Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA170910 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Molecular Classification of AIDS-Related Lymphomas
| PRJNA119689 | ENA
Project description:Gene expression profiling (GEP) of ARL patient samples was done to determine whether gene expression signatures derived from HIV- lymphomas retained their ability to molecularly classify HIV+ lymphomas. The GEP-based predictors robustly classified ARL tumors, distinguishing molecular Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL), as well as activated B-cell-like (ABC) and germinal center B-cell-like (GCB) molecular subtypes of DLBCL. Gene expression profiles were used to identify coordinately regulated gene sets and pathways that differ between HIV+ and HIV- lymphomas of corresponding molecular subtype. Frozen tumor biopsies were obtained from 20 HIV-positive patients with an AIDS-defining lymphoma. Cases were ascertained at the University of Nebraska Medical Center and through the NCI AIDS and Cancer Specimen Resource tumor bank. Sufficient RNA for hybridization to Affymetrix U133 plus 2 arrays was obtained on 17 ARL cases. Details of all 20 HIV-positive patients can be found in the supplementary file below. Third party array data from HIV- lymphomas of corresponding molecular subtype were used for the comparison and molecular classification of the HIV+ cases in this study. The third party HIV- lymphoma samples include the following. [1] HIV- lymphoma, BL cases: 84 samples profiled on the Affymetrix HG U133 Plus 2 array. The data are publicly available on the website companion to Dave et al. NEJM 2006; Volume 354:13-24 (http://llmpp.nih.gov/BL/) and were used 'as is' (ie, not reanalyzed). [2] HIV- lymphoma, DLBCL cases: 200 of the 414 cases in Series GSE10846 (listed in the supplementary file below). These included all R-CHOP treated cases of either ABC or GCB subtype. These data were also used as is. These data were published in Lenz et al. NEJM 2008; Volume 359: 2313-2323.
2012-07-17 | E-GEOD-17372 | biostudies-arrayexpress
Project description:The tumor virus landscape of AIDS-related lymphomas
| PRJNA280845 | ENA
Project description:Third Party Annotation (TPA) genome maintained by SGD
| PRJNA43747 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below. [Third party comment] Samples with identical non-normalized expression values are identified at: https://colab.research.google.com/drive/1swvQGf-ZLAWnZw-7bOCmsypzzAnCDGUR#scrollTo=mIqv_oTHc6ns
2013-10-31 | GSE42834 | GEO
Project description:Gene expression profiling (GEP) of ARL patient samples was done to determine whether gene expression signatures derived from HIV- lymphomas retained their ability to molecularly classify HIV+ lymphomas. The GEP-based predictors robustly classified ARL tumors, distinguishing molecular Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL), as well as activated B-cell-like (ABC) and germinal center B-cell-like (GCB) molecular subtypes of DLBCL. Gene expression profiles were used to identify coordinately regulated gene sets and pathways that differ between HIV+ and HIV- lymphomas of corresponding molecular subtype. Frozen tumor biopsies were obtained from 20 HIV-positive patients with an AIDS-defining lymphoma. Cases were ascertained at the University of Nebraska Medical Center and through the NCI AIDS and Cancer Specimen Resource tumor bank. Sufficient RNA for hybridization to Affymetrix U133 plus 2 arrays was obtained on 17 ARL cases. Details of all 20 HIV-positive patients can be found in the supplementary file linked below.
2010-03-07 | E-GEOD-17189 | biostudies-arrayexpress
Project description:To identify new candidate genes for neurocristopathies, a Long-SAGE library has been made from human neural crest cells (hNCC) derived from a normal embryo at Carnegie stage 13. Data analysis indicates the expression of a number of genes in multiple GO functional classes that were anticipated based on animal studies and/or human disease. An average linkage hierarchical clustering was performed using SAGE data from hNCC and 14 other normal tissues and cell lines. This and other analyses indicate a high degree of molecular identity between hNCC and the two human embryonic stem cells (hES) lines included, compared to the other tissue or cell types included, including more tissue-restricted stem cells, such as mesenchymal stem cells, or hNCC derivatives such as Schwann cells. Keywords: Cell type comparison Total RNA was extracted from a confluent 10 cm dish of hNCC (line N5) from a female human embryo at 28-32 dpf (Carnegie stage 13). Half the RNA was used to construct a SAGE bank with long tags using NlaIII and MmeI. Data was then compared to currently publicly available SAGE data from fourteen banks made from normal human tissues for hierarchical clustering. Third-party GEO accession numbers for human SAGE data: GSM41360, hES3; GSM41362, hES4; GSM48250, sciatic nerve; GSM48251, Schwann cells (in vitro); GSM31931, brain substantia nigra; GSM824, muscle; GSM785, liver; GSM708, kidney; GSM676, brain white matter; GSM761, brain cerebellum; GSM762, lung. Other third-party data: Cancer Genome Anatomy Project http://cgap.nci.nih.gov/SAGE/SAGELibraryFinder: SAGE_Prostate_normal_B_2 (prostate) Umbilical cord- and bone marrow-derived mesenchymal stem cell data had been downloaded from currently broken links http://bit.fmrp.usp.br/uc-msc_tags/ and http://bit.fmrp.usp.br/msc_tags/ as referenced in Panepucci et al. (2004) Stem Cells 22:1263-1278; DOI: 10.1634/stemcells.2004-0024 (UC-MSC) and Silva et al. (2003) Stem Cells 21:661-669.
2008-08-07 | E-GEOD-8368 | biostudies-arrayexpress
Project description:The distinction between the Burkitt lymphoma and diffuse large B-cell lymphoma is imprecise using current diagnostic criteria. We applied transcriptional and genomic profiling to molecularly define Burkitt lymphoma. Gene expression profiling employing Affymetrix GeneChips (U133A) was performed in 220 mature aggressive B-cell lymphomas, including a core group of eight Burkitt lymphomas, which fulfilled all diagnostic criteria of the WHO classification. A molecular signature of Burkitt lymphoma was generated. Chromosomal abnormalities were detected by interphase fluorescence in-situ hybridization and array comparative genomic hybridization. The molecular Burkitt lymphoma signature identified 44 cases. Fifteen of these cases lacked a morphology typical for Burkitt/Burkitt-like lymphoma. The vast majority (88%) of the 176 lymphomas without the molecular Burkitt lymphoma signature represented diffuse large B-cell lymphomas. In 20% of these cases a MYC break was detectable which was associated with complex chromosomal changes. Our molecular definition of Burkitt lymphoma sharpens and extends the spectrum of Burkitt lymphoma. In mature aggressive B-cell lymphomas without a Burkitt lymphoma signature, a chromosomal break in the MYC locus proved to be associated with adverse clinical outcome. Experiment Overall Design: 220 diffuse large B-cell lymphoma and Burkitt lymphoma samples hybridized to 221 HGU133A Affymetrix GeneChips
2008-06-13 | E-GEOD-4475 | biostudies-arrayexpress