We report here that human mitochondria contain small RNA including microRNA, piRNA, tRNA, rRNA, and RNA repeats. Mitochondria from human cells were purified and RNA isolated. Small RNAs were purified, library generated and analyzed by Illumina Hiseq 2000 system. The sequencing generated 19.5 and 17.7 million reads from HEK-293 and HeLa respectively. 91% and 97% sequences of HEK293 and HeLa respectively were annotated to various classes of small RNA. The total percentage of 4.21 and 2.58 sequences from HEK293 and HeLa respectively was found to be of miRNA. Further, we found only 1.2 % sequences from both the libraries aligned to mitochondrial genome. These results suggest that there is efficient transport of nuclear encoded small RNA to mitochondria. The small RNA in mitochondria may regulate critical cellular processes. Overall design: Analyzing the smallRNA in human mitochondria from two human cell lines (HEK-293 and HeLa).
Systematic analysis of small RNAs associated with human mitochondria by deep sequencing: detailed analysis of mitochondrial associated miRNA.
Specimen part, Cell line, Subject
View SamplesBy conditionally deleting BRD4 at various stages of thymic differentiation, we have established that BRD4 deficiency selectively affects a unique developmental subpopulation of thymocytes. Overall design: We examined by RNA-seq the effect on gene expression of BRD4 deletion in ex vivo DN, ISP, DP, CD4 and CD8 thymocyte subpopulations. The analysis was also performed on WT or BRD4 deleted ISP and DP thymocytes cultured for 16 hours at 37oC In this analysis, the conditional deletion of BRD4 (cKO) is achieved using the LCK-cre Transgene.
Immature CD8 Single-Positive Thymocytes Are a Molecularly Distinct Subpopulation, Selectively Dependent on BRD4 for Their Differentiation.
Specimen part, Treatment, Subject
View SamplesThe aim of this study was to minimize the number of candidate genes responsible for salt tolerance between a pair of rice varieties (CSR27 and MI48) with contrasting level of salt tolerance by bulked segregant analysis of their recombinant inbred lines. Microarray analysis of RNA extracted from the tolerant and susceptible parents without and with stress showed 798 and 2407 differentially expressed genes, respectively. The number of differentially expressed genes was drastically reduced to 70 and 30, by pooling the RNAs from ten extreme tolerant and ten extreme susceptible RILs due to normalization of irrelevant differentially expressed genes between the parents.
Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.).
No sample metadata fields
View SamplesThe aim of this study was to identify candidate genes responsible for grain number per panicle between a pair of rice varieties (Pusa 1266 and Pusa Basmati 1) by combining QTL analysis with expression analysis. Microarray analysis of RNA extracted from the panicle primordia showed 2741 differentially expressed genes. The differentially expressed genes were shortened to 18 on the basis of their occurance in the QTL region (responsible for grain number regulation) detected in RIL population derived from Pusa 1266 and Pusa Basmati 1.
Identification of candidate genes for grain number in rice (Oryza sativa L.).
No sample metadata fields
View SamplesLiver stage of malaria parasite exports SLTRiP and PB268 to the cytosol of parasite infected host cell. To know the host genes perturbed by WT-PBANKA, SLTRiP-KO and PB268-KO parasite growth, we did transcriptomic sequencing of infected host cells. We did mRNA sequencing of four samples for comparative analysis of WT and PB-knockout parasites infected host cells at 22 hours of post sporozoites infection. Overall design: mRNA profiles of Plasmodium PBANKA, PBSLTRiP-KO, PB268-KO parasite infected and uninfected HepG2 cells after 22hrs of sporozoites infections were generated by deep sequencing using Illumina GAIIx.
A Sporozoite- and Liver Stage-expressed Tryptophan-rich Protein Plays an Auxiliary Role in Plasmodium Liver Stage Development and Is a Potential Vaccine Candidate.
No sample metadata fields
View SamplesAbiotic stresses like drought, salinity, high and low temperature, and submergence are major factors that limit the crop productivity. Hence, identification of genes associated with stress response in crops is a prerequisite for improving their tolerance to adverse environmental conditions. In this study, we have analyzed the expression profiles of three genotypes WT, TaVAP mutant and TaVAPOE plants in Arabidopsis thaliana in col-0 background using microarray technology to identify the genes differentially expressed under control conditions.
Gene encoding vesicle-associated membrane protein-associated protein from Triticum aestivum (TaVAP) confers tolerance to drought stress.
Specimen part
View SamplesTwenty one day old seedlings of the mutant and WT grown in hydroponic culture in three replications were subjected to 25% PEG stress for one hour. The leaf samples of stressed and control seedlings were collected and preserved in liquid nitrogen for RNA isolation. Total RNA from four samples i.e. mutant control (MC), mutant stress (MS), Nagina22 control (NC) and Nagina22 stress (NS) was extracted by following the manufacturer‰۪s instructions provided with SV Total RNA isolation system Kit (PROMEGA, USA). All the steps starting from cRNA preparation to hybridization were conducted following the instructions of Affymetrix (AffymetrixGeneChip Expression Analysis Technical Manual). Chips were washed and stained in the Affymetrix Fluidics Station 450, and then scanned using the Affymetrix Gene Chip Scanner 3000. The cell intensity data files (.CEL) generated by the Gene Chip Operating Software (GCOS 1.2).
Physiological, anatomical and transcriptional alterations in a rice mutant leading to enhanced water stress tolerance.
None
Specimen part
View SamplesLeaf samples were used. We exposed young seedlings to NaCl and drought.
Identification of cis-regulatory elements associated with salinity and drought stress tolerance in rice from co-expressed gene interaction networks.
Specimen part
View SamplesThe aim of the study was to identify candidate genes responsible for drought tolerance trait between a pair of wheat varieties ( WL711 and C306) and correspondng progeny bulks (10 drought susceptible RILs and 10 drought tolerant RILs) by combining QTLs analysis with expression analysis. Microarray analysis of RNA extracted from the flag leaves showed large number of differentially expressed genes. The number of differentially expressed genes was reduced to 37 on the basis of their occurance in a major QTL region (responcible for drought tolerance) detected in RIL population derived from WL711 and C306.
Genomic associations for drought tolerance on the short arm of wheat chromosome 4B.
Specimen part
View SamplesGene expression profiling was performed on CNS tissue from neonatal mice carrying the T9H translocation and maternal or paternal duplication of proximal Chromosomes 7 and 15. Our analysis revealed the presence of two novel paternally expressed intergenic transcripts at the PWS/AS locus. The transcripts were termed Pec2 and Pec3 for paternally expressed in the CNS.Our analysis also revealed imprinting of Magel2, Mkrn3, Ndn,Ube3a and Usp29, as well as Pec2 and Pec3 in embryonic brain, 15.5 dpc, and provided a survery of biallelically expressed genes on proximal Chromosomes 7 and 15 in embryonic and neonatal CNS.
Novel paternally expressed intergenic transcripts at the mouse Prader-Willi/Angelman Syndrome locus.
No sample metadata fields
View Samples