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SRP001305
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- Pan troglodytes, Homo sapiens
- 23 Downloadable Samples
Sentrix HumanRef-8 v2 Expression BeadChip
Description
The signaling pathways orchestrating both the evolution and development of language in the human brain remain unknown. To date, the transcription factor FOXP2 is the only gene implicated in Mendelian forms of human speech and language dysfunction1,2. It has been proposed, that the amino acid composition in the human variant of FOXP2 has undergone accelerated evolution, and this change occurred around the time of language emergence in humans3,4. However, this remains controversial, and whether the acquisition of these amino acids in human FOXP2 has any functional consequence in human neurons remains untested. Here, we demonstrate that these two amino acids confer new functionality in terms of differential transcriptional regulation, and extend these observations to in vivo brain, showing that several of the differential FOXP2 targets significantly overlap with genes different between human and chimpanzee brain. We also identify novel relationships among the differentially expressed genes with additional critical regulators of neuronal development. These data provide support for the functional relevance of changes that occur on the human lineage by showing that the two amino acids unique to human FOXP2 can lead to significant differences in gene expression patterns across brain evolution, with direct consequences for human brain development and disease. Since FOXP2 has an important role in the use of language in humans, the identified targets may have a critical function in the development and evolution of language circuitry in humans.
Publication Title
Human-specific transcriptional regulation of CNS development genes by FOXP2.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- IlluminaGenomeAnalyzer
Description
Comprehensive RNA-seq experiments in control and PRMT5 and WDR77 shRNA infected cells delineate the role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis Overall design: RNA-seq was used to measure gene expression levels in scrambled control, PRMT5 and WDR77 short hairpin RNA (shRNA) infected human breast cancer cells
Publication Title
The PRMT5/WDR77 complex regulates alternative splicing through ZNF326 in breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
- IlluminaGenomeAnalyzer
Description
Comprehensive RNA-seq experiments in DMSO and HPTB (inhibitor of PRMT5) treated cells delineate the role of PRMT5 complex in promoting breast cancer oncogenesis Overall design: RNA-seq was used to measure gene expression levels in DMSO and HPTB (inhibitor of PRMT5) treated human breast cancer cells
Publication Title
The PRMT5/WDR77 complex regulates alternative splicing through ZNF326 in breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Illumina HiSeq 4000
Description
Deposition of histone variant H2A.Z by the SWR1 chromatin-remodeling complex is critical for the appropriate expression of many genes in eukaryotes, yet, despite its importance, the composition of the Arabidopsis SWR1 complex has not been thoroughly analyzed. Here we have identified the interacting partners of a conserved Arabidopsis SWR1 subunit, actin-related protein 6 (ARP6). We isolated 9 predicted components, identifying subunits implicated in histone acetylation and interacting partners implicated in chromatin biology. We found that the methyl-CpG-binding domain 9 (MBD9) subunit functioned synergistically with ARP6 to control flowering time. MBD9, in combination with ARP6, was involved in the SWR1-mediated incorporation of the majority of H2A.Z. MBD6 was further required for deposition of H2A.Z at a distinct subset of loci. MBD9 was preferentially bound to nucleosome-depleted regions at the 5' of genes containing high levels of activating histone marks. Our data suggests a model for MBD9 in recruiting the SWR1 complex to open chromatin of actively transcribing genes. Overall design: Total RNA was extracted from 13 DAG shoots grown on 1%MS supplemented with 1% sucrose under long day conditions. Four replicates, grown on separate plates were collected for each genotype. Each replicate conisted of three seedlings. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo). For RNA-Seq, 1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina).
Publication Title
Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- IlluminaHiSeq2000
Description
hnRNP M and Rbfox proteins are subunits of the Large Assembly of Splicing Regulators (LASR). The purpose of this study is to investigate how these two splicing factors affect each others'' role in regulating splice site choices in pre-mRNA. hnRNP M is knocked down by RNAi in Flp-In T-REx 293 cells (Invitrogen), whereas Rbfox1 is expressed inducibly under tetracycline control from construct integrated into the genome at the FRT site. Using this system, splicing and expression profiles of cells expressing and/or lacking these proteins are compared on a whole genome level by RNA-seq technology. Overall design: The experiment was performed in Flp-In T-REx 293, Rbfox2 knockout cells (clone 7), in which the Rbfox2 ORF was disrupted in the first constitutive exon (exon 3), thus these cells do not produce endogenous Rbfox protein. In addition to this, cells expressing Flag-tagged Rbfox1 under tetracycline control from a pcDNA5/FRT/TO construct inserted into the FRT site were generated. hnRNP M was knocked down to 10% of the normal levels by transient expression of two RNA hairpins targeting separate 3'' UTR regions. A non-targeting hairpin served as control. Four separate cell populations: not expressing Rbfox with normal levels fo hnRNP M; expressing Rbfox1 with normal hnRNP M levels; not expressing Rbfox, hnRNP M expression reduced by 90%; expressing Rbfox1, hnRNP M reduced by 90% were each grown independently in triplicates. Total RNA was collected from these cells and further treated with DNase I to avoid DNA contamination. Illumina TruSeq stranded mRNA kit was used to generate strand-specific libraries. These libraries were subjected to 50bp paired-end sequencing (Illumina HiSeq2000 platform). In parallel, a fraction of each cell population was lysed in RIPA buffer for protein analysis.
Publication Title
Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 10 Downloadable Samples
- Illumina HiSeq 2000
Description
Cbx3 (HP1?) that is a member of the heterochromatin protein 1 family play important roles in development and differentiation. To determine the regulatroy mechanisms of Cbx3 during neural differentiation from ESCs to NPCs, we performed RNA-seq analysis of ESCs or ESC-derived NPCs depleted for Cbx3 or Cbx3-assocatied Mediator subunit Med26. Overall design: ESCs or ESC-derived NPCs were transfected with control siRNA targeting to luciferase or siRNA mediated knockdown of Cbx3 or Med26. RNAs were extracted from control or knockdown group and subjected to library preparation and deep sequencing.
Publication Title
Cbx3 maintains lineage specificity during neural differentiation.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 7 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Gene Expression in d5 wound-edge tissues of MFG-E8 WT and MFG-E8 KO mice
Publication Title
Correction of MFG-E8 Resolves Inflammation and Promotes Cutaneous Wound Healing in Diabetes.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 21 Downloadable Samples
- IlluminaHiSeq2500
Description
We identified a novel recurrent genetic lesion in T-LGL. Mutations of the tumour suppressor gene TNFAIP3 causing amino-acid exchanges or protein truncations were seen in 3/39 cases (8%). Overall design: RNA sequencing (Illumina HiSeq 2500) of 5 index patients with paired tumor and non-tumor samples.
Publication Title
Recurrent alterations of TNFAIP3 (A20) in T-cell large granular lymphocytic leukemia.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 69 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Mind-body practices that elicit the relaxation response (RR) have been used worldwide for millennia to prevent and treat disease. The RR is believed to be the counterpart to stress response and is characterized by decreased oxygen consumption, increased exhaled nitric oxide, and reduced psychological distress. Individuals experiencing chronic psychological stress have the opposite pattern of physiology and a characteristic transcriptional profile. We hypothesized that consistent, long-term practice of RR techniques results in characteristic changes in gene expression. We tested this hypothesis by assessing the transcriptional profile of whole blood in healthy, long-term practitioners of daily RR practice (group M) in comparison to healthy controls (group N1). The signature obtained has been validated on new subject data.
Publication Title
Genomic counter-stress changes induced by the relaxation response.
Sample Metadata Fields
No sample metadata fields
View Samples