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Mus musculus
157 Downloadable Samples
Illumina HiSeq 1000
Description
Post-transcriptional regulation of cellular mRNA is essential for protein synthesis. Here we describe the importance of mRNA translational repression and mRNA subcellular location for protein expression during B lymphocyte activation and the DNA damage response. Cytoplasmic RNA granules are formed upon cell activation with mitogens, including stress granules that contain the RNA binding protein Tia1. Tia1 binds to a subset of transcripts involved in cell stress, including p53 mRNA, and controls translational silencing and RNA granule localization. DNA damage promotes mRNA relocation and translation in part due to dissociation of Tia1 from its mRNA targets. Upon DNA damage, p53 mRNA is released from stress granules and associates with polyribosomes to increase protein synthesis. Global analysis of cellular mRNA abundance and translation indicates that this is an extended ATM-dependent mechanism to increase protein expression of key modulators of the DNA damage response. Overall design: Splenic B cells from C57BL/6Babr mice were isolated and activated with LPS for 48 hours prior induction or not of DNA damage with etoposide. After 4 hours, cells were treated with cycloheximide (100 microgrames per ml) for 3 minutes. Then, cytoplasmic extracts were collected. Polysome fractionation in sucrose gradients (10-50% sucrose) was performed for isolation of mRNA associated to monosomes (fractions 4 to 7), light polysomes (fractions 8 to 10) or heavy polysomes (fractions 11 to 16). The ATM kinase inhibitor KU55933 was added 1 hour prior induction of DNA damage with etoposide.
Publication Title
Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples
GSE37562- Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
Transient siRNA-mediated knockdown of hnRNP L, followed by cycloheximide treatment to eliminate NMD.
Publication Title
Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function.
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
Comparison of control vs SAFB1 knockdown
Publication Title
iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function.
Sample Metadata Fields
Disease, Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
- NextSeq 500
Description
Human male infertility has long been associated with genetic defects that affect nuclear RNA binding proteins, yet what RNA targets these proteins control or why their absence causes infertility remain poorly defined. Here we find that genetic knockout of the mouse nuclear RNA binding protein gene Hnrnpgt causes azoospermia. Knockout male germ cells arrest during the highly transcriptionally active stage of meiotic prophase with altered meiotic nuclear RNA processing patterns. Hnrnpgt knockout most notably leads to the inclusion of previously unidentified cryptic exons that could otherwise disable gene function and poison the meiotic transcriptome. Hnrnpgt target genes include Esco1 and Kdm4d, which encode proteins that are important for chromosome function, and Hnrnpgt null germ cells have altered centromere clustering and H3K9me3 distribution patterns. Our data reveal a nuclear RNA processing programme that is critical for meiotic metaphase entry. Overall design: Gene expression profiling by RNA-Seq of mouse testes 18 days post-partum. Samples from C57BL/6 background, either wild type (n=3) or HnRNPGT Cre-Lox knockout (n=3).
Publication Title
An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 15 Downloadable Samples
- Illumina HiSeq 1000
Description
Post-transcriptional regulation of mRNA by the RNA binding protein HuR is required in B cells for the germinal centre reaction and for the production of class-switched antibodies in response to T-independent antigens. Transcriptome-wide examination of RNA isoforms, abundance and translation in HuR-deficient B cells, together with direct measurements of HuR-RNA interaction, revealed that HuR-dependent mRNA splicing affects hundreds of transcripts including the dihydrolipoyl succinyltransferase (Dlst), a subunit of the aketoglutaratedehydrogenase (aKGDH) enzyme. In the absence of HuR, defective mitochondrial metabolism results in high levels of reactive oxygen species and B cell death. Our study shows how post-transcriptional processes control the balance of energy metabolism required for B cell proliferation and differentiation. Overall design: Sequencing analysis of B cell transcriptome using Illumina TruSeq mRNA sample prep kit and Illumina platform. RNA was isolated from ex-vivo or LPS-activated (48h) splenic B cells from HuRflox/flox x mb1wt control or HuRflox/flox x mb1cre mice. 3-4 biological replicates per genotype and condition.
Publication Title
The RNA-binding protein HuR is essential for the B cell antibody response.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 3 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
The LH surge triggers dramatic transcriptional changes in genes associated with ovulation and luteinization. The present study investigated the spatiotemporal expression of nuclear factor interleukin-3 (NFIL3), a transcriptional regulator of the bZIP transcription factor superfamily, and its potential role in the ovary during the periovulatory period. NFIL3, also known as E4-binding protein 4 or NFIL3/E4BP4, was originally identified as a transcriptional repressor based on its DNA-binding activity at the promoter of the gene encoding the adenovirus E4 protein. Immature female rats were injected with PMSG, treated with hCG, and ovaries or granulosa cells were collected at various times after hCG. Nfil3 mRNA was highly induced both in intact ovaries and granulosa cells after hCG treatment. In situ hybridization demonstrated that Nfil3 mRNA was highly induced in theca-interstitial cells at 4-8 h after hCG, localized to granulosa cells at 12 h, and decreased at 24 h. Over-expression of NFIL3 in granulosa cells inhibited the induction of prostaglandin-endoperoxide synthase 2 (Ptgs2), progesterone receptor (Pgr), epiregulin (Ereg), and amphiregulin (Areg) and down regulated levels of prostaglandin E2. The inhibitory effect on Ptgs2 induction was reversed by NFIL3 siRNA treatment. In theca-interstitial cells the expression of hydroxyprostaglandin dehydrogenase 15-(NAD) (Hpgd) was also inhibited by NFIL3 over-expression. Data from luciferase assays demonstrated that NFIL3 over-expression decreased the induction of the Ptgs2 and Areg promoter activity. EMSA and ChIP analyses indicated that NFIL3 binds to the promoter region containing the DNA binding sites of CREB and C/EBP?. In summary, hCG induction of NFIL3 expression may modulate the process of ovulation and theca-interstitial and granulosa cell differentiation by regulating expression of PTGS2, PGR, AREG, EREG, and HPGD, potentially through interactions with CREB and C/EBP? on their target gene promoters.
Publication Title
A role for nuclear factor interleukin-3 (NFIL3), a critical transcriptional repressor, in down-regulation of periovulatory gene expression.
Sample Metadata Fields
Sex
View Samples- Mus musculus
- 44 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Type 1 diabetes is a multigenic disease caused by T-cell mediated destruction of the insulin producing -cells. Although conventional (targeted) approaches of identifying causative genes have advanced our knowledge of this disease, many questions remain unanswered. Using a whole molecular systems study, we unraveled the genes/molecular pathways that are altered in CD4 T-cells from young NOD mice prior to insulitis (lymphocytic infiltration into the pancreas). Many of the CD4 T-cell altered genes lie within known diabetes susceptibility regions (Idd), including several genes in the diabetes resistance region Idd13 and two genes (Khdrbs1 and Ptp4a2) in the CD4 T-cell diabetogenic activity region Idd9/11. Alterations involved apoptosis/cell proliferation and metabolic pathways (predominant at 2 weeks), inflammation and cell signaling/activation (predominant at 3 weeks), and innate and adaptive immune responses (predominant at 4 weeks). We identified several factors that may regulate these abnormalities: IRF-1, HNF4A, TP53, BCL2L1 (lies within Idd13), IFNG, IL4, IL15, and prostaglandin E2, which were common to all 3 ages; AR and IL6 to 2 and 4 weeks; and Interferon (IFN-I) and IRF-7 to 3 and 4 weeks. Others were unique to the various ages (e. g. MYC, JUN, and APP to 2 weeks; TNF, TGFB1, NFKB, ERK, and p38MAPK to 3 weeks; and IL12 and STAT4 to 4 weeks). Our data suggest that diabetes resistance genes in Idd13 and Idd9/11, and BCL2L1, IL6-AR and IFNG-IRF-1-IFN-I/IRF-7-IL12 pathways play an important role in CD4 T-cells in the early pathogenesis of autoimmune diabetes. Thus, the alternative approach of investigation at the molecular systems level has captured new information, which combined with validation studies, offers the opportunity to test hypotheses on the role played by the genes/molecular pathways identified in this study, to understand better the mechanisms of autoimmune diabetes in CD4 T-cells, and to develop new therapeutic strategies for the disease.
Publication Title
Molecular pathway alterations in CD4 T-cells of nonobese diabetic (NOD) mice in the preinsulitis phase of autoimmune diabetes.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Iron-deficiency repsonses in Arabidopsis are controlled by several bHLH transcription factors. FIT, for example has been shown to direct iron-uptake responses. However, the role of shoot and root expressed genes bHLH100 and bHLH101 has not be clarified. We used microarray to study what genes might be miss-regulated in the double mutant bhlh100/bhlh101 background
Publication Title
Arabidopsis bHLH100 and bHLH101 control iron homeostasis via a FIT-independent pathway.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples