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accession-icon GSE8059
resting and IL2 activated human natural killer cells
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The aim of the study was to investigate the activation of human NK cells by IL2 through analyzing the global gene expression at different time points (0, 2, 8 and 24 hours) after culture with the cytokine IL2 at 100 IU/ml. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected by immunomagnetic beads and re-examined by flow-cytometry to ensure greater than 90% purity .

Publication Title

Genome wide transcriptional analysis of resting and IL2 activated human natural killer cells: gene expression signatures indicative of novel molecular signaling pathways.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE22759
Expression data from cell lines originating from patients with multiple myeloma, plasmacytoma and diffuse large B-cell lymphoma
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

A predictive gene list for response to high dose melphalan therapy in patients diagnosed with multiple myeloma is generated by combining results from dose response experiments and microarray data using a B-cell line panel and the introduction of multivariate regression techniques.

Publication Title

Generation of a predictive melphalan resistance index by drug screen of B-cell cancer cell lines.

Sample Metadata Fields

Cell line

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accession-icon GSE40311
A model system for assessing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

A model system for assessing and comparing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells.

Sample Metadata Fields

Cell line

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accession-icon SRP015013
A model system for assessing the ability of tag sequencing to detect genes specific for malignant B-cells
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer

Description

The purpose of this study was to develop a quantification method that can be used to assess the ability of tag-seq to detect malignant B-cell transcripts. The data support that tumour cell concentration is an important variable with fundamental impact on gene expression pattern. Overall design: We analysed eight serial dilutions of the malignant B-cell line, OCI-Ly8, into the embryonic kidney cell line, HEK293, by tag-sequencing. No technical replicates were performed.

Publication Title

A model system for assessing and comparing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells.

Sample Metadata Fields

Cell line, Subject

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accession-icon GSE40309
A model system for assessing the ability of exon microarray to detect genes specific for malignant B-cells
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer

Description

The purpose of this study was to develop a quantification method that can be used to assess the ability of exon microarray to detect malignant B-cell transcripts.

Publication Title

A model system for assessing and comparing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells.

Sample Metadata Fields

Cell line

View Samples
accession-icon GSE19069
Molecular signatures in peripheral T-cell lymphoma (PTCL)
  • organism-icon Homo sapiens
  • sample-icon 147 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Molecular signatures to improve diagnosis in PTCL and prognostication in angioimmunoblastic T-cell lymphoma (AITL). Gene expression profiling of PTCL patient samples was performed to investigate whether molecular signatures can be used to identify distinct entities of PTCL.

Publication Title

Molecular signatures to improve diagnosis in peripheral T-cell lymphoma and prognostication in angioimmunoblastic T-cell lymphoma.

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE110548
Exon expression profiling of de novo diffuse large B-cell lymphoma samples
  • organism-icon Homo sapiens
  • sample-icon 37 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)

Description

Exon expression profiling was performed on 37 clinical DLBCL samples and subsequently analyzed using alternative splice analysis of vairance (asANOVA) implemented in Partek Genomics Suite in order to identify alternative spliced genes.

Publication Title

Expression of NOTCH3 exon 16 differentiates Diffuse Large B-cell Lymphoma into molecular subtypes and is associated with prognosis.

Sample Metadata Fields

Treatment

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accession-icon GSE68878
Gene expression profiles of normal B-cell subsets from sternal bone marrow
  • organism-icon Homo sapiens
  • sample-icon 38 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [CDF: huex10st_Hs_ENSG_18.0 (huex10st)

Description

Mononuclear cells were isolated from the sternal bone marrow and prepared for multiparametric flow cytometry using an optimized and validated protocol. B-cell subsets of PreBI, PreBII, Immature, Naive, Memory and Plasma cells were isolated and a al of 38 gene expression profiles were generated using the HuEx-1_0-st-v2-micro array chip from Affymetrix to characterize the gene expression in the individual subpopulations.

Publication Title

Long Noncoding RNA Expression during Human B-Cell Development.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon GSE69033
Long noncoding RNA expression during human B-cell development
  • organism-icon Homo sapiens
  • sample-icon 30 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [CDF: huex10st_Hs_ENSG_18.0 (huex10st)

Description

Long noncoding RNAs (lncRNAs) have emerged as important regulators of diverse cellular processes, but their roles in the developing immune system are poorly understood. In this study, we analysed lncRNA expression during human B-cell development by array-based expression profiling of eleven distinct flow-sorted B-cell subsets, comprising pre-B1, pre-B2, immature, naive, memory, and plasma cells from bone marrow biopsies (n=7), and naive, centroblast, centrocyte, memory, and plasmablast cells from tonsil tissue samples (n=6), respectively. A remapping strategy was used to assign the array probes to 37630 gene-level probe sets, reflecting the most recent updates in genomic and transcriptomic databases, which enabled expression profiling of 19579 long noncoding RNAs, comprising 3947 antisense RNAs, 5277 lincRNAs, 7625 pseudogenes, and 2730 additional lncRNAs. As a first step towards inferring the functions of the identified lncRNAs in developing B-cells, we analysed their co-expression with well-characterized protein-coding genes, a method known as guilt by association. By using weighted gene co-expression network analysis, we identified 272 lincRNAs, 471 antisense RNAs, 376 pseudogene RNAs, and 64 lncRNAs within seven sub-networks associated with distinct stages of B-cell development, such as early B-cell development, B-cell proliferation, affinity maturation of antibody, and terminal differentiation. These data provide an important resource for future studies on the functions of lncRNAs in development of the adaptive immune response, and the pathogenesis of B-cell malignancies that originate from distinct B-cell subpopulations.

Publication Title

Long Noncoding RNA Expression during Human B-Cell Development.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon GSE53798
Expression data from malignant human B-cell cell lines
  • organism-icon Homo sapiens
  • sample-icon 26 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We used global gene expression profiles from human B-cell cell lines to generate gene expression signatures for prediction of response to the drugs cyclophosphamide, doxorubicin or vincristine. The signatures were validated in two publicly available clinical cohorts.

Publication Title

Predicting response to multidrug regimens in cancer patients using cell line experiments and regularised regression models.

Sample Metadata Fields

Disease, Cell line

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refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

fund-icon Fund the CCDL

Developed by the Childhood Cancer Data Lab

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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