Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative intraindividual transcriptome analysis of B-precursor ALL of childhood

ABSTRACT: The objective of this study was the assessment of transcriptional dysregulation in particular with regard to B-cell differentiation factors. Most studies focus on cross-section analyses of various leukemia subtypes to identify differentially regulated genes lacking suitable reference models. Here we applied comparative intraindividual transcriptome analysis of B-precursor ALL of childhood, which introduces a side-by-side analysis of leukemic cells and matched normal lymphoblasts from the same individual in complete continuous remission after the end of re-induction therapy. This approach reduces noise by eliminating interindividual variability. Comparative matched pair analysis of (single sorted) initial leukemia and single sorted lymphoblasts isolated from the same individual, n=4 pairs, reference samples are the single sorted normal lymphoblasts. Please note that there are sorted samples form only three of the patients. Due to experimental circumstances, a "sorted" sample from the last patient was not included.

ORGANISM(S): Homo sapiens

SUBMITTER: Thomas Streichert

PROVIDER: E-GEOD-42221 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparative intraindividual transcriptome analysis of B-precursor ALL of childhood

Project description:The objective of this study was the assessment of transcriptional dysregulation in particular with regard to B-cell differentiation factors. Most studies focus on cross-section analyses of various leukemia subtypes to identify differentially regulated genes lacking suitable reference models. Here we applied comparative intraindividual transcriptome analysis of B-precursor ALL of childhood, which introduces a side-by-side analysis of leukemic cells and matched normal lymphoblasts from the same individual in complete continuous remission after the end of re-induction therapy. This approach reduces noise by eliminating interindividual variability.

2013-09-17 | GSE42221 | GEO

The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.

Project description:Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However, purifying them from within the bulk tumor has been challenging, so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC-transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells (more precisely referred to as leukemia propagating cells within our transplantation model). In addition, the side population within the leukemia evolves with serial transplantation, increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non-side population cells when transplanted into syngeneic recipients. RNA-sequencing analysis of sorted side population cells compared to non-side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt-signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt-signaling were significantly upregulated in the side population. Overall, these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt-pathway as a likely genetic driver of leukemia stem cell fate.

2021-12-10 | GSE123665 | GEO

Expression data from CUTLL1 cells infected with shHES1

Project description:To formally address the biological activity of HES1 in vitro, we measured the transcriptional effect of HES1 inactivation infectiing CUTLL1 leukemia cell lines with shHES1 HES1 knockdown triggered apoptosis in human T-ALL lymphoblasts. We show that HES1 inactivation induces programmed cell death in leukemia lymphoblasts

2015-05-07 | GSE65872 | GEO

Expression data from CUTLL1 cells infected with shHES1

2015-05-07 | E-GEOD-65872 | biostudies-arrayexpress

Oral Cavity Cancer Compared to Adjacent "Normal" Tissue [Validation Set]

Project description:Oral Cavity Cancer Comparative analysis of gene expression using Affymetrix U133 plus 2.0 microarrays to compare differences between oral cancer samples (most HPV-) and adjacent "normal" mucosa. We have 24 matched pairs of tumor and normal from the same patient

2012-12-05 | E-GEOD-42743 | biostudies-arrayexpress

B-cell chronic lymphocytic leukemia side population cells

Project description:Analysis of Hoechst dye 33342-effluxing side population (SP) cells from B-CLL peripheral blood mononuclear cells. 9 biological replicates from B-CLL patients sorted into CD5+CD19+ SP and non-SP subsets. Two color comparative gene expression using Agilent microarrays.

2011-09-26 | E-GEOD-30171 | biostudies-arrayexpress

Homo sapiens

Project description:Comparative intraindividual transcriptome analysis of B-precursor ALL of childhood

| PRJNA179347 | ENA

Single-cell chromatin accessibility data using scATAC-seq

Project description:A single hematopoietic stem cell can give rise to all blood cells with remarkable fidelity. Here, we define the chromatin accessibility and transcriptional landscape controlling this process in thirteen primary cell types that traverse the hematopoietic hierarchy. Exploiting the finding that enhancer landscapes better reflect cell identity than mRNA levels, we enable "enhancer cytometry" for accurate enumeration of pure cell types from complex populations. We further reveal the lineage ontogeny of genetic elements linked to diverse human diseases. In acute myeloid leukemia, chromatin accessibility reveals distinctive regulatory evolution in pre-leukemic HSCs (pHSCs), leukemia stem cells, and leukemic blasts. These leukemic cells demonstrate unique lineage infidelity, confirmed by single cell regulomes. We further show that pHSCs have a competitive advantage that is conferred by reduced chromatin accessibility at HOXA9 targets and is associated with adverse patient outcomes. Thus, regulome dynamics can provide diverse insights into human hematopoietic development and disease. Single-cell ATAC-seq of LMPPs, Monocytes, LSCs and Luekemic blast cells.

2016-06-01 | E-GEOD-74310 | biostudies-arrayexpress

Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer

Project description:Intraindividual tumor heterogeneity may reduce the efficacy of molecularly guided systemic therapy for cancers that have metastasized. To determine whether the genomic alterations in a single metastasis provide a reasonable assessment of the major oncogenic drivers of other dispersed metastases in an individual, we analyzed multiple tumors from men with disseminated prostate cancer through whole-exome sequencing, array comparative genomic hybridization (CGH) and RNA transcript profiling [GSE74685], and we compared the genomic diversity within and between individuals. Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile 171 CRPC tumors from 63 patients. RNA was amplified prior to hybridization against a common reference pool of prostate tumor cell lines. Custom Agilent 415K whole human CGH microarrays were used to profile 149 CRPC tumors from 60 patients. Genomic DNA from tumors was hybridized against a pool of reference normal male DNA.

2016-02-16 | E-GEOD-77930 | biostudies-arrayexpress

Functional and Molecular Single-Cell Analyses Implicate PRDM14 in the Initiation of a Novel B-1 Cell Malignancy - Single Cell RNA sequencing experiments

Project description:Description: Molecular mechanisms underlying high-risk subtypes of leukemia remain elusive. PR domain-containing 14 (Prdm14) is a potent oncogene implicated in the initiation of many cancers, including leukemia. Here, we interrogate the heterogeneity of Prdm14-expressing cell types in a mouse model of T-cell acute lymphoblastic leukemia (T-ALL). We identified an abnormal B-1 cell-like population in pre-leukemic bone marrow. B-1 cells are a self-renewing population of unconventional B cells established during embryonic development. This dataset contains single-cell transcriptomic profiling of four samples. Cells from R26PR;Mx1-cre mice were sorted on GFP expression (“GFP+” and “GFP-” samples) or on a pro-B-1-like immunophenotype of CD11b- CD19+ CD127+ Sca-1+ (“Pre-leukemia” sample). As a control, immunophenotype-matched cells from R26PR mice were analyzed by scRNA-seq after sorting on CD11b- CD19+ CD127+ Sca-1+ (“Control” sample) (Supplemental Figure 2). Accordingly, we conducted scRNA-seq of four total samples: “GFP+”, “GFP-“, “Pre-leukemia”, and “Control”. The GFP+ and GFP- samples provide the cellular context to the bone marrow samples.

2024-06-29 | E-MTAB-13160 | biostudies-arrayexpress

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