients undergoing transformation to a diffuse large B-cell lymphoma (DLBCL) morphology for which the clinical outcomes are poor. To elucidate the differences in copy number profiles between FL and tFL groups, we performed Affymetrix SNP 6.0 Array analysis on 31 paired FL-tFL cases. We wanted to identify and compare recurrent somatic copy number alterations (CNAs) between the two groups (FL vs. tFL). In addition, the concordance and discordance in the copy neutral loss of heterozygosity (cnLOH) between the two groups were also investigated to identify recurrent target gene regions. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from follicular lymphoma (FL), transformed follicular lymphoma (tFL) and matching germline (GL) sample (if available). Copy number analysis of Affymetrix SNP 6.0 Array were performed on 91 DNA samples, consisting of 31 patients. Among the 31 patients, 19 had matching germline samples, while 12 had no germline samples. The Log R Ratio (LRR) values and the B Allele Frequency (BAF) values were subsequently calculated to search for copy number aberrations and copy neutral (CN)-LOH in the FL and tFL samples. Paired and unpaired analyses were performed accordingly.

2013-10-01 | E-GEOD-42525 | biostudies-arrayexpress

Single cell genome sequencing of murine and human leukemia cells to identify copy number variations in individual cells

Project description:Single cell genome sequencing of murine and human leukemia cells to identify copy number variations in individual cells

| PRJEB13742 | ENA

Transcriptional profiles of murine E13 epidermal cells and P4 epidermal basal cells

Project description:Transcriptional profiles of murine E13 epidermal cells and P4 epidermal basal cells

| PRJNA494644 | ENA

Transcriptional profiles of murine E13 epidermal cells and P4 epidermal basal cells

Project description:Transcriptional profiling of mouse epidermal cells at embryonic day 13 (E13) compared with epidermal basal cells at postnatal day 4 (P4), both isolated from Krt14-H2BGFP mouse skin. Goal was to identify the genes differentially expresssed in E13 epidermal cells vs P4 epidermal basal cells.

2018-10-05 | GSE120824 | GEO

Adult High Grade B-cell Lymphoma with Burkitt Lymphoma Signature: Genomic features and Potential Therapeutic Targets

Project description:Gene expression profiling of RNA and SNP array profiling of DNA was performed on Burkitt lymphoma samples to identify genes and pathways affected by DNA copy number alterations and expression changes.

2021-03-09 | GSE168422 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data