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accession-icon GSE60901
Comparison of small RNA-seq and microarray analysis for determining the effects of acute prenatal ethanol exposure on microRNA expression and its amelioration by environmental manipulation
  • organism-icon Rattus norvegicus
  • sample-icon 94 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Gene 1.0 ST Array (ragene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Effects of Acute Prenatal Exposure to Ethanol on microRNA Expression are Ameliorated by Social Enrichment.

Sample Metadata Fields

Sex

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accession-icon GSE60819
Effects of acute prenatal exposure to ethanol on microRNA expression are ameliorated by environmental manipulation.
  • organism-icon Rattus norvegicus
  • sample-icon 94 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Gene 1.0 ST Array (ragene10st)

Description

In this study, we tested if miRNAs are altered in amygdala and ventral striatum as a consequence of prenatal ethanol exposure and/or social enrichment. miRNA samples from 72 male and female adolescent rats were analyzed by RNA-Seq analysis and Affymetrix miRNA arrays. Several miRNAs showed significant changes due to prenatal ethanol exposure or social enrichment in one or both brain regions. Some of the miRNA changes caused by ethanol were reversed by social enrichment. The top predicted gene targets of these miRNAs were mapped and subjected to pathway enrichment analysis. We also directly examined the evidence for modulation of target mRNAs in whole transcriptome microarray data from the same rats. Among the pathways most strongly affected were p53, CREB, Glutamate and GABA signaling. Together, our data suggest a number of novel epigenetic mechanisms for social enrichment to reverse the effects of ethanol exposure.

Publication Title

Effects of Acute Prenatal Exposure to Ethanol on microRNA Expression are Ameliorated by Social Enrichment.

Sample Metadata Fields

Sex

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accession-icon GSE26024
Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarray
  • organism-icon Mus musculus
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

C57BL/6J (B6) and DBA/2J (D2) are two of the most commonly used inbred mouse strains in neuroscience research. However, the only currently available mouse genome is based entirely on the B6 strain sequence. Subsequently, oligonucleotide microarray probes are based solely on this B6 reference sequence, making their application for gene expression profiling comparisons across mouse strains dubious due to their allelic sequence differences, including single nucleotide polymorphisms (SNPs). The emergence of next-generation sequencing (NGS) and the RNA-Seq application provides a clear alternative to oligonucleotide arrays for detecting differential gene expression without the problems inherent to hybridization-based technologies. Using RNA-Seq, an average of 22 million short sequencing reads were generated per sample for 21 samples (10 B6 and 11 D2), and these reads were aligned to the mouse reference genome, allowing 16,183 Ensembl genes to be queried in striatum for both strains. To determine differential expression, 'digital mRNA counting' is applied based on reads that map to exons. The current study compares RNA-Seq (Illumina GA IIx) with two microarray platforms (Illumina MouseRef-8 v2.0 and Affymetrix MOE 430 2.0) to detect differential striatal gene expression between the B6 and D2 inbred mouse strains. We show that by using stringent data processing requirements differential expression as determined by RNA-Seq is concordant with both the Affymetrix and Illumina platforms in more instances than it is concordant with only a single platform, and that instances of discordance with respect to direction of fold change were rare. Finally, we show that additional information is gained from RNA-Seq compared to hybridization-based techniques as RNA-Seq detects more genes than either microarray platform. The majority of genes differentially expressed in RNA-Seq were only detected as present in RNA-Seq, which is important for studies with smaller effect sizes where the sensitivity of hybridization-based techniques could bias interpretation.

Publication Title

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays.

Sample Metadata Fields

Sex, Specimen part

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accession-icon SRP004777
Evaluating striatal expression differences between the C57BL/6J and DBA/2J inbred mouse strains using RNA-Seq and microarrays.
  • organism-icon Mus musculus
  • sample-icon 21 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II

Description

C57BL/6J (B6) and DBA/2J (D2) are two of the most commonly used inbred mouse strains in neuroscience research. However, the only currently available mouse genome is based entirely on the B6 strain sequence (NCBI m37, April 2007). Subsequently, oligonucleotide microarray probes are based solely on this B6 reference sequence, making their application for gene expression profiling comparisons across mouse strains dubious due to their allelic sequence differences, including single nucleotide polymorphisms (SNPs). The emergence of next-generation sequencing (NGS) and the RNA-Seq application provides a clear alternative to oligonucleotide arrays for detecting differential gene expression without the problems inherent to hybridization-based technologies. Using RNA-Seq, an average of 22 million short sequencing reads were generated per sample for 21 samples (10 B6 and 11 D2), and these reads were aligned to the mouse reference genome, allowing 16,183 Ensembl genes to be queried in striatum for both strains. To determine differential expression, 'digital mRNA counting' is applied based on reads that map to exons. The current study compares RNA-Seq (Illumina GA IIx) with two microarray platforms (Illumina MouseRef-8 v2.0 and Affymetrix MOE 430 2.0) to detect differential striatal gene expression between the B6 and D2 inbred mouse strains. We show that by using stringent data processing requirements that differential expression as determined by RNA-Seq is concordant with both the Affymetrix and Illumina platforms in more instances than it is concordant with only a single platform, and that instances of discordance with respect to direction of fold change were rare. The large dynamic range of RNA-Seq detects thousands more genes than were observed with microarray analyses. This additional information gained by using this technology illustrates the value of RNA-Seq.

Publication Title

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE18935
Effects on small RNA MgrR in Escherichia coli
  • organism-icon Escherichia coli k-12
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon Affymetrix E. coli Genome 2.0 Array (ecoli2)

Description

MgrR is a newly characterized Hfq dependent small RNA RNA. The expression of MgrR is regulated by Two component system, PhoPQ regulon, which senses low Mg2+ in environment. It has been reported that Hfq-binding sRNAs base pair with target RNAs, frequently leading to rapid degradation of target messages or, less frequently, to stabilization, both of which can be assayed by using microarrays. In order to search for the target genes of MgrR, we therefore examined the consequences of MgrR expression on mRNA abundance under two conditions. In condition 1, the chromosomal copy of mgrR was deleted and MgrR was expressed for 15 from an induced plac-mgrR plasmid and compared to cells carrying a vector induced for the same period. In condition 2, the expression of mRNAs was compared in wild-type cells (mgrR+) and the mgrR deletion strain, both grown in LB; because MgrR levels are fairly high under our normal growth conditions, this allowed analysis of both the direct and indirect (long-term) effects of MgrR.

Publication Title

A PhoQ/P-regulated small RNA regulates sensitivity of Escherichia coli to antimicrobial peptides.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE115379
Genetic signatures of retinal ganglion cells revealed through single cell profiling [non-dissociated RGC]
  • organism-icon Mus musculus
  • sample-icon 29 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

This study aimed to characterize the transcriptomes of adult retinal ganglion cells (RGCs). The physiological properties of these cells were characterized first in non-dissociated retinal tissue. With that information recorded, the cells were isolated for transcriptome profiling.

Publication Title

Molecular signatures of retinal ganglion cells revealed through single cell profiling.

Sample Metadata Fields

Specimen part

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accession-icon GSE92948
GPCR19 agonist increases in number of immune-regulatory myeloid cells and their expression of immune checkpoint molecule
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

GPCR19 pathway has been implicated in regulating various inflammation. However, the exact mechanism of immune regulation by GPCR19 pathway has not been elucidated in detail.

Publication Title

Taurodeoxycholate Increases the Number of Myeloid-Derived Suppressor Cells That Ameliorate Sepsis in Mice.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE11594
Expression data from dark grown Arabidopsis Wild type (Wt, col-o) and pif1-2 (At2g20810, Salk_072677) mutant seedlings
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Arabidopsis bHLH transcription factor PIF1 has been shown function as a negative regulator of Chlorophyll biosynthesis. Pif1-2 mutant accumulate more protochlorophylide during prolonged dark growth condations, therefore the comparation between Wt and pif1-2 mutant will help us find the PIF1 target genes in Chlorophyll biosynthesis pathway at genome wide level under the dark grown conditions.

Publication Title

PIF1 directly and indirectly regulates chlorophyll biosynthesis to optimize the greening process in Arabidopsis.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP026129
Late life rapamycin treatment reverses age-related heart dysfunction
  • organism-icon Mus musculus
  • sample-icon 20 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

We report the mRNA profile of aged mice (24 months old) fed either a control diet or a diet containing Rapamycin (14 ppm) for 3 months. After drug treatement, the hearts of the mice were removed and total mRNA was removed from the tissue. Analysis revealed that there were 700 significantly differentially expressed genes between the control fed group and the Rapamycin diet group by our analysis. Overall design: Heart tissue samples from age-matched control mice (n=10) and rapamycin fed mice (n=10) were extracted for total RNA. The samples were sequenced using Illumina HiSeq 2000 (50 basepair paired-end sequencing). The sequencing yielded quality scores greater than 30 with an average of 10 million reads per sample. 34,293 genes were mapped back to the MGSCv37 C57BL/6J mouse genome (maximum paired distance=300 and minimum=130, minimum number of reads per mapping = 5, maximum number of mismatches= 2, with the reads being mapped to unique sites in the genome).

Publication Title

Late-life rapamycin treatment reverses age-related heart dysfunction.

Sample Metadata Fields

Age, Specimen part, Treatment, Subject

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accession-icon GSE119747
Comparison of enteroendocrine cells and pancreatic -cells using gene expression profiling and insulin gene methylation
  • organism-icon Mus musculus
  • sample-icon 38 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

In this study, similarities between EECs and -cells were evaluated in detail. To obtain specific subtypes of EECs, cell sorting by flow cytometry was conducted from STC-1 cells (a heterogenous EEC line), and each single cell was cultured and passaged. Five EEC subtypes were established according to hormone expression, measured by quantitative RT-PCR and immunostaining: L, K, I, G and S cells expressing glucagon-like peptide-1, glucose-dependent insulinotropic polypeptide, cholecystokinin, gastrin and secretin, respectively.

Publication Title

Comparison of enteroendocrine cells and pancreatic β-cells using gene expression profiling and insulin gene methylation.

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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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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