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accession-icon SRP070828
Identification Of Candidate Anti-Cancer Molecular Mechanisms Of Compound Kushen Injection Using Functional Genomics
  • organism-icon Homo sapiens
  • sample-icon 27 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

Compound Kushen Injection (CKI) has been clinically used in China for over 15 years to treat various types of solid tumours. However, because such Traditional Chinese Medicine (TCM) preparations are complex mixtures of plant secondary metabolites, it is essential to explore their underlying molecular mechanisms in a systematic fashion. We have used the MCF-7 breast cancer cell line as an initial in vitro model to identify CKI induced changes in gene expression. Cells were treated with CKI for 24 and 48 hours at two concentrations (1.0 and 2.0 mg/mL), and 5-Fluorouracil (5-FU) was used to treat cells as a positive control. Cell proliferation and apoptosis activity were measured with XTT and Caspase-3 assays respectively. Transcriptome data of cells treated with CKI or 5-FU for 24 and 48 hours were acquired using high-throughput Illumina RNA-seq technology. In this report we show that CKI inhibited MCF-7 cell proliferation and induced apoptosis in a dose-dependent fashion. We integrated and applied a series of transcriptome analysis methods, including gene differential expression analysis, pathway over-representation analysis, de novo identification of long non-coding RNAs (lncRNA) as well as co-expression network reconstruction, to identify candidate anti-cancer molecular mechanisms of CKI. Multiple pathways were perturbed and the cell cycle was identified as the potential primary target pathway of CKI in MCF-7 cells. CKI may also induce apoptosis in MCF-7 cells via a p53 independent mechanism. In addition, we identified novel lncRNAs and showed that many of them might be expressed as a response to CKI treatment. Overall, we have comprehensively investigated the utility of transcriptome analysis with high-throughput sequencing to characterise the molecular response of cancer cells to a TCM drug, and provided a practical guideline for future molecular studies of TCM. Overall design: High-depth paired-end RNA-seq from MCF-7 cell line. Each sample contains 3 biological replicates.

Publication Title

Identification of candidate anti-cancer molecular mechanisms of Compound Kushen Injection using functional genomics.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP149798
Genome wide analysis of upper spinal cords with training after spinal cord hemisection injury
  • organism-icon Rattus norvegicus
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1500

Description

The goal of this study is to elucidate the influence of treadmill training on transcriptome of the upper lumbar spinal cord after thoracic spinal cord hemisection. mRNA profiles of spinal cords at 23 days-post injury with/without treadmill training were generated. The expression levels of 650 genes in the trained animal were increased ( > 2-fold) compared to untrained animals. Our study represents the detailed analysis of transcriptomes of spinal cord distal to the hemisected lesion after treadmill training, with biologic replicates, generated by RNA-seq technology. Overall design: The effect of training after spinal cord injury (T9) on the transcriptome of intact upper spinal cord was investigated.

Publication Title

Locomotor Training Increases Synaptic Structure With High NGL-2 Expression After Spinal Cord Hemisection.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE14220
The nuclear actin-related protein Arp6 contributes to the radial positioning of chromosome territories.
  • organism-icon Gallus gallus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Chicken Genome Array (chicken)

Description

The chromatin of individual chromosomes is organized into chromosome territories (CTs) in the interphase nucleus. The spatial arrangement of CTs is non-random and evolutionarily conserved. The gene-dense and gene-poor CTs are positioned in the nuclear center and periphery, respectively. As candidates for key molecules involved in nuclear organization, we have investigated the nuclear actin-related proteins (Arps), which include the evolutionarily conserved actin-family together with conventional actin. We used a conditional knockout system with chicken DT40 cells to analyze the functions of the actin-related protein Arp6. Consistent with a previous identification of Arp6 in the SRCAP chromatin remodeling complex, the histone variant H2AZ was significantly decreased in the chromatin of Arp6-deficient cells. Most importantly, Arp6-deficient cells had impaired radial positioning of both gene-poor macrochromosome and gene-rich microchromosome CTs. A transcription microarray analysis of the cells suggests that the radial positioning of CTs impacts only a limited number of genes and plays an active role in repression, rather than in induction. As far as we know, this report is the first observation that an inner nuclear protein is required for the radial distribution of CTs, and will provide new insight into the mechanisms and physical significance of the positioning of CTs in the nucleus.

Publication Title

The actin family member Arp6 and the histone variant H2A.Z are required for spatial positioning of chromatin in chicken cell nuclei.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE35430
Expression data from H2A.Z-1 and H2A.Z-2 double KO cells
  • organism-icon Gallus gallus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Chicken Genome Array (chicken)

Description

The histone variant H2A.Z is evolutionarily conserved from yeast to vertebrates. H2A.Z regulates gene expression when localized to promoter region. Recently, we identified two genes encoding H2A.Z, H2A.Z-1 and H2A.Z-2 in vertebrate genome. However, it is not clear that both H2A.Z-1 and H2A.Z-2 were required for the function of H2A.Z in gene regulation. To address this issue, we generated the H2A.Z-1 and H2A.Z-2 double knock out (KO) cells in chicken DT40 cells. The expression pattern of H2A.Z-1 and H2A.Z-2 double KO cells was compared with WT cells to characterize the genes regulated by H2A.Z-1 and H2A.Z-2.

Publication Title

The actin family member Arp6 and the histone variant H2A.Z are required for spatial positioning of chromatin in chicken cell nuclei.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE12404
Expression data from Arabidopsis Seed Compartments at 5 discrete stages of development
  • organism-icon Arabidopsis thaliana
  • sample-icon 87 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

Specimen part

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accession-icon GSE11262
Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
  • organism-icon Arabidopsis thaliana
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We collected globular stage seed compartments from 5 or 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of an Arabidopsis seed containing a globular stage embryo. For the purposes of this study we broke down the seed into 8 capturable compartments: embyro proper, suspensor, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat, general seed coat, and whole seeds.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE15160
Expression data from Arabidopsis seed compartments at the heart stage.
  • organism-icon Arabidopsis thaliana
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We collected heart stage seed compartments from 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing heart stage embryos. For the purposes of this study we captured 6 compartments: embryo proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat and seed coat, as well sets of serial sections encompassing the entire heart stage seed.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

Specimen part

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accession-icon GSE12403
Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
  • organism-icon Arabidopsis thaliana
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We collected linear-cotyledon stage seed compartments from 5 to 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing linear-coyledon-stage embryos. For the purposes of this study we captured 7 compartments: embyro proper, cellularized endosperm, chalazal endosperm, chalazal seed coat, general seed coat, whole seeds and micropylar endosperm.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE15165
Expression data from Arabidopsis seed compartments at the mature green stage.
  • organism-icon Arabidopsis thaliana
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We collected mature green seed compartments from 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing mature green-stage embryos. For the purposes of this study we captured 6 compartments: embryo proper, micropylar endosperm, cellularized peripherial endosperm, chalazal endosperm, chalazal seed coat and seed coat, as well sets of serial sections encompassing the entire mature green stage seed.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE12402
Expression data from Arabidopsis seed compartments at the pre-globular stage
  • organism-icon Arabidopsis thaliana
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We collected pre-globular stage seed compartments from 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of seeds containing pre-globular-stage embryos was identified as those seeds containing embryo propers made up of between 2 and 8 cells. For the purposes of this study we captured 6 compartments: embyro proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat and general seed coat. Serial sections of entire seeds were also captured for comparison.

Publication Title

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed.

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)

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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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