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SRP032669
Mus musculus
8 Downloadable Samples
Illumina Genome Analyzer IIx
Description
N6-methyladenosine (m6A) has been recently identified as a conserved epitranscriptomic modification of eukaryotic mRNAs, but its features, regulatory mechanisms, and functions in cell reprogramming are largely unknown. Here, we report m6A modification profiles in the mRNA transcriptomes of four cell types with different degrees of pluripotency. Comparative analysis reveals several features of m6A, especially gene- and cell-type-specific m6A mRNA modifications. We also show that microRNAs (miRNAs) regulate m6A modification via a sequence pairing mechanism. Manipulation of miRNA expression or sequences alters m6A modification levels through modulating the binding of METTL3 methyltransferase to mRNAs containing miRNA targeting sites. Increased m6A abundance promotes the reprogramming of mouse embryonic fibroblasts (MEFs) to pluripotent stem cells; conversely, reduced m6A levels impede reprogramming. Our results therefore uncover a role for miRNAs in regulating m6A formation of mRNAs and provide a foundation for future functional studies of m6A modification in cell reprogramming. Overall design: m6A-seq in ESC, iPSC, NSC and sertoli cells.
Publication Title
m(6)A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 32 Downloadable Samples
- Illumina HiSeq 2500
Description
Total RNA-seq analysis of mouse liver following LNA treatment in vivo to identify mRNA targets of mmu-miR-802-5p and mmu-miR-1948-5p. Overall design: Male and female 9-wk ICR mice were injected with LNAs complementary to mmu-miR-1948-5p and mmu-miR-802-5p, respectively. Liver RNA was analyzed by RNA-seq 3 days or 6 days after LNA treatment.
Publication Title
Functional Roles of Sex-Biased, Growth Hormone-Regulated MicroRNAs miR-1948 and miR-802 in Young Adult Mouse Liver.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The inflammatory response plays out over time in a reproducible and organized manner after an initiating stimulus. Here we showed that the genes activated in cultured mouse fibroblasts in response to the proinflammatory cytokine tumor necrosis factorcan be divided roughly into three groups, each with different induction kinetics. Whereas differential transcription is important in determining the grouping of these genes, differential mRNA stability also exerted strong influence in some cases overriding that of transcriptional control elements on the temporal order of gene expression. mRNA transcripts expressed early after TNF stimulation have abundant AU-rich elements in their 3'-untranslated regions whereas those expressed later are contain fewer AU-rich sequences. Thus mRNA stability and transcriptional control, two intrinsic characteristics of genes, control the kinetics of proinflammatory cytokine-induced gene expression.
Publication Title
The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 4000
Description
High amount of Eomes might drive T cell exhaustion. In order to understand how Eomes contributes to exhaustion of CD8+ T cell in the TME, we conducted transcriptional analysis of control OT-I cells and Eomes-overexpressing OT-I cells Overall design: Eomes was cloned into a retroviral expression vector (RVKM) which also encodes an IRES-hCD2 cassette. This vector was transfected into Pheonix to package retrovirus. The empty vector was used as a control. CD8+ T cells were isolated from spleen and lymph nodes of OT-I mice using Dynabeads Flowcomp mouse CD8 kit (Invitrogen). Then the cells were stimulated with SIINFEKL peptide (OVA257-264) at 2.5 ng/mL in the presence of 10U/mL IL-2 for 24 hr. Retroviral supernatants were harvested, filtered, and supplemented with 6µg/mL polybrene. OT-I T cell cultures were spinduced with the retroviral supernatant for 90 min at 1800 rpm, 32ºC. 48 hr later, hCD2+ cells were sorted prior to re-stimulation. hCD2+ OT-I cells were plated at 40,000 cells/well in 96-well plates and re-stimulated with 2.5ng/mL OVA with 10U/mL IL-2 for 3 days before harvested for RNAseq analysis. Total RNA was extracted from re-stimulated control or Eomes-overexpressing OT-I cells and sent to BGI Genomics for library construction. The library products were sequenced via Illumina Hiseq4000 by BGI Genomics. The sequencing reads were filtered by SOAPnuke without quality problems. Genome mapping was done by HISAT. Clean reads were mapped to the mm10 reference genome using Bowtie2, and gene expression indicated by RPKM (Reads Per Kilobases per Million reads) was calculated by RSEM. Differentially expressed genes (DEG) were detected with PoissonDis by at least 1.5 fold change and FDR lower than 0.01.
Publication Title
High Levels of Eomes Promote Exhaustion of Anti-tumor CD8<sup>+</sup> T Cells.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We used microarrays to detail the global programme of gene expression to identify TNF-induced genes that are negatively regulated by EHMT1
Publication Title
EHMT1 protein binds to nuclear factor-κB p50 and represses gene expression.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
Gene expression in intact and hypophysectomized adult mouse liver was assayed by RNA-seq analysis of total liver RNA, as part of a study of growth hormone regulation of hepatic lincRNAs. Overall design: Eight independent pools: two intact males, two intact females, two hypophysectomized males and two hypophysectomized females, comprised of total RNA isolated from 3-5 individual livers / pool, were prepared and used for unstranded RNA-seq.
Publication Title
Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 7 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Cumulus oophorus cells play an essential role in oocyte development. CBX4 is a member of the Polycomb complex, which plays a role in regulating cellular differentiation.
Publication Title
Contribution of CBX4 to cumulus oophorus cell phenotype in mice and attendant effects in cumulus cell cloned embryos.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
Gene expression in adult male mouse liver was assayed by nuclear RNA-seq, as part of a study of hepatic lincRNAs. Overall design: Three independent pools, comprised of nuclear RNA isolated from 4 individual male livers per pool, were prepared and used for RNA-seq.
Publication Title
Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Gene expression in adult female mouse liver was assayed by nuclear RNA-seq, as part of a study of hepatic lincRNAs. Overall design: Three independent pools, comprised of nuclear RNA isolated from 4 individual livers per pool, were prepared and used for unstranded RNA-seq.
Publication Title
Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- IlluminaHiSeq2000
Description
Gene expression in adult male and female mouse liver was assayed by RNA-seq, as part of a study on hepatic lincRNAs. Overall design: Total liver RNA was prepared from 12 individual male and 12 individual female mice. Four independent pools, comprised of RNA isolated from 6 individual male or female livers (2 pooled biological replicates for each sex) were then prepared and used for RNA-seq.
Publication Title
Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone.
Sample Metadata Fields
No sample metadata fields
View Samples