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GSE41050
Homo sapiens
14 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
DNA methylation has been comprehensively profiled in normal and cancer cells, but the dynamics that form, maintain and reprogram differentially methylated regions remain enigmatic. We show that methylation patterns within populations of cells from individual somatic tissues are heterogeneous and polymorphic. Using in vitro evolution of immortalized fibroblasts for over 300 generations, we track the dynamics of polymorphic methylation at regions developing significant differential methylation on average. The data indicate that changes in population-averaged methylation occur through a stochastic process that generates a stream of local and uncorrelated methylation aberrations. Despite the stochastic nature of the process, nearly deterministic epigenetic remodeling emerges on average at loci that lose or gain resistance to methylation accumulation. Changes in the susceptibility to methylation accumulation are correlated with changes in histone modifications and CTCF occupancy. Characterizing epigenomic polymorphism within cell populations is therefore critical for understanding methylation dynamics in normal and cancer cells.
Publication Title
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 188 Downloadable Samples
Illumina HiSeq 2500
Description
Background: The main bottleneck for genomic studies of tumors is the limited availability of fresh frozen (FF) samples collected from patients, coupled with comprehensive long-term clinical follow-up. This shortage could be alleviated by using existing large archives of routinely obtained and stored Formalin-Fixed Paraffin-Embedded (FFPE) tissues. However, since these samples are partially degraded, their RNA sequencing is technically challenging. Results: In an effort to establish a reliable and practical procedure, we compared three protocols for RNA sequencing using pairs of FF and FFPE samples, both taken from the same breast tumor. In contrast to previous studies, we compared the expression profiles obtained from the two matched sample types, using the same protocol for both. Three protocols were tested on low initial amounts of RNA, as little as 100 ng, to represent the possibly limited availability of clinical samples. For two of the three protocols tested, poly(A) selection (mRNA-seq) and ribosomal-depletion, the total gene expression profiles of matched FF and FFPE pairs were highly correlated. For both protocols, differential gene expression between two FFPE samples was in agreement with their matched FF samples. Notably, although expression levels of FFPE samples by mRNA-seq were mainly represented by the 3'-end of the transcript, they yielded very similar results to those obtained by ribosomal-depletion protocol, which produces uniform coverage across the transcript. Further, focusing on clinically relevant genes, we showed that the high correlation between expression levels persists at higher resolutions. Conclusions: Using the poly(A) protocol for FFPE exhibited, unexpectedly, similar efficiency to the ribosomal-depletion protocol, with the latter requiring much higher (2-3 fold) sequencing depth to compensate for the relative low fraction of reads mapped to the transcriptome. The results indicate that standard poly(A)-based RNA sequencing of archived FFPE samples is a reliable and cost-effective alternative for measuring mRNA-seq on FF samples. Expression profiling of FFPE samples by mRNA-seq can facilitate much needed extensive retrospective clinical genomic studies. Overall design: We perform an unbiased evaluation of RNA-seq of archived tumor tissues by comparing the same library preparation methods for both FF and FFPE matched tumor samples and for small amounts of total RNA starting material. We have 3 matched FF/FFPE tumor samples with a moderate archival time of about 4-5 years (T1=T3), and additional 3 FFPE tumor samples archived for more than 10 years (T4-T6). all samples were tested with two protocols: illumina Truseq RNA after poly(A) selection (mRNA-seq); and Truseq after ribosomal depletion (RiboZero). Several initial amounts of starting material was tested for eacg protocol.
Publication Title
mRNA-seq whole transcriptome profiling of fresh frozen versus archived fixed tissues.
Sample Metadata Fields
Specimen part, Disease, Subject
View Samples- Mus musculus
- 412 Downloadable Samples
- NextSeq 500
Description
Primary RNASeq data for progenitor, resident, and stimulated (C.alb, LPS, injury, APAP+ starved overnight and pIC) mononuclear phagocytes from fourteen organs. Overall design: RNASeq data for over 400 samples comprising of 130 populations submitted by 16 labs (both non-ImmGen and ImmGen labs) from 8 locations around the world for ImmGen OpenSource Mononuclear Project. Samples were sorted in these facilities using ImmGen's stringent ULI protocol and shipped to one location for library preparation and sequencing. Contributor: Immunological Genome Project Consortium
Publication Title
ImmGen report: sexual dimorphism in the immune system transcriptome.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 190 Downloadable Samples
- NextSeq 500
Description
Primary RNA Seq data for 11 diverse immunocyte populations from male and female mice of varying ages stimulated with different dose of IFN and sequenced using ImmGen's standard ultra-low input RNA-seq pipeline Overall design: RNASeq data for 11 cell populations from male and female mice generated by ImmGen labs to study sexual differences in the immune system (companion ATACseq datasets are found in GSE100738). These mice comprised of varying ages, including 6-8weeks and 2- 20months old. In addition, mice were stimulated with 1K and 10K Type 1 interferon to understand sex specific responses. contributor: Immunological Genome Project Consortium
Publication Title
ImmGen report: sexual dimorphism in the immune system transcriptome.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Alveolar rhabdomyosarcoma (aRMS) is an aggressive sarcoma of skeletal muscle characterized by expression of the PAX3-FOXO1 fusion gene. Despite its discovery over almost 20 years ago, PAX3-FOXO1 remains an enigmatic tumor driver. Previously, we reported that PAX3-FOXO1 supports aRMS initiation by enabling bypass of cellular senescence. Here, we show that bypass occurs in part by PAX3-FOXO1-mediated upregulation of RASSF4, a Ras-association domain family (RASSF) member, which then suppresses the evolutionarily conserved mammalian Hippo/Mst1 pathway. RASSF4 loss-of-function activates Hippo/Mst1 and inhibits downstream YAP, causing aRMS cell cycle arrest and senescence. This is the first evidence for an oncogenic role for RASSF4, and a novel mechanism for Hippo signaling suppression in human cancer.
Publication Title
Alveolar rhabdomyosarcoma-associated PAX3-FOXO1 promotes tumorigenesis via Hippo pathway suppression.
Sample Metadata Fields
Cell line, Treatment
View Samples- Triticum aestivum
- 36 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
Transcripomic analysis of leaf gene expression in S and N-deficient winter wheat during grain development. Tissue was harvested at anthesis and 7, 14 and 21 days post anthesis from experimental field plots.
Publication Title
Co-ordinated expression of amino acid metabolism in response to N and S deficiency during wheat grain filling.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject, Time
View Samples- Homo sapiens
- 10 Downloadable Samples
- Illumina HiSeq 2500
Description
Mutations in GRIN2B are associated with intellectual disability in humans. We generated iPSC derived mature cortical neurons with mutations in GRIN2B and compared them to isogenic control cells. We found that both loss of function (LOF) and reduced dosage (RD) mutations in GRIN2B lead to reduced expression of NMDAR genes and increased expression of marker of immaturity, including KI67 and MET. Overall design: Examination of transcriptome in iPSC-derved mature neurons with and without the presence of mutations in GRIN2B
Publication Title
Disruption of GRIN2B Impairs Differentiation in Human Neurons.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 29 Downloadable Samples
- Illumina HiSeq 2500
Description
To probe the tissue source (cancer cell VS stromal cell) of gene expression in the mixed tumor samples, we took advantage of a set of Urothelial Cancer patient-derived xenograft (PDX) models given that the transcriptome in these models is a mixture of human RNA (derived from cancer cells) and mouse RNA (derived from stromal cells). Overall design: The cohort includes 5 different patient-derived PDX models, 3 replicates for each model, and thus a total of 15 samples
Publication Title
EMT- and stroma-related gene expression and resistance to PD-1 blockade in urothelial cancer.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- NextSeq 500
Description
RNA sequencing of PLZF+ and PLZF- ?d T cell subsets from adipose tissue for gene expression analysis Overall design: PLZF+ and PLZF- ?d T cells were sorted from adipose tissue of PLZF-GFP mice for subsequent RNA sequencing and gene-expression analysis. Two replicates for each subset pooled from 10 mice each were used for the study.
Publication Title
γδ T cells producing interleukin-17A regulate adipose regulatory T cell homeostasis and thermogenesis.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples