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MetabolomicsA multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6 (NMR assay)

Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that capt...

2020-02-14 | MTBLS1320 | MetaboLights
TranscriptomicsCytoplasmic Assembly and Selective Nuclear Import of Arabidopsis ARGONAUTE4/siRNA Complexes
Here we profiled small RNAs from whole cell, cytoplasmic and nuclear extracts from three-week-old Arabidopsis seedlings. We unexpectedly found that nuclear functional hc-siRNAs are predominantly present in the cytoplasm. Samples from Arabidopsis thaliana whole cell, cytoplasmic and nuclear extract...
ORGANISM(S): Arabidopsis thaliana 
2012-07-12 | E-GEOD-36500 | biostudies-arrayexpress
TranscriptomicsTMV-derived Small RNAs Reveals Role for Arabidopsis thaliana RNA-dependent RNA Polymerases in Viral siRNA Biogenesis
Using a crucifer-infecting strain of Tobacco Mosaic Virus (TMV-Cg) and Arabidopsis thaliana as a model system, we analyzed the viral small RNA profile in wild-type plants as well as rdr mutants by applying small RNA deep sequencing technology. Over 100,000 TMV-Cg-specific small RNA reads, mostly of...
ORGANISM(S): Youcai mosaic virus 
2009-03-24 | E-GEOD-12918 | biostudies-arrayexpress
TranscriptomicsDeep Sequencing of Human Nuclear and Cytoplasmic Small RNAs Reveals an Unexpectedly Complex Subcellular Distribution of miRNAs and tRNA 3' Trailers
Background: MicroRNAs (miRNAs) are 22-nt small non-coding regulatory RNAs that have generally been considered to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs localize to and function in the nucleus. Methodology/Pr...
ORGANISM(S): Homo sapiens 
2010-07-14 | E-GEOD-22918 | biostudies-arrayexpress
TranscriptomicsNuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans
We have recently shown that transcription initiation RNAs (tiRNAs) are derived from sequences downstream of transcription start sites. Here we report the identification of a second class of nuclear-specific ~17-18 nucleotide small RNA whose 3M-bM-^@M-^Y ends map precisely to the splice donor site of...
ORGANISM(S): Homo sapiens 
2010-07-01 | E-GEOD-20664 | biostudies-arrayexpress
TranscriptomicsThe little elongation complex (LEC) regulates small nuclear RNA transcription
The Eleven-nineteen Lysine-rich Leukemia (ELL)-containing Super Elongation Complex (SEC) containing P-TEFb is a key regulator in the expression of HOX genes in Mixed Lineage Leukemia (MLL)-based leukemia. We have identified an SEC-like complex in Drosophila, as well as a distinct ELL-containing comp...
ORGANISM(S): Drosophila melanogaster 
2011-12-22 | E-GEOD-32120 | biostudies-arrayexpress
TranscriptomicsRNA profiling in mouse haemopoiesis
RNA profiling of mouse haemopoetic lineages RNA profiling of mouse haemopoetic lineages. For the isolation and sequencing of ouse granulocyte nuclei, bone marrow from C57BL/6J was harvested from the femur, tibia and spine using a mortar and pestle in PBS supplemented with 2% (v/v) FCS and mature gra...
ORGANISM(S): Mus musculus 
2010-07-01 | E-GEOD-20683 | biostudies-arrayexpress
ProteomicsProteins that interact with PHAX and UAP56 from HeLa nuclear extracts
HeLa nuclear extracts and RNase A were incubated with GST-PHAX and FLAG-UAP56 in the presence of ATP. The mixture was subjected to immunoprecipitation. The bound proteins were eluted with FLAG peptide. The eluate was subjected to GST pull-down. The bound proteins were treated with HRV 3C protease. S...
ORGANISM(S): Homo Sapiens (human) 
2025-06-28 | PXD053480 | JPOST Repository
TranscriptomicsEndogenous shRNAs, siRNAs, and Other Microprocessor-independent, Dicer-dependent Small RNAs in Mouse ES Cells
Canonical microRNAs (miRNAs) require two processing steps: the first by the Microprocessor, a complex of DGCR8 and Drosha, and the second by Dicer. dgcr8delta/delta mouse embryonic stem cells (mESCs) have less severe phenotypes than dicer1delta/delta mESCs, suggesting a physiological role for Microp...
ORGANISM(S): Mus musculus 
2008-09-09 | E-GEOD-12521 | biostudies-arrayexpress
TranscriptomicsProfile of small RNA transcriptome during cortical development in the Rat
Small non-coding RNAs play important roles in regulating gene expression during development and disease. However, a comprehensive analysis of small RNAs in developing brain is largely lacking. By using next-generation sequencing technique, we carried out a systematic analysis of small RNA transcript...
ORGANISM(S): Rattus norvegicus 
2012-06-25 | E-GEOD-27576 | biostudies-arrayexpress
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