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SRP185814
Arabidopsis thaliana
36 Downloadable Samples
Illumina HiSeq 2000
Description
Cold stress response is extensively studied process in plants. However most studies explore only limited set of organs and developmental stages (leaves or seedlings). In order to gain insight into organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+4ºC) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq. It showed that gene expression is highly organ-specific. The results on differential expression in leaves are congruent with current knowledge on stress response pathways, in particular, the role of CBF genes. In other organs, both essence and dynamics of gene expression changes are different. We show the involvement of genes that are confined to narrow expression patterns in non-stress conditions into stress response. In particular, the genes that control cell wall modification in pollen, are activated in leaves. In seeds, predominant pattern is the change of lipid metabolism. We found that stress response is highly organ-specific and highlighted the processes that are involved in this process in each type of organs.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part
View Samples- Danio rerio
- 2 Downloadable Samples
- IlluminaHiSeq2000
Description
Differential Expression between testis and ovary in two months of fish
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 2 Downloadable Samples
- IlluminaHiSeq2000
Description
Differential expression between WT and CD82a from Morpholino-treated embyro of Danio rerio
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Glycine max
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
No description.
Publication Title
No associated publication
Alternate Accession IDs
None
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
Alternate Accession IDs
None
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
Alternate Accession IDs
None
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
Alternate Accession IDs
None
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
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part
View Samples- Zea mays
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
The research of maize freezing tolerance.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part
View Samples- Bubalus bubalis, Bos taurus, Bos grunniens
- 9 Downloadable Samples
Affymetrix Bovine Genome Array (bovine)
Description
Sex condition has been demonstrated to alter meat quality and sex is a major factor that affects the fatty acid composition of lipids of carcass dissectible or intramuscular depot fats. But the possible genetic molecular mechanism of gender causing meat quality differences is not well defined. Qinchuan cattle, Qinghai yak and Guangxi buffalo are three typical indigenous species of cattle in China. Obivious differences of meat quality exist among the three species of cattle. Few studies have been conducted to elucidate the muscle tissue expression of genes involved in pathways and mechanisms leading to meat quality differences beyond the phenotype properties of beef.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Specimen part
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