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accession-icon GSE39877
Expression data from skeletal muscles of flies with muscle-specific overexpression of Foxo or Mnt
  • organism-icon Drosophila melanogaster
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-39877

Sample Metadata Fields

Sex, Specimen part, Treatment

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accession-icon SRP061691
In vivo transcriptional activation using CRISPR-Cas9 in Drosophila
  • organism-icon Drosophila melanogaster
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina 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.

Alternate Accession IDs

GSE71430

Sample Metadata Fields

Specimen part, Treatment, Subject

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accession-icon SRP132041
CG7358 mutant Drosophila melanogaster sequencing
  • organism-icon Drosophila melanogaster
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina 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.

Alternate Accession IDs

GSE110047

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE73354
Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization
  • organism-icon Drosophila melanogaster
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-73354

Sample Metadata Fields

Cell line

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accession-icon SRP064105
Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization [RNA-Seq]
  • organism-icon Drosophila melanogaster
  • sample-icon 32 Downloadable Samples
  • Technology Badge IconIllumina 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.

Alternate Accession IDs

GSE73353

Sample Metadata Fields

Cell line, Subject

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accession-icon GSE73335
Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization [Microarray Expression]
  • organism-icon Drosophila melanogaster
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-73335

Sample Metadata Fields

Cell line

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accession-icon SRP190499
Time series RNA-seq analyses of Drosophila S2R+ cells after insulin stimulation
  • organism-icon Drosophila melanogaster
  • sample-icon 24 Downloadable Samples
  • Technology Badge IconIllumina 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.

Alternate Accession IDs

GSE129292

Sample Metadata Fields

Specimen part, Treatment, Subject, Time

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accession-icon GSE31702
CD4+ T cell gene expression in B6 vs B6.Sle1c2 mice
  • organism-icon Mus musculus
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-31702

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon SRP001305
Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform
  • organism-icon Drosophila melanogaster
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina 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.

Alternate Accession IDs

GSE17171

Sample Metadata Fields

Cell line, Subject

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accession-icon SRP056148
Sex hormones have pervasive effects on thymic epithelial cells
  • organism-icon Mus musculus
  • sample-icon 29 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The goal of our study was to evaluate at the systems-level, the effect of sex hormones on thymic epithelial cells (TECs). To this end, we sequenced the transcriptome of cortical and medullary TECs (cTECs and mTECs) from three groups of 6 month-old mice: males, females and males castrated at four weeks of age. In parallel, we analyzed variations in the size of TEC subsets in those three groups between 1 and 12 months of age. We report that sex hormones have pervasive effects on the transcriptome of TECs: the number of differentially expressed genes was 1,440 in cTECs and 1,783 in mTECs. Sexual dimorphism was particularly conspicuous in cTECs. Male cTECs displayed low proliferation rates that correlated with low expression of Foxn1 and its main targets. Furthermore, male cTECs expressed relatively low levels of genes instrumental in thymocyte expansion (e.g., Dll4) and positive selection (Psmb11 and Ctsl). Nevertheless, cTECs were more abundant in males than females. Accumulation of cTECs in males correlated with differential expression of genes regulating cell survival and cell differentiation. Unexpectedly, we observed that female and male sex hormones repressed promiscuous gene expression in mTECs. Since sex hormones did not affect the expression of Aire per se, they must impinge on the activity of unidentified regulator(s) of promiscuous gene expression in mTECs. The sexual dimorphism of TECs highlighted here may be mechanistically linked to the well-recognized sex differences in susceptibility to infections and autoimmune diseases. Overall design: Cortical and medullary thymic epithelial cells from 6 month-old male, female and castrated male mice were sequenced in 3 replicates (but only 2 replicates for castrated male mTECs).

Publication Title

Thymic Mesenchymal Cells Have a Distinct Transcriptomic Profile.

Alternate Accession IDs

GSE66873

Sample Metadata Fields

No sample metadata fields

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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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