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GSE27485
Mus musculus
18 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Gene expression from Wild-type and NFAT5 knock-out Mouse Embryonic Fibroblasts
Publication Title
Transcriptional regulation of gene expression during osmotic stress responses by the mammalian target of rapamycin.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Caenorhabditis elegans
- 4 Downloadable Samples
Illumina Genome Analyzer IIx
Description
Deep sequencing of transcriptomes allows quantitative and qualitative analysis of many RNA species in a sample, with parallel comparison of expression levels, splicing variants, natural antisense transcripts, RNA editing and transcriptional start and stop sites the ideal goal. By computational modeling, we show how libraries of multiple insert sizes combined with strand-specific, paired-end (SS-PE) sequencing can increase the information gained on alternative splicing, especially in higher eukaryotes. Despite the benefits of gaining SS-PE data with paired ends of varying distance, the standard Illumina protocol allows only non-strand-specific, paired-end sequencing with a single insert size. Here, we modify the Illumina RNA ligation protocol to allow SS-PE sequencing by using a custom pre-adenylated 3’ adaptor. We generate parallel libraries with differing insert sizes to aid deconvolution of alternative splicing events and to characterize the extent and distribution of natural antisense transcription in C. elegans. Despite stringent requirements for detection of alternative splicing, our data increases the number of intron retention and exon skipping events annotated in the Wormbase genome annotations by 127 % and 121 %, respectively. We show that parallel libraries with a range of insert sizes increase transcriptomic information gained by sequencing and that by current established benchmarks our protocol gives competitive results with respect to library quality. Overall design: Sequencing of mRNA from C. elegans with libraries of four differing insert sizes
Publication Title
Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes.
Sample Metadata Fields
Specimen part, Disease, Cell line, Subject
View Samples- Homo sapiens
- 38 Downloadable Samples
- Illumina HumanRef-8 v3.0 expression beadchip
Description
Gene expression analyis of two neonatal fibroblasts (BJ and HFF1), one adult dermal fibroblasts (NFH2), two BJ-derived human iPSCs (iB4 and iB5), two HFF1-derived iPSCs (iPS 2 and iPS4), four NFH2-derived iPSCs (OiPS3, OiPS6, OiPS8, OiPS16), one amniotic fluid cells and three derived iPSCs (lines 4, 5, 6, 10, and 41), two human ES cells (H1 and H9), neonatal fibroblasts transduced with the four retroviral factors (OKSM) after 24h, 48h, and 72h, neonatal fibroblasts treated with EDHB for 24h, 48h, and 72h, neonatal fibroblasts transduced with four factors and treated with EDHB for 24h, 48h, and 72h, neonatal fibroblasts knocked down for HIF1A (HIF1-KD) and for a scrambled sequence (SCR-KD)
Publication Title
HIF1α modulates cell fate reprogramming through early glycolytic shift and upregulation of PDK1-3 and PKM2.
Sample Metadata Fields
Age, Specimen part, Cell line
View Samples- Zea mays
- 22 Downloadable Samples
- Illumina HiSeq 2000
Description
Endosperm is an absorptive structure that supports embryo development or seedling germination in angiosperms. The endosperm of cereals is a main source of food, feed, and industrial raw materials worldwide. However, the gene regulatory networks that control endosperm cell differentiation remain largely unclear. As a first step toward characterizing these networks, we profiled the mRNAs in five major cell types of the differentiating endosperm and in the embryo and four maternal compartments of the kernel. Comparisons of these mRNA populations revealed the diverged gene expression programs between filial and maternal compartments, and an unexpected close correlation between embryo and the aleurone layer of endosperm. Gene co-expression network analysis identified co-expression modules associated with single or multiple kernel compartments including modules for the endosperm cell types, some of which showed enrichment of previously identified temporally activated and/or imprinted genes. Detailed analyses of a co-expression module highly correlated with the basal endosperm transfer layer (BETL) identified a regulatory module activated by MRP-1, a regulator of BETL differentiation and function. These results provide a high-resolution atlas of gene activity in the compartments of the maize kernel and help to uncover the regulatory modules associated with the differentiation of the major endosperm cell types. Overall design: RNAs from ten compartments of the maize kernel including the central starchy endosperm (CSE), conducting zone (CZ), aleurone (AL), basal endosperm transfer layer (BETL), embryo-surrounding region (ESR), nucellus (NU), pericarp (PE), placenta-chalazal region (PC), the vascular region of the pedicel (PED), and the embryo (EMB) were isolated at 8 days after pollination (DAP) using laser-capture microdissection and sequenced using an Illumina HiSeq 2000 platform.
Publication Title
RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
In recent years, several approaches have been taken in the peptide-based immunotherapy of metastatic renal cell carcinoma (RCC), although little is known about HLA presentation on metastases compared to primary tumor and normal tissue of RCC. In this study we compared primary tumor, normal tissue and metastases with the aim of identifying similarities and differences between these tissues. We performed this comparison for two RCC patients on the level of the HLA ligandome using mass spectrometry and for three patients on the level of the transcriptome using oligonucleotide microarrays. The quantitative results show that primary tumor is more similar to metastasis than to normal tissue, both on the level of HLA ligand presentation and mRNA. We were able to characterize a total of 142 peptides in the qualitative analysis of HLA-presented peptides. Six of them were significantly overpresented on metastasis, among them a peptide derived from CD151; fourteen were overpresented on both primary tumor and metastasis compared to normal tissue, among them an HLA ligand derived from tumor protein p53. Thus, we could demonstrate that peptide-based immunotherapy might affect tumor as well as metastasis of RCC, but not healthy kidney tissue. Furthermore we were able to identify several peptides derived from tumor-associated antigens that are suitable for vaccination of metastatic RCC.
Publication Title
HLA ligand profiles of primary renal cell carcinoma maintained in metastases.
Sample Metadata Fields
Sex
View Samples- Arabidopsis thaliana
- 87 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 28 Downloadable Samples
- Affymetrix Arabidopsis Genome Array (ag)
Description
This series contain all stages Arabidopsis plant development. Stages of development includes unfertilized ovule, 24-Hr post-fertilization seed, globular stage seed, cotyledon stage seed, mature green seed, post-mature green seed, post-germination seedling, rosette leaf, root, stem, and floral bud.
Publication Title
Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 17 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We collected globular stage seed compartments from 5 or 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of an Arabidopsis seed containing a globular stage embryo. For the purposes of this study we broke down the seed into 8 capturable compartments: embyro proper, suspensor, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat, general seed coat, and whole seeds.
Publication Title
Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We collected heart stage seed compartments from 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing heart stage embryos. For the purposes of this study we captured 6 compartments: embryo proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat and seed coat, as well sets of serial sections encompassing the entire heart stage seed.
Publication Title
Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 14 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We collected linear-cotyledon stage seed compartments from 5 to 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing linear-coyledon-stage embryos. For the purposes of this study we captured 7 compartments: embyro proper, cellularized endosperm, chalazal endosperm, chalazal seed coat, general seed coat, whole seeds and micropylar endosperm.
Publication Title
Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.
Sample Metadata Fields
No sample metadata fields
View Samples