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| Status |
Public on Mar 29, 2015 |
| Title |
Robust enumeration of cell subsets from tissue expression profiles (HGU133Plus2) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen, and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unknown mixture content, and closely related cell types. CIBERSORT should enable large-scale analysis of RNA specimens for cellular biomarkers and therapeutic targets (http://cibersort.stanford.edu).
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| Overall design |
To evaluate the performance of CIBERSORT, RNA was extracted from the following primary human samples: (i) 14 disaggregated lymph node biopsies from patients with follicular lymphoma (FL), (ii) pre- and/or post-immunotherapy PBMC samples from 3 patients with extranodal marginal zone lymphoma (EMZL) or diffuse large B cell lymphoma (DLBCL), and (iii) B or T cells purified from the tonsils of 5 healthy normal controls.
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| Contributor(s) |
Newman AM, Liu C, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA |
| Citation(s) |
25822800 |
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| Submission date |
Jan 21, 2015 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Aaron M Newman |
| E-mail(s) |
amnewman@stanford.edu
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| Organization name |
Stanford University
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| Department |
Institute for Stem Cell Biology and Regenerative Medicine & Division of Oncology, Stanford School of Medicine
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| Lab |
Alizadeh Lab (http://alizadehlab.stanford.edu)
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| Street address |
265 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (28)
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| GSM1587830 |
PBMCs, post-RCHOP, 3 |
| GSM1587831 |
FL lymph node biopsy, untreated, 1063 |
| GSM1587832 |
FL lymph node biopsy, untreated, 1080 |
| GSM1587833 |
FL lymph node biopsy, untreated, 575 |
| GSM1587834 |
FL lymph node biopsy, untreated, 581 |
| GSM1587835 |
FL lymph node biopsy, untreated, 598 |
| GSM1587836 |
FL lymph node biopsy, untreated, 639 |
| GSM1587837 |
FL lymph node biopsy, untreated, 664 |
| GSM1587838 |
FL lymph node biopsy, untreated, 666 |
| GSM1587839 |
FL lymph node biopsy, untreated, 695 |
| GSM1587840 |
FL lymph node biopsy, untreated, 706 |
| GSM1587841 |
FL lymph node biopsy, untreated, 726 |
| GSM1587842 |
FL lymph node biopsy, untreated, 731 |
| GSM1587843 |
FL lymph node biopsy, untreated, 944 |
| GSM1587844 |
FL lymph node biopsy, untreated, 959 |
| GSM1587845 |
Normal tonsil B cells, 1 |
| GSM1587846 |
Normal tonsil B cells, 3 |
| GSM1587847 |
Normal tonsil B cells, 4 |
| GSM1587848 |
Normal tonsil B cells, 5 |
| GSM1587849 |
Normal tonsil B cells, 6 |
| GSM1587850 |
Normal tonsil T cells, 1 |
| GSM1587851 |
Normal tonsil T cells, 3 |
| GSM1587852 |
Normal tonsil T cells, 4 |
| GSM1587853 |
Normal tonsil T cells, 5 |
| GSM1587854 |
Normal tonsil T cells, 6 |
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| This SubSeries is part of SuperSeries: |
| GSE65136 |
Robust enumeration of cell subsets from tissue expression profiles |
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| Relations |
| BioProject |
PRJNA273241 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE65135_RAW.tar |
127.2 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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