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SRP063496
Homo sapiens
73 Downloadable Samples
IlluminaHiSeq2000
Description
RNA sequencing was performed on RNA isolated from baseline biopsies from UC patients enrolled in the Phase II EUCALYPTUS study of etrolizumab. Gene expression differences were identified in a subset of anti-TNF naïve patients that achieved clinical remission at 10 weeks in response to etrolizumab. Overall design: Baseline colonic biopsies from UC patients treated with etrolizumab were sequenced by the Illumina HiSeq 2000 Sequencing System.
Publication Title
Association Between Response to Etrolizumab and Expression of Integrin αE and Granzyme A in Colon Biopsies of Patients With Ulcerative Colitis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 153 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Samples were taken from colorectal cancers in surgically resected specimens in 155 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133Plus 2.0 arrays. Our MSI/MSS classifier was applied to these samples.
Publication Title
DNA copy-number alterations underlie gene expression differences between microsatellite stable and unstable colorectal cancers.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 72 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Samples were taken from colorectal cancers in surgically resected specimens from 74 patients. The expression profiles were determined using Affymetrix Human Genome U133Plus 2.0 arrays. Our MSI/MSS classifer was applied to these samples.
Publication Title
DNA copy-number alterations underlie gene expression differences between microsatellite stable and unstable colorectal cancers.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 117 Downloadable Samples
- Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)
Description
The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), characterized by aneuploidy and poor outcome, is unknown. Here, using complementary genome-wide profiling approaches, we show that hypodiploid ALL comprises two major subtypes that differ in the severity of aneuploidy, transcriptional profile and submicroscopic genetic alterations. Near haploid cases with 24-31 chromosomes frequently harbor alterations targeting receptor tyrosine kinase- and Ras signaling (71%) and IKZF3 (AIOLOS; 13%). In contrast, low hypodiploid ALL cases with 32-39 chromosomes are characterized by TP53 alterations (88%), almost half of which are present in non-tumor cells, and have alterations of IKZF2 (HELIOS; 53%) and RB1 (41%). Both near haploid and low hypodiploid tumors exhibit activation of Ras and PI3K signaling pathways, and are sensitive to PI3K inhibition, indicating that these drugs should be explored as a new therapeutic strategy for this frequently lethal form of leukemia.
Publication Title
The genomic landscape of hypodiploid acute lymphoblastic leukemia.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 41 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Gene expression profiling was performed of Pax5 wild type bone marrow subsets from common lymphoid progenitors through to Hardy stage F cells. These cells were obtained by flow sorting of bone marrow.
Publication Title
The genomic landscape of hypodiploid acute lymphoblastic leukemia.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
We''ve recently shown that we can accelerate disease in a model of SLE (the NZB/W F1 model) using an anti-Ox40 mAb treatment regimen. The disease acceleration is rapid (within 2 weeks) but its unclear, mechanistically, how OX40 functions to promote disease. To that end we want to perform RNASeq on the sorted OX40-expressing CD4 T cells during treatment to understand how they function in response to OX40 signaling in vivo Overall design: RNASeq was performed on FACS sorted CD4 T cells from the spleen and kidney of NZB/W F1 lupus mice following anti-Ox40 agonist mAb treatment and disease acceleration
Publication Title
The Ox40/Ox40 Ligand Pathway Promotes Pathogenic Th Cell Responses, Plasmablast Accumulation, and Lupus Nephritis in NZB/W F1 Mice.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
We''ve recently shown that we can accelerate disease in a model of SLE (the NZB/W F1 model) using an anti-Ox40 mAb treatment regimen. The disease acceleration is rapid (within 2 weeks) but its unclear, mechanistically, how Ox40 promotes disease. To that end we performed RNASeq on in vitro cultured CD4 T cells during Ox40 and TCR stimulation (in a reductionist setting) to understand how Ox40 signaling impacts cellular phenotype and function, including with and without TCR stimulation Overall design: RNASeq was performed on in vitro cultured CD4 T cells from the spleen of NZB/W F1 lupus prone mice, following anti-Ox40 mAb and anti-CD3/CD28 bead stimulation
Publication Title
The Ox40/Ox40 Ligand Pathway Promotes Pathogenic Th Cell Responses, Plasmablast Accumulation, and Lupus Nephritis in NZB/W F1 Mice.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 19 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA was purified from lung tissue and isolated Alveolar type II cells. The "SAMPLE_ID" sample description is a sample identifier internal to Genentech. The ID of this project in Genentech''s ExpressionPlot database is PRJ0007671 Overall design: RNA from lung and Alveolar type II cells of the following mutant mice: (1) SpcCreERT2;RosatdTomato n=5 ; (2) SpcCreERT2;RosatdTomato;Etv5ko/loxp n= 5
Publication Title
Transcription factor Etv5 is essential for the maintenance of alveolar type II cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA was purified from lung tissue and isolated Alveolar type II cells. The "SAMPLE_ID" sample description is a sample identifier internal to Genentech. The ID of this project in Genentech''s ExpressionPlot database is PRJ0005064 Overall design: RNA from lung and Alveolar type II cells of the following mutant mice: (1) KRaswt/d12;RosaCreERT2 n=4 (2) KRaswt/d12; Etv5loxp/loxp;RosaCreERT2 n=4 (3) KRaswt/d12; Etv4KO/KO; Etv5loxp/loxp;RosaCreERT2 n=4
Publication Title
Transcription factor Etv5 is essential for the maintenance of alveolar type II cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 384 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Analysis of the transcriptome of mouse models of prostate cancer to assemble a mouse prostate cancer interactome.
Publication Title
Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy.
Sample Metadata Fields
Treatment
View Samples