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GSE79660
Homo sapiens
12 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
These data show distinct interactions between these two drugs on CLL cells in vitro with an ex vivo treatment
Publication Title
Lenalidomide Induces Interleukin-21 Production by T Cells and Enhances IL21-Mediated Cytotoxicity in Chronic Lymphocytic Leukemia B Cells.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples GSE59545- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
p65-/-Ras cells show delayed tumor formation in SCID mice. However, after prolonged latency, tumor formation was observed from these mice. To understand the changes of NF-kB regulated genes before and after tumor formation, RNA from p65+/+Ras, p65+/+RasTumor, p65-/-Ras, p65-/-RasTumor cells were isolated and microarray were performed.
Publication Title
NF-κB functions in tumor initiation by suppressing the surveillance of both innate and adaptive immune cells.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 13 Downloadable Samples
Illumina HiSeq 2500
Description
Recurrent mutations in RNA splicing factors SF3B1, U2AF1, and SRSF2 have been reported in hematologic cancers including myelodysplastic syndromes (MDS) and chronic lymphocytic leukemia (CLL). However, SF3B1 is the only splicing associated gene to be found mutated in CLL and has been shown to induce aberrant splicing. To investigate if any other genomic aberration caused similar transcriptome changes, we clustered RNASeq samples based on an alternative 3' splice site (ss) pattern previously identified in SF3B1-mutant CLL patients. Out of 215 samples, we identified 37 (17%) with alternative 3' ss usage, the majority of which harbored known SF3B1 hotspot mutations. Interestingly, 3 patient samples carried previously unreported in-frame deletions in SF3B1 around K700, the most frequent mutation hotspot. To study the functional effects of these deletions, we used various minigenes demonstrating that recognition of canonical 3' ss and alternative branchsite are required for aberrant splicing, as observed for SF3B1 p.K700E. The common mechanism of action of these deletions and substitutions result in similar sensitivity of primary cells towards splicing inhibitor E7107. Altogether, these data demonstrate that novel SF3B1 in-frame deletion events identified in CLL result in aberrant splicing, a common biomarker in spliceosome-mutant cancers. Overall design: 13 CLL samples, 5 SF3B1 WT, 5 SF3B1 p.K700E, and 3 with in-frame deletions around the K700 position of SF3B1
Publication Title
Novel <i>SF3B1</i> in-frame deletions result in aberrant RNA splicing in CLL patients.
Sample Metadata Fields
Disease, Disease stage, Subject
View Samples- Mus musculus
- 36 Downloadable Samples
- NextSeq 500
Description
We developed a UPPL (Upk3a-CreERT2;p53f/f;Ptenf/f;Rosa26LSL-Luc) mouse model of bladder cancer and compared it with the existing BBN (N-butyl-N-(4-hydroxybutyl)nitrosamine) mouse model of blader cancer. We cultured UPPL and BBN primary tumor cells as cell lines along with MB49 cancer cell lines and KT immortalized normal urothelial cell lines and implanted them back into mice as cell-line derived tumors. Overall design: RNASeq analysis was performed on 9 UPPL primary tumors, 11 BBN primary tumors, 1 UPPL cell line, 1 BBN cell line, 1 MB49 cell line, 3 KT cell lines, 4 UPPL cell-line derived tumors, 2 BBN cell-line derived tumors, and 4 MB49 cell-line derived tumors
Publication Title
Molecular Subtype-Specific Immunocompetent Models of High-Grade Urothelial Carcinoma Reveal Differential Neoantigen Expression and Response to Immunotherapy.
Sample Metadata Fields
Disease, Treatment, Subject
View Samples- Mus musculus, Homo sapiens
- 16 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Pluripotent stem cells reveal erythroid-specific activities of the GATA1 N-terminus.
Sample Metadata Fields
Specimen part, Cell line, Time
View Samples- Homo sapiens
- 17 Downloadable Samples
- Illumina HiSeq 2000
Description
IGHV mutation status is a well-established prognostic factor in chronic lymphocytic leukemia, and also provides crucial insights into tumor cell biology and function. Currently, determination of IGHV transcript sequence, from which mutation status is calculated, requires a specialized laboratory procedure. RNA sequencing is a method that provides high resolution, high dynamic range transcriptome data that can be used for differential expression, isoform discovery, and variant determination. In this paper, we demonstrate that unselected next-generation RNA sequencing can accurately determine the IGH@ sequence, including the complete sequence of the complementarity-determining region 3 (CDR3), and mutation status of CLL cells, potentially replacing the current method which is a specialized, single-purpose Sanger-sequencing based test. Overall design: CLL cells were sequenced by mRNA-seq on the Illumina platform then subjected to the costom bioinformatic pipeline Ig-ID which yields IGH data
Publication Title
Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 13 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We generated human induced pluripotent stem cells (iPSCs) from trisomy 21 (T21) and euploid patient tissues with and without GATA1 mutations causing exclusive expression of truncated GATA1, termed GATA1short (GATA1s). Transcriptome analysis comparing expression levels of genes in GATA1s vs. wtGATA1-expressing progenitors demonstrated that GATA1s impairs erythropoiesis and enhances megakaryopoiesis and myelopoiesis in both T21 and euploid contexts in the iPSC-model system.
Publication Title
Pluripotent stem cells reveal erythroid-specific activities of the GATA1 N-terminus.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
We modeled human Trisomy 21 primitive hematopoiesis using induced pluripotent stem cells (iPSCs). Primitive multipotent progenitor populations generated from Trisomy 21 iPSCs showed normal proliferative capacity and megakaryocyte production, enhanced erythropoiesis and reduced myeloid development compared to euploid iPSCs.
Publication Title
Trisomy 21-associated defects in human primitive hematopoiesis revealed through induced pluripotent stem cells.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We used microarrays to analyze gene expression following treatment of leukemic B cells with the Hsp90 inhibitor 17-DMAG.
Publication Title
Hsp90 inhibition increases SOCS3 transcript and regulates migration and cell death in chronic lymphocytic leukemia.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Treatment
View Samples- Mus musculus
- 3 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We transduced mouse Gata1- megakaryocyte-erythroid progenitors with MIGRI-GFP vector expressing GATA1fl or GATA1s cDNAs. GFP-positive cells expressing one of the two isoforms of GATA1 were isolated by FACS 42 hours following transduction and used for microarray transcriptome analysis. At this time point, there was no apparent difference in the cell surface phenotypes between GATA1fl and GATA1s-expressing cells. Transcriptome data for G1ME/GATA1fl at 42h were deposited previously under GSE14980 (GSM374049, GSM374050, GSM374051), whereas G1ME/GATA1s at 42h are deposited here.
Publication Title
Pluripotent stem cells reveal erythroid-specific activities of the GATA1 N-terminus.
Sample Metadata Fields
Specimen part
View Samples