HeLa cell polyA- RNA-seq
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Karla Neugebauer
PROVIDER: E-GEOD-58450 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Coilin iCLIP data revealed 42 novel human snoRNAs of intronic origin. To validate their expression and estimate abundance of novel and annotated snoRNAs, we performed RNA-seq on polyA- and rRNA-depleted RNA isolated from HeLa cells. Results show that expression of novel snoRNAs is comparable to the previously annotated snoRNAs.
2014-11-06 | GSE58450 | GEO
Project description:We seqeunced mRNA from the bacterial pathogen 'Candidatus Liberibacter solanacearum" during its association with the psyllid vector Bactericera cockerelli. Total RNA was purified from psyllids, insect and bacterial rRNAs were depleted. PolyA RNA was purified using Dynabeads. PolyA purified RNA and depleted RNA were sequenced.
2014-07-21 | E-GEOD-57808 | biostudies-arrayexpress
Project description:The paired-end next-generation sequencing of all small RNAs of less than 200 nucleotides in length from four different human cell lines (SKOV3ip1, MCF-7, BJ-Tielf, INOF) allowed us to determine the exact sequence(s) and variations of human box C/D snoRNAs (small nucleolar RNAs), revealing processing patterns of this class of molecules. Two distinct groups of box C/D snoRNAs were identified based on the position of their ends with respect to their characteristic boxes and the terminal base pairing potential. Short box C/D snoRNAs start sharply 4 or 5 nucleotides upstream of their box C and end 2 or 3 nucleotides downstream of their box D. In contrast, long box C/D snoRNAs start 5 or 6 nucleotides upstream of their box C and end 4 or 5 nucleotides downstream of their box D, increasing the likelihood of formation of a k-turn between their boxes C and D. Sequencing of SKOV3ip1 cells following the depletions of NOP58, a core box C/D snoRNA-binding protein and of RBFOX2, a splicing factor, shows that the short box C/D snoRNA forms are significantly more affected by the depletion of RBFOX2 while the long snoRNA forms, which display more canonical box C/D snoRNA features, are significantly more affected by the depletion of NOP58. Together the data suggest that box C/D snoRNAs are divided into at least two groups of RNA with distinct maturation and functional preferences. Small RNAs (<200 nucleotides) were isolated from different human cell lines that were either untreated or depleted of NOP58 or RBFOX2 using specific siRNAs. The resulting libraries were multiplexed and paired-end sequenced using Illumina HiSeq.
2014-07-01 | E-GEOD-55946 | biostudies-arrayexpress
Project description:To investigate location of Cajal bodies (CB) inside the cell nucleus, we created a stable cell line expressing the GFP version of CB-marker protein coilin at endogenous levels and performed ChIP-seq with anti-EGFP antibody. ChIP-seq revealed close association of CBs wih U3 genes, snRNA genes and histone genes in histone cluster 1 and 2. 1 biological replicate of coilin ChIP-seq and input sample
2014-11-06 | E-GEOD-58449 | biostudies-arrayexpress
Project description:Our ChIP resuls suggested that coilin association with U3, snRNA and histone genes might be dependent on coilin-RNA interaction. We used iCLIP of coilin-GFP expressed in HeLa and P19 cell lines at endogenous levels to identify coilin RNA targets and investigate RNA-binding specificity. P19 cells expressing GFP fused to a nuclear localization signal (GFP-NLS) was used as a negative control. iCLIP results revealed that coilin binds several classes of ncRNA including snRNAs, U3 snoRNA and scaRNAs. Interestlignly the majority of coilin targets were intronic snoRNAs, suggesting a novel role of CBs in snoRNA biogenesis. 5 biological replicates from P19 and 2 biological replicates from HeLa cells after UV-crosslinking. Negative control samples prepared from GFP-NLS fusion protein are stored uder accession E-MTAB-747.
2014-11-06 | E-GEOD-58448 | biostudies-arrayexpress
Project description:Our data suggest that all SR proteins contribute to mRNA export via NXF1. To identify endogenous export targets we depleted all seven SR proteins individually from P19 WT cells prepared cytoplasmic fractions. We sequenced the cytoplasmic fraction and as a control whole celll RNA from the identical sample. Knockdown of seven SR Proteins plus control, total RNA and cytoplasmic RNA, polyA+ enriched, 2 biological replicates per condition, 2 technical replicates per condition
2016-03-07 | E-GEOD-69733 | biostudies-arrayexpress
Project description:Massive-scale RNA-seq on rRNA-depleted samples allowed us to survey in a specific cell type, affected in Down syndrome, the complete set of coding and non-coding RNA species - emerging as novel contributors to pathogenic mechanisms - to an unprecedented level of resolution and sensitivity. In particular, we demonstrated the deregulation of crucial gene pathways by quantitatively measuring the expression of known RefSeq genes. Moreover, we identified novel regions of active transcription falling outside already annotated loci, and investigated also the expression of non-polyadenilated long, as well as short, non coding RNAs. In addition, we found novel splice isoforms for a large subset of genes, and novel extended UTRs, both 5' and 3', for known genes - possibly representing novel miRNA targets or regulatory sites for gene transcription, respectively. 2 RNA samples examined: 1 euploid control and 1 trisomic sample.
2011-05-04 | E-GEOD-27443 | biostudies-arrayexpress
Project description:The Microprocessor complex (DGCR8/Drosha) is required for microRNA (miRNA) biogenesis but also binds and regulates the stability of several types of cellular RNAs. Of particular interest, DGCR8 controls the stability of mature small nucleolar RNA (snoRNA) transcripts independently of Drosha, suggesting the existence of alternative DGCR8 complex/es with other nucleases to process a variety of cellular RNAs. Here, we found that DGCR8 co-purifies with subunits of the nuclear exosome, preferentially associating with its hRRP6-containing nucleolar form. Importantly, we demonstrate that DGCR8 is essential for the recruitment of the exosome to snoRNAs and to human telomerase RNA. In addition, we show that the DGCR8/exosome complex controls the stability of the human telomerase RNA component (hTR/TERC). Altogether, these data suggests that DGCR8 acts as a novel adaptor to recruit the exosome complex to structured RNAs and induce their degradation. [i] Examination of the RNA binding profile of hRRP6 (also known as EXOSC10) via iCLIP. [ii] HeLa cells were transiently depleted of hRRP6 or DGCR8 using siRNAs. For a control an non-targetting (siNon) siRNA was used. Three biological replicates of each samples were sent for RNA sequencing.
2015-12-10 | E-GEOD-73376 | biostudies-arrayexpress
Project description:Background RNA sequencing (RNA-seq) is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the proliferation of library construction methods, understanding the bias it introduces is incomplete but critical to realizing its value. Results Here we present a method, in vitro transcription sequencing (IVT-seq), for identifying and assessing the technical biases in RNA-seq library generation and sequencing at scale. We created a pool of > 1000 in vitro transcribed (IVT) RNAs from a full-length human cDNA library and sequenced them with poly-A and total RNA-seq, the most common protocols. Because each cDNA is full length and we show IVT is incredibly processive, each base in each transcript should be equivalently represented. However, with common RNA-seq applications and platforms, we find ~50% of transcripts have > 2-fold and ~10% have > 10-fold differences in within-transcript sequence coverage. Strikingly, we also find > 6% of transcripts have regions of high, unpredictable sequencing coverage, where the same transcript varies dramatically in coverage between samples, confounding accurate determination of their expression. To get at causal factors, we used a combination of experimental and computational approaches to show that rRNA depletion is responsible for the most significant variability in coverage and that several sequence determinants also strongly influence representation. Conclusions In sum, these results show the utility of IVT-seq in promoting better understanding of bias introduced by RNA-seq and suggest caution in its interpretation. Furthermore, we find that rRNA-depletion is responsible for substantial, unappreciated biases in coverage. Perhaps most importantly, these coverage biases introduced during library preparation suggest exon level expression analysis may be inadvisable. 5 rRNA-depleted samples with duplicates, 1 polyA selected, 1 total RNA, and 1 plasmid library all without replicates.
2014-05-21 | E-GEOD-50445 | biostudies-arrayexpress
Project description:To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted total RNA were harvested across six developmental stages and subjected to high throughput sequencing. The maternally loaded transcriptome is highly diverse and consists of both polyadenylated and deadenylated transcripts. Many maternal genes show peak expression in the oocyte and include genes which are known to be the key regulators of events like oocyte maturation and fertilization. Of all the transcripts that increase in abundance between an early blastula and larval stages, about 30% of the embryonic genes are induced by fourfold or more by the late blastula stage and another 35% by late gastrulation. Using a gene model validation and discovery pipeline, we identified novel transcripts, the majority of which show hallmarks of being long non-coding RNAs both in terms of their coding potential and gene structure. Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development
2013-11-12 | E-GEOD-43652 | biostudies-arrayexpress