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GSE39877
Drosophila melanogaster
9 Downloadable Samples
Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Skeletal muscle senescence influences whole organism aging, yet little is known on the relay of pro-longevity signals from muscles to other tissues. We performed an RNAi screen in Drosophila for muscle-released cytokines (?myokines?) regulating lifespan and identified Myoglianin, the homolog of human Myostatin. Myoglianin is induced in skeletal muscles by the transcription factor Mnt and together they constitute an inter-organ signaling module that regulates lifespan, age-related muscle dysfunction, and protein synthesis across aging tissues. Both Mnt and Myoglianin activate already in young age the protective decline in protein synthesis that is typical of old age, while knock-down of Myoglianin impairs this process. Mechanistically, Mnt decreases the expression of nucleolar components in muscles while also decreasing nucleolar size in distant tissues via Myostatin/p38 MAPK signaling. Our results highlight a myokine-dependent inter-organ longevity pathway that coordinates nucleolar function and protein synthesis across aging tissues.
Publication Title
Intertissue control of the nucleolus via a myokine-dependent longevity pathway.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Drosophila melanogaster
- 8 Downloadable Samples
Illumina HiSeq 2000
Description
Identifying putative transcription factor target genes by combining CRISPR/Cas9-based transcriptional activation with RNAseq in Drosophila S2R+ cells. This study focuses on the transcription factors Twist and Snail, singly and together. Overall design: RNA from Drosophila cells following CRISPR/Cas9-based activation of Twist, Snail, or Twist and Snail together, compared with non-targeting sgRNA. Two biological replicates for each experiment
Publication Title
In Vivo Transcriptional Activation Using CRISPR/Cas9 in Drosophila.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
To understand the function of gene CG7358 in Drosophila melanogaster, including indentification of those genes whose expression levels or alternative splicing are affected by CG7358. Overall design: 6 samples are analyzed, including 3 replicates for CG7358 mutant and the other 3 for wild type fly
Publication Title
Xio is a component of the <i>Drosophila</i> sex determination pathway and RNA <i>N</i><sup>6</sup>-methyladenosine methyltransferase complex.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Drosophila melanogaster
- 18 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization.
Sample Metadata Fields
Cell line
View Samples- Drosophila melanogaster
- 32 Downloadable Samples
- Illumina HiSeq 2000
Description
To characterize the sequence of events associated with RasV12 immortalization of Drosophila embryonic cells, we generated transcriptional time series during cell line establishment, from primary cultures until passage (P) 19. Overall design: We generated three transcriptional time series from three cell lines (R1, R4 and R5) by sampling the cultures at successive stages, early (P2-4), intermediate (P4-11), and late (P16-19), characterized by different passage times. Time points for the R1 time-series were: P2, P3, P4, P5, P7, P8, P10, P11, P16, P17 and P19; for the R4 time-series: P2, P3, P4, P5, P6, P7, P9, P11, P12, P16, P17 and P19; and for the R5 time-series: P2, P3, P4, P6, P7, P8, P16, P17 and P19
Publication Title
Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization.
Sample Metadata Fields
Cell line, Subject
View Samples- Drosophila melanogaster
- 18 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
To characterize the sequence of events associated with RasV12 immortalization of Drosophila embryonic cells, we generated transcriptional time series during cell line establishment, from primary cultures until passage (P) 19.
Publication Title
Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization.
Sample Metadata Fields
Cell line
View Samples- Drosophila melanogaster
- 24 Downloadable Samples
- Illumina HiSeq 4000
Description
Purpose: identifying genes responding to insulin stimulation in S2R+ cells through whole transcriptome RNA-seq analyses Methods: Total RNA was extracted from S2R+ cells using TRIzol® reagent (Invitrogen). After assessing RNA quality with an Agilent Bioanalyzer, libraries were constructed with Illumina TruSeq mRNA Library Prep Kit , libraries were sequenced using an Illumina HiSeq 4000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center). Results: Using an time series data analysis workflow incorporating polynormials , we identified 1254 temproally differentially expressed genes responding to insulin stimulation in the S2R+ cells. Overall design: the pre-starved S2R+ cells ( with serum free medium) were stimulated with insulin; triplicate samples were collected at basline and every 20minutes time interval up to three hours; transcriptome profiling
Publication Title
Interspecies analysis of MYC targets identifies tRNA synthetases as mediators of growth and survival in MYC-overexpressing cells.
Sample Metadata Fields
Specimen part, Treatment, Subject, Time
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
- Illumina Genome Analyzer II
Description
Drosophila melanogaster expresses three classes of small RNAs, which are classified according to their mechanisms of biogenesis. MicroRNAs are ~22-23-nt, ubiquitously expressed small RNAs that are sequentially processed from hairpin-like precursors by Drosha/Pasha and Dcr-1/Loquacious complexes. MicroRNAs usually associate with AGO1 and regulate the expression of protein-coding genes. Piwi-interacting RNAs (piRNAs) of ~24-28-nt associate with Piwi-family proteins and can arise from single-stranded precursors. piRNAs function in transposon silencing and are mainly restricted to gonadal tissues. Endo-siRNAs are found in both germline and somatic tissues. These ~21-nt RNAs are produced by a distinct Dicer, Dcr-2, and do not depend on Drosha/Pasha complexes. They predominantly bind to AGO2 and target both mobile elements and protein-coding genes. Surprisingly, a subset of endo-siRNAs strongly depend for their production on the dsRNA-binding protein Loquacious (Loqs), thought generally to be a partner for Dcr-1 and a co-factor for miRNA biogenesis. Endo-siRNA production depends on a specific Loqs isoform, Loqs-PD, which is distinct from the one, Loqs-PB, required for the production of microRNAs. Paralleling their roles in the biogenesis of distinct small RNA classes, Loqs-PD and Loqs-PB bind to different Dicer proteins, with Dcr-1/Loqs-PB complexes and Dcr-2/Loqs-PD complexes driving microRNA and endo-siRNA biogenesis, respectively. Small RNA profiling by high throughput sequencing Overall design: Total RNA was isolated using Trizol reagent (Invitrogen) and size-fractionated by PAGE into 19-24nt. These were independently processed and sequenced using the Illumina GAII platform. In total, six libraries were analyzed.
Publication Title
Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina Genome Analyzer II
Description
Regulation of genes that initiate and amplify inflammatory programs of gene expression is achieved by signal-dependent exchange of co-regulator complexes that function to read, write and erase specific histone modifications linked to transcriptional activation or repression. Here, we provide evidence for an unexpected role of trimethylated histone H4 lysine 20 (H4K20me3) as a repression checkpoint that restricts expression of toll like receptor 4 (TLR4) target genes in macrophages. H4K20me3 is deposited at the promoters of a subset of these genes by the SMYD5 histone methyltransferase through its association with NCoR co-repressor complexes. Signal-dependent erasure of H4K20me3 is required for effective gene activation and is achieved by NF-KB-dependent delivery of the histone demethylase PHF2. Liver X receptors antagonize TLR4-dependent gene activation by maintaining NCoR/SMYD5-mediated repression. These findings reveal a histone H4K20 tri-methylation/de-methylation strategy that integrates positive and negative signaling inputs that control immunity and homeostasis. Overall design: mRNA profiling from thioglycollate-elicited mouse macrophages treated with siRNA for Control, Smyd5 and Phf2 for 48 hours followed by 4 hours of LPS treatment.
Publication Title
Control of proinflammatory gene programs by regulated trimethylation and demethylation of histone H4K20.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Sle1c is a sublocus of the NZM2410-derived Sle1 major susceptibility locus. We have previously shown that Sle1c contributes to lupus pathogenesis by conferring CD4+ T cell-intrinsic hyperactivation and increased susceptibility to chronic graft-versus-host disease (cGVHD) that mapped to the centromeric portion of the locus. In this study, we have refined the centromeric sublocus to a 675Kb interval, termed Sle1c2. Recombinant congenic strains expressing Sle1c2 exhibited a T cell-intrinsic CD4+ T cell hyperactivation and cGVHD susceptibility, similar to mice with the parental Sle1c.
Publication Title
Murine lupus susceptibility locus Sle1c2 mediates CD4+ T cell activation and maps to estrogen-related receptor γ.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples