Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

5ef4b8a4-0162-4273-a8a2-9bd2f8055e85 - samples

ABSTRACT: This data set includes bam files of WGS of 36 paired lymphomas in immune-privileged sites and normal controls.

PROVIDER: EGAD00001007753 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Whole-genome sequencing of lymphomas in immune-privileged sites

Project description:To characterize the genetic alterations in lymphomas in immune-privileged sites (IP-DLBCLs), we performed whole-genome sequencing (WGS) of 22 primary central nervous system lymphomas (PCNSLs), 8 primary testicular lymphomas (PTLs) and 6 secondary CNS lymphomas.

| EGAS00001005367 | EGA

ATM deficiency in the absence of T cells promotes the development of NF-kB-dependent B cell lymphomas [Gene Expression]

Project description:Our model removes T cells as targets for lymphomagenesis as well as eliminating T cell-dependent immune surveillance. These mice exclusively develop early onset IgM+ B cell lymphomas that histologically and genetically resemble the activated B cell-like (ABC) subset of human diffuse large B cell lymphomas (DLBCL). This dataset includes the comparison of B-cell lymphomas (tumors) from ATMKO.CD3eKO RNA expression levels with normal spleens from both ATMKO.CD3eKO and ATMWT.CD3eKO non-tumor bearing mice.

2015-07-18 | GSE59576 | GEO

Whole Genome Sequencing of Tongue cancer samples and cell line

Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).

2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress

ATM deficiency in the absence of T cells promotes the development of NF-kB-dependent B cell lymphomas [aCGH]

Project description:Our model removes T cells as targets for lymphomagenesis as well as eliminating T cell-dependent immune surveillance. These mice exclusively develop early onset IgM+ B cell lymphomas that histologically and genetically resemble the activated B cell-like (ABC) subset of human diffuse large B cell lymphomas (DLBCL). This dataset includes the array CGH of B-cell lymphomas (tumors) from ATMKO.CD3eKO mice.

2015-07-18 | GSE59577 | GEO

Optimization and Clinical Validation of a Pathogen Detection Microarray

Project description:This series includes microarrays from 36 patient samples and 2 cell-culture controls, used to optimize and validate the pathogen detection microarray (Wong, et. al. 2007) Keywords: viral pathogen detection

2007-05-29 | GSE7779 | GEO

Whole membrane proteome for depletion of Bam subunits in F. johnsoniae

Project description:In Gram-negative bacteria the outer membrane (OM) is the first line of defence against antimicrobial agents and immunological attacks. A key part of OM biogenesis is the insertion of OM proteins (OMPs) by the β-barrel–assembly machinery (BAM). Here we report the cryo-electron microscopy (cryoEM) structure of a BAM complex isolated from Flavobacterium johnsoniae, a member of the Bacteroidota, a phylum that includes key human commensals and major anaerobic pathogens. This BAM complex is extensively modified from the canonical Escherichia coli system and includes an extracellular canopy that overhangs the substrate folding site and a subunit that inserts into the BAM pore. We find that the novel subunits involved in forming the extracellular canopy, BamG and BamH, are required for BAM function and conserved across the Bacteroidota, suggesting that they form an essential extension to the canonical BAM core in this phylum. For BamH, isolation of a suppressor mutation allows the separation of its essential and non-essential functions. The need for a highly remodelled and enhanced BAM complex reflects the unusually complex membrane proteins found in the OM of the Bacteroidota.

2025-08-04 | PXD065907 | Pride

Expression data from myositis muscles

Project description:Immune cell infiltration in myositis were by examining microarray expression profiles in muscle biopsies from 31 myositis patients and 5 normal controls. Muscle samples from 36 subjects (5 normal controls, 5 NM, 8 DM, 8 PM and 10 IBM) were studied

2012-11-01 | E-GEOD-39454 | biostudies-arrayexpress

c73c1e32-9a9c-44e6-973c-32c5fbd807c9 - samples

Project description:This data set includes 72 mate pair sequenced osteosarcomas (36 as part of a discovery cohort and 36 as part of a validation cohort). It also includes RNA-sequencing data on 67 osteosarcomas (mostly overlapping with the above mate pair sequenced cases) and 13 osteoblastomas used as controls for gene expression levels.

| EGAD00001005307 | EGA

Expression patterns of cDNAs in gamma-irradiation induced T-cell lymphomas

Project description:This set of data contains the expression levels of cDNAs in T-cell lymphoblastci lymphomas induced by gamma-irradiation. These tumor samples were compared to normal thymuses Keywords: Tumor profiles, comparison of tumoral versus wilf-type tissues, lymphomas and leukemias

2008-06-26 | GSE10859 | GEO

Gamma-irradiation induced T-cell lymphomas (miRNA study)

Project description:This set of data contains the expression levels of cDNAs in T-cell lymphoblastic lymphomas induced by gamma-irradiation. These tumor samples were compared to normal thymuses Keywords: Tumor profiles, comparison of tumoral versus wild-type tissues, lymphomas and leukemias

2008-06-26 | GSE10891 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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