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accession-icon SRP008258
Human mitochondria hub of small RNAs: Analysis by deep Sequencing
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

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).

Publication Title

Systematic analysis of small RNAs associated with human mitochondria by deep sequencing: detailed analysis of mitochondrial associated miRNA.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon SRP131016
Effect of BRD4 deletion on the Transcriptome of Different Thymocyte Subpopulations
  • organism-icon Mus musculus
  • sample-icon 36 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

By 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.

Publication Title

Immature CD8 Single-Positive Thymocytes Are a Molecularly Distinct Subpopulation, Selectively Dependent on BRD4 for Their Differentiation.

Sample Metadata Fields

Specimen part, Treatment, Subject

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accession-icon GSE16108
Transcription profiling of parental lines and bulked salt sensitive and salt tolerant RILs derived from 2 rice varieties
  • organism-icon Oryza sativa indica group
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

The 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.

Publication Title

Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.).

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE15912
Whole genome transcriptome profiling of Pusa 1266 and Pusa Basmati 1 in panicle primordia stage
  • organism-icon Oryza sativa
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

The 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.

Publication Title

Identification of candidate genes for grain number in rice (Oryza sativa L.).

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP034011
Transcriptomic analysis of Plasmodium PBANKA, PBSLTRiP-KO, PB268-KO parasite infected and uninfected host cell
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIlluminaGenomeAnalyzerIIx

Description

Liver 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.

Publication Title

A Sporozoite- and Liver Stage-expressed Tryptophan-rich Protein Plays an Auxiliary Role in Plasmodium Liver Stage Development and Is a Potential Vaccine Candidate.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE86848
Role of TaVAP in stress tolerance in plants
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Abiotic 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.

Publication Title

Gene encoding vesicle-associated membrane protein-associated protein from Triticum aestivum (TaVAP) confers tolerance to drought stress.

Sample Metadata Fields

Specimen part

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accession-icon GSE10584
Comparison of gene expression in erythroblasts with the In(Lu) phenotype with normal erythroblasts.
  • organism-icon Homo sapiens
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

In order to elucidate the molecular mechanism giving rise to the rare In(Lu) type of Lu(a-b-) blood group phenotype we compared the transcriptome of normal and In(Lu) erythroblasts at different stages of maturation. Many erythroid-specific genes had reduced transcript levels suggesting the phenotype resulted from a transcription factor abnormality. A search for mutations in erythroid transcription factors revealed mutations in the promoter or coding sequence of EKLF in 21 of 24 individuals with the In(Lu) phenotype. In all cases the mutant EKLF allele occurred in the presence of a normal EKLF allele. Individuals with the In(Lu) phenotype have no reported pathology indicating that one functional EKLF allele is sufficient to sustain human erythropoiesis. These data provide the first description of inactivating mutations in human EKLF and the first demonstration of a blood group phenotype resulting from mutations in a transcription factor.

Publication Title

Mutations in EKLF/KLF1 form the molecular basis of the rare blood group In(Lu) phenotype.

Sample Metadata Fields

No sample metadata fields

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accession-icon E-MTAB-3230
Comparative transcriptome study of enhanced water stress tolerant (ewst1) mutant of rice variety Nagina22
  • organism-icon Oryza sativa
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Twenty 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).

Publication Title

Physiological, anatomical and transcriptional alterations in a rice mutant leading to enhanced water stress tolerance.

Sample Metadata Fields

Specimen part

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accession-icon GSE16561
Gene expression analysis of peripheral whole blood RNA following ischemic stroke
  • organism-icon Homo sapiens
  • sample-icon 63 Downloadable Samples
  • Technology Badge IconIllumina HumanRef-8 v3.0 expression beadchip

Description

The purpose of this project was to elucidate gene expression in the peripheral whole blood of acute ischemic stroke patients to identify a panel of genes for the diagnosis of acute ischemic stroke. Peripheral blood samples were collected in Paxgene Blood RNA tubes from stroke patients who were >18 years of age with MRI diagnosed ischemic stroke and controls who were non-stroke neurologically healthy. The results suggest a panel of genes can be used to diagnose ischemic stroke, and provide information about the biological pathways involved in the response to acute ischemic stroke in humans.

Publication Title

Genomic biomarkers and cellular pathways of ischemic stroke by RNA gene expression profiling.

Sample Metadata Fields

Sex, Age, Race

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accession-icon GSE71717
Expression data from Human Ishikawa cells treated with Genistein
  • organism-icon Homo sapiens
  • sample-icon 60 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This study provides a comprehensive evaluation of changes in gene expression during treatment with Genistein in vitro.

Publication Title

Dose- and Time-Dependent Transcriptional Response of Ishikawa Cells Exposed to Genistein.

Sample Metadata Fields

Treatment

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...

refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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