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GSE150581
Vitis vinifera
24 Downloadable Samples
Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Grapevine rootstock 1616C shoots were sterilized and cultured on Murashige & Skoog (MS) medium containing 2% sucrose (w/v). Plantlets were grown in a growth chamber with a 16-h light/8-h dark cycle for 10 weeks at 25 °C.
Publication Title
Salt stress induces endoplasmic reticulum stress-responsive genes in a grapevine rootstock.
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 59 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We aimed to compare the gene expression profiles of patients with degenerative MR in SR and AFib. We used Affymetrix human gene expression microarrays for each atrium sample. We chose most homogenous groups to compare, cause of the noise overshadows in high-throughput analysis when investigating complex diseases.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Toll-like receptors (TLR), pattern-recognition receptors responsible for the recognition of various microorganisms and tissue-derived danger signals, are indispensable components of the innate immune system. It is important to note that the expression of TLRs during fetal period is developmentally regulated in such a way that the expression of TLRs increases in a steady-state manner with increasing fetal weight. Although it is well established that assisted reproduction is associated with reduced fetal growth in various species, it remains to be determined whether or not ART alters the expression of TLRs as well as genes involved in TLR-signaling pathway within this critical period of life. Given that the portal of pathogen entry into a neonate is primarily through the respiratory tract, we aimed in the present study to test if the expression of genes involved in TLR-signaling pathway is altered in the lung tissue of fetuses generated through in vitro culture and embryo transfer.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The use of nucleic acids from formalin-fixed paraffin-embedded (FFPE) tissues for high-throughput molecular techniques, such as microarray gene expression profiling has become widespread in molecular research area. However, working with FFPE tissues is challenging because of degradation, cross-linking with proteins, and RNA chemical modifications. Also, there is no generally accepted procedure for RNA extraction to microarray analysis. Thus, there is a need for a standardized workflow for FFPE samples to study microarray transcriptome profiling. Therefore, the main purpose of this study was to conduct a standardized process from deparaffinization to RNA extraction and microarray gene expression analysis. Firstly, deparaffinization procedure was optimized for FFPE samples and then Trizol, PicoPure RNA isolation kit, and Qiagen RNeasy FFPE kit performances were compared in terms of yield and purity. Finally, two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P) were also evaluated to determine which combination gives the best percentage of present call. Our optimization study shows that the Qiagen RNeasy FFPE kit with modified deparaffinization step gives better results (RNA quantity and quality) than the other two isolation kits. The Ribo-SPIA protocol and U133_X3P array combination gave a significantly higher percentage of present calls than the 3 IVT cDNA amplification and labeling system. However, no significant differences were found between the two array platforms. These results present a workflow for microarray gene expression profiling of FFPE tissues. The findings also indicate that sufficient quality gene expression data can be obtained from FFPE-derived RNA.
Publication Title
Optimization of gene expression microarray protocol for formalin-fixed paraffin-embedded tissues.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We profiled transcripts from sorted phloem cells of wild-type and apl mutants to identify the genes regulated by APL in phloem.
Publication Title
Plant development. Arabidopsis NAC45/86 direct sieve element morphogenesis culminating in enucleation.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 3 Downloadable Samples
Illumina HiSeq 4000
Description
Cervical cancer cell line C33A
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Cell line, Treatment, Race
View Samples- Mus musculus
- 3 Downloadable Samples
- NextSeq 500
Description
In the terms of vaccine efficacy and duration of protection in malaria vaccination is major concern against malaria. On the other hand, it is facing complications in development and administration to the host. However, whole sporozoites vaccination (WSV) is far more efficacious than any other alternative strategy. We have found that the intermittent sporozoite challenge to immune mice following RAS vaccination extends the longevity of sterile protection by maintaining CD8+T cell memory responses to LS infection and also helps in CD8a+DCs accumulation and activation in liver. Consequently, there has been great interest in elucidating and understating the sterile immunological response at mechanistic level. The information we have generated can then potentially be used in generation of next generation vaccine with improved efficacy and duration of protection. In this work, to elucidate the host initial immune response underlying the protective effects of a WSV in shaping the protected sterile protection and advances its immunogenicity in the future, a high-throughput RNA sequencing technology was used to investigate the immunization related gene expression patterns of mouse immunized with radiation attenuated sporozoites (RAS) vaccine.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Arabidopsis thaliana
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
Introduction: The Plant Organelle RNA Recognition (PORR) domain proteins are nucleus-encoded RNA-binding proteins that have acquired specific roles in organelle RNA metabolism as splicing factors of chloroplast group II introns. LEFKOTHEA (At5g62990) is a nuclear gene encoding a PORR domain protein that carries a transit peptide (TP) and monopartite or bipartite nuclear localization signals (NLS). These motifs result in dual-targeting of LEFKOTHEA to the nucleus and chloroplasts implying a role in the splicing of chloroplast group II introns and nuclear pre-mRNA introns. Therefore, we examined the splicing efficiency of plastid and nuclear genes in lefko2 mutant.Methods: The lefko2 mutant was isolated from a genetic screen of an M2 EMS-mutagenized Arabidopsis thaliana Columbia (Col-0) background seed population. The lefko2 mutant allele has a white cotyledon phenotype caused by a G to A mutation in the coding region resulting in a Glycine (G) 373 to Aspartic acid (D) conversion. Total RNA was extracted using plant RNA kit spin columns with an on-column DNase treatment from lefko2 mutant and wild-type Arabidopsis cotyledons. The quantity and integrity of the RNA was assessed using a NanoDrop 1000 spectrophotometer and agarose gel electrophoresis. RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer's instructions (Illumina). Sequencing was performed on an Illumina HiSeq 2000 instrument at BGI (Beijing Genomics Institute). Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10). RNA-seq data were analyzed using the SOAP (Release 2.121) with parameters “-s 40 -l 32 -v 3 -r 2” and the TopHat/Cufflinks pipeline (version 2) with parameters “-p 16 --solexa1.3-quals --segment-length 30 --segment-mismatches 2 -r 20 --mate-std-dev 20 --library-type fr-unstranded”. We generated 480 million paired-end reads (101 bp in length) for each sample. On average, about 90% of these reads could be unambiguously aligned to the TAIR10 reference genome sequence. Alternative splicing events were detected for lefko2 and wild-type using Spladder. Intron retention events detected in wild-type were filtered out from lefko2 or vice-versa, and visualized using the Integrative Genomics Viewer (IGV) tool.Results: Splicing defects were observed in numerous nuclear genes of lefko2 cotyledons compared to wild type. Among them, intron retention (IR) events were the most prominent. Further, the fidelity of 5' splice site (5'SS) donor and 3'SS acceptor splicing was disturbed in lefko2 cotyledons. To less extend, exon skipping (ES) defects were also detected.Conclusions: Detailed nuclear splicing events were widely observed in lefko2 cotyledons demonstrating a prevalent role of LEFKOTHEA in the splicing of nuclear pre-mRNA introns.Overall design: RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer's instructions (Illumina). Sequencing was performed on an Illumina HiSeq 2500 instrument at BGI (Beijing Genomics Institute).
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
View Samples- Pseudomonas aeruginosa
- 1 Downloadable Sample
- Illumina HiSeq 2500
Description
The study was conducted to understand the effect of Solanum torvum root extract upon Pseudomonas aeruginosa signaling system . Extract could suppress quorum sensing genes due to which the bacteria remains attenuated inside a host.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Saccharomyces cerevisiae
- 16 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Effect of FLO8 or MSS11 deletion and -overexpression on yeast transcript profiles compared to wild type in laboratory yeast strains 1278b and S288c.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples