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accession-icon SRP041736
Transcriptome Proflings of 347 Single cells from 10 Distinct Populations
  • organism-icon Homo sapiens
  • sample-icon 576 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

Analyze the transcriptomes of 347 cells from 10 distinct populations in both of low-coverage (~0.27 million reads per cell) and high-coverage (~5 million reads per cell) to identify cell-type-specific biomarkers, and to compare gene expression across samples specifically for cells of a given type as well as to reconstruct developmental lineages of related cell types.

Publication Title

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP038765
Drosophila melanogaster Transcriptome in cold stress
  • organism-icon Drosophila melanogaster
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer IIx

Description

Investigate the genetic mechanism bebind cold stress for insects.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part, Cell line

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accession-icon SRP212246
Atorvastatin targets islet mTOR signaling via regulating small G proteins to reduce functional ß-cell mass
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Statins, the cholesterol lowering agents, can increase diabetes incidence and impair glucose tolerance via its detrimental effects on non-hepatic tissues, such as pancreatic islet, but underlying mechanism has not been clarified. In atorvastatin-treated high fat diet mice, we found reduced pancreatic ß-cell size, ß-cell mass, mature insulin granules and reduced insulin secretion along with the deteriorated glucose tolerance. Transcriptome profiling of primary pancreatic islets showed inhibitory effects of atorvastatin on expression of genes encoding key pancreatic transcription factors, mTOR signaling pathway and small G proteins (sGPs).

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part, Cell line, Treatment

View Samples
accession-icon SRP073799
Transcriptome of highly purified mouse spermatogenic cell populations
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Spermatogenesis is a complex differentiation process that involves the successive and simultaneous execution of three different gene expression programs: mitotic proliferation of spermatogonia, meiosis, and spermiogenesis. Testicular cell heterogeneity has hindered its molecular analyses. Moreover, the characterization of short, poorly represented cell stages such as initial meiotic prophase ones (leptotene and zygotene) has remained elusive, despite their crucial importance for understanding the fundamentals of meiosis.We have developed a flow cytometry-based approach for obtaining highly pure stage-specific spermatogenic cell populations, including early meiotic prophase. Here we combined this methodology with next generation sequencing, which enabled the analysis of meiotic and postmeiotic gene expression signatures in mouse with unprecedented reliability. Interestingly, we found that a considerable number of genes involved in early as well as late meiotic processes are already on at early meiotic prophase, with a high proportion of them being expressed only for the short time lapse of lepto-zygotene stages. Besides, we observed a massive change in gene expressionpatterns during medium meiotic prophase (pachytene) when mostly genes related to spermiogenesis and sperm function are already turned on. This indicates that the transcriptional switch from meiosis to post-meiosis takes place very early, during meiotic prophase, thus disclosing a higher incidence of post-transcriptional regulationin spermatogenesis than previously reported. Moreover, we found that a good proportion of the differential gene expression in spermiogenesis corresponds to up-regulation of genes whose expression starts earlier, at pachytene stage; this includes transition protein- and protamine-coding genes, which have long been claimed to switch on during spermiogenesis. In addition, our results afford new insights concerning X chromosome meiotic inactivation and reactivation. This work provides for the first time an overview of the time course for the massive onset and turning off of the meiotic and spermiogenic genetic programs. Importantly, our data represent a highly reliable information set about gene expression in pure testicular cell populations including early meiotic prophase, for further data mining towards the elucidation of the molecular bases of male reproduction in mammals.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part, Cell line

View Samples
accession-icon SRP092882
Drosophila allele specific expression
  • organism-icon Drosophila melanogaster
  • sample-icon 66 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

This study crossed Drosophila melanogaster genotypes from four populations to the reference genome line. RNAseq data was then generated to study natural variation in allele specific expression.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part, Cell line

View Samples
accession-icon GSE29986
gene expression analyses of pediatric lymphoblastic lymphomas and leukemias
  • organism-icon Homo sapiens
  • sample-icon 36 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

T-cell acute lymphoblastic leukemia (T-ALL) and lymphoma (T-LBL) share common morphologic and immunophenotypic features and are treated with similar therapeutic approaches. Nonetheless, they show distinct clinical presentations suggesting that they may represent two different biological entities. In order to investigate T-LBL and T-ALL biological characteristics we used transcriptional profiling approache. Genome-wide gene expression profiling, performed on 20 T-LBL and 10 T-ALL diagnostic specimens, showed that the two malignancies shared a large fraction of their transcriptional profile while a subset of genes appeared to be differentially expressed in T-LBL versus T-ALL. This gene signature included genes involved in chemotactic responses and angiogenesis which might play a role in the different tumor cell localization suggesting that T-LBL and T-ALL could be two distinct diseases with unique transcriptional characteristics.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-29986

Sample Metadata Fields

Specimen part, Disease

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accession-icon E-MEXP-1415
Transcription profiling time series of leaves from winter wheat grown under S and N-deficient conditions
  • organism-icon Triticum aestivum
  • sample-icon 36 Downloadable Samples
  • Technology Badge Icon Affymetrix Wheat Genome Array (wheat)

Description

Transcripomic analysis of leaf gene expression in S and N-deficient winter wheat during grain development. Tissue was harvested at anthesis and 7, 14 and 21 days post anthesis from experimental field plots.

Publication Title

Co-ordinated expression of amino acid metabolism in response to N and S deficiency during wheat grain filling.

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part, Disease, Disease stage, Subject, Time

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accession-icon E-MEXP-583
Transcription profiling of human normal progenitor cells mutated for RUNX1-RUNX1 during myeloid and erythroid development to identify genes disregulated by RUNX1-RUNX1
  • organism-icon Homo sapiens
  • sample-icon 32 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

In order to identify genes dysregulated by the aberrant transcriptional activity of RUNX1-RUNX1T1, we used microarrays to determine the effect of this mutation on gene expression during myeloid and erythroid development of normal human progenitor cells.

Publication Title

Transcriptional dysregulation mediated by RUNX1-RUNX1T1 in normal human progenitor cells and in acute myeloid leukaemia.

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part

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accession-icon E-MEXP-550
Transcription profiling of Arabidopsis response to UV-B
  • organism-icon Arabidopsis thaliana
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Seven-day-old white-light-grown Arabidopsis seedlings were exposed for 15 minutes to polychromatic radiation with decreasing short-wave cut-off in the UV range, transferred back to the standard growth chamber and samples were taken 1 and 6 hours after the start of irradiation.

Publication Title

Genome-wide analysis of gene expression reveals function of the bZIP transcription factor HY5 in the UV-B response of Arabidopsis.

Alternate Accession IDs

None

Sample Metadata Fields

Age, Time

View Samples
accession-icon SRP056612
Homo sapiens Transcriptome or Gene expression
  • organism-icon Homo sapiens
  • sample-icon 20 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 4000, Illumina HiSeq 3000, NextSeq 500

Description

Gene expression profile in Calu-3 cells infected with MERS-CoV or SARS-CoV

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

View Samples
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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)

fund-icon Fund the CCDL

Developed by the Childhood Cancer Data Lab

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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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