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accession-icon SRP053172
Zea mays subsp. mays Transcriptome or Gene expression
  • organism-icon Zea mays
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1000

Description

Transcriptomic analysis of ZmUbi:ZmNAC111 transgenic maize under under well-watered and 2h dehydration stress conditions

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part

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accession-icon SRP132132
Arabidopsis thaliana strain:Col-0 Raw sequence reads
  • organism-icon Arabidopsis thaliana
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

This study is aimed to compare the gene expression between wild type and 35S:6MYC-HARP1 in response to wounding treatment.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Age, Specimen part, Treatment

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accession-icon SRP052846
Mus musculus breed:mix C57/bl6-129sv Transcriptome or Gene expression
  • organism-icon Mus musculus
  • sample-icon 3 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

CD19 positive B cells were sorted from spleens in wild type mice and conditional konckout PRMT7 mice. RNA-seq experiments were performed to identify the differential expressing genes.

Publication Title

Histone Arginine Methylation by PRMT7 Controls Germinal Center Formation via Regulating Bcl6 Transcription.

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP067820
Global discovery of long noncoding RNAs during bovine adipogenic differentiation
  • organism-icon Bos taurus
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Adipogenesis is a complex and precisely orchestrated process mediated by a network of adipogenic regulatory factors. The recent explosion of knowledge have demonstrated that long noncoding RNA are involved in adipogenic gene regulatory network. However, existing annotations of lncRNAs involved in adipogenic differentiation are derived from preadipocyte cell lines, researches using primary cultures of farm animals are obviously required. To comprehensively identify lncRNAs with potential functions during bovine adipogenesis, in the present study we performed Ribo-Zero-Seq to survey the transcriptome landscape of in vitro cultured bovine preadipocytes and differentiated adipocytes. A stringent set of 2882 lncRNAs were finally identified. The 2882 lncRNAs shared many of the features of their mammalian counterparts: relatively shorter in length, significantly lower expression levels and fewer in exon number than RefSeq protein coding transcripts. Comparison of the lncRNAs expression profiles identified 16 specifically regulated lncRNAs during adipogenic differentiation. Integrative computational analyses associated these lncRNAs with several signaling pathways involved in lipid metabolism, including steroid biosynthesis, PPAR signaling pathway, glycolysis/gluconeogenesis, and fatty acid metabolism. Our data provide a valuable genomic resource for the identification of lncRNAs with potential functions in adipogenic differentiation.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part

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accession-icon SRP142026
Saccharomyces cerevisiae Raw sequence reads
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 34 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

As an ancient winning strategy of microorganisms, glucose repression mechanism has become specialized to perfection in Saccharomyces cerevisiae. The galactose (GAL) metabolism network is stringently regulated by glucose repression in yeast and has been a classic system for studying gene regulation. We show here that the population of S. cerevisiae living in fermented milks has autonomously reinstated an ancient version of the structural GAL genes through introgression. The introgressed GAL network has completely abolished the glucose repression and conversed from a strictly inducible to a constitutive system through coordinative polygenic changes in the regulatory components of the network, including transitions in the upstream repressing sequence site of GAL4 that impair Mig1p-mediated repression and loss of function of the inducer Gal3p and the repressor Gal80p. In addition, the introgressed GAL2 gene has been duplicated while the native HXT6 and HXT7 genes have been inactivated, resulting in galactose-over-glucose preference and elevated galactose utilization rate. Relying on the reverse evolution of the GAL network, the non-lactose fermenting yeast has become a dominant species co-existing with other lactose fermenting microorganisms in fermented milks. Our results also provide new clues for developing yeast strains devoid of barriers to co-utilization of different sugars.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part, Disease, Cell line

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accession-icon SRP165652
Homo sapiens Genome sequencing
  • organism-icon Homo sapiens
  • sample-icon 3 Downloadable Samples
  • Technology Badge IconIon Torrent S5

Description

This study presented the preliminary mechanistic studies of teniposide analogs for toxicity reduction

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon SRP151834
RNA-seq results of WT and CKIP-1 KO mouse macrophages
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The differential expression of gene in bone marrow derived macrophages from Ckip-1 KO mice and WT mice.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part, Cell line

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accession-icon SRP018010
DNA topoisomerase I and antisense transcription
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

DNA Topoisomerase I (Top1) relaxes DNA supercoiling and is inhibited with high specificity by camptothecin, a natural product of chinese tree Camptotheca acuminata with anticancer activity. Topoisomerase activity is required at transcribing regions to modulate DNA supercoils generated by RNA polymerases. However, Top1 functions at promoters and molecular responses to CPT are not fully understood. We found that camptothecin increases antisense RNA polymerase II transcripts at active divergent CpG-island promoters in a replication-independent manner. Kinetics investigations of the formation of Top1-DNA cleavage complexes and non-B DNA structures showed that CPT interferes with Top1 modulation of negative DNA supercoiling at promoters. The present findings will be a resource to establish the role of such antisense RNAs in transcription regulation and to discover additional components of the response pathway. Moreover, the transcriptional camptothecin effects can be the molecular basis of the therapeutic activity in cancer as well as neurological syndromes.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE34022
Expression data of interferon-alpha treated Huh-7 cells
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Hepatitis C virus (HCV) infection is primarily treated with a pegylated interferon alpha based therapy, a regime that induces antiviral effects through the upregulation of many interferon-stimulated genes (ISGs). Whilst a number of anti-HCV ISGs have previously been identified, others may also be involved.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-34022

Sample Metadata Fields

Cell line

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accession-icon GSE86379
Expression data from BPH resistant and susceptible rice varieties
  • organism-icon Oryza sativa
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Bph6 is a gene that confers rice high resistance to its devastating pest BPH. Understanding the molecular responses of the resistant and susceptible varieties would pave the way to controlling the pest more effectively.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-86379

Sample Metadata Fields

Specimen part

View Samples
...

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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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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