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Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human Embryonic Stem cells

ABSTRACT: Cytoplasmic polyadenylated RNA from human embryonic stem cells (HES2) was separated on a 1.2% agarose and gel slices were excised corresponding to the following sizes: 0 to 0.5 kb; 0.5-2 kb; 2-3.5 kb; 3.5-6.5 kb and 6.5-20+ kb. Slices were dissolved and extracted RNA (1% of each fraction) was run on the Agilent Bioanalyser (Agilent) to confirm the correct size distribution and yield. Library molecules were clonally amplified onto one micron magnetic beads according to the SOLiD Template Bead Preparation protocol and sequenced using a SOLiD Analyzer according to manufacturer's instructions. Human ES cells size fractionated mRNA

ORGANISM(S): Homo sapiens

SUBMITTER: Sean Grimmond

PROVIDER: E-GEOD-24355 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome.

Mercer Tim R TR Dinger Marcel E ME Bracken Cameron P CP Kolle Gabriel G Szubert Jan M JM Korbie Darren J DJ Askarian-Amiri Marjan E ME Gardiner Brooke B BB Goodall Gregory J GJ Grimmond Sean M SM Mattick John S JS

Genome research 20101102 12

The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo cleavage and secondary 5' capping. Here, we show that post-transcriptional cleavage of RNA contributes to the diversification of the transcriptome by generating a range of small RNAs and long coding and noncoding RNAs. Using genome-wide histone ...[more]

PMID: 21045082

Publication: 1/2

Similar Datasets

Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human Embryonic Stem cells

Project description:Cytoplasmic polyadenylated RNA from human embryonic stem cells (HES2) was separated on a 1.2% agarose and gel slices were excised corresponding to the following sizes: 0 to 0.5 kb; 0.5-2 kb; 2-3.5 kb; 3.5-6.5 kb and 6.5-20+ kb. Slices were dissolved and extracted RNA (1% of each fraction) was run on the Agilent Bioanalyser (Agilent) to confirm the correct size distribution and yield. Library molecules were clonally amplified onto one micron magnetic beads according to the SOLiD Template Bead Preparation protocol and sequenced using a SOLiD Analyzer according to manufacturer's instructions.

2010-10-20 | GSE24355 | GEO

HES2 embryonic stem cells (ESCs) grown in standard conditions and FACs sorted for GCTM-2 and CD9

Project description:HES2 ESCs were grown in standard ES culture conditions. After 1 week, these cells were FACs sorted for the presence of GCTM-2 and CD9. Keywords: Sorted cell comparison Three consecutive passages of HES2 cells were grown and subjected to FACs sorting. For each, 4 sorted populations of cells (p4, p5, p6, p7) were collected and these were subjected to microarray. A total of 12 samples: 3 replicates each of p4, p5, p6, and p7.

2010-04-08 | E-GEOD-13201 | biostudies-arrayexpress

Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human Embryonic Stem cells (part 2)

Project description:Recent RNA-sequencing studies have shown remarkable complexity in the mammalian transcriptome. The ultimate impact of this complexity on the predicted proteomic output is less well defined. We have undertaken a strand-specific RNA sequencing of multiple cellular RNA fractions (>18Gb) to uncover the transcriptional complexity of human ES cells. We have shown that human ES cells display a high degree of transcriptional diversity, with more than half? of active genes generating RNAs that differ from conventional gene models. We found evidence that more than >1000 genes express long 5’ and/or extended 3’ UTRs, which was confirmed by “virtual northern” analysis. Exhaustive sequencing the membrane-polysome and cytosolic/untranslated fractions of hESC was used to identify RNAs encoding peptides destined for secretion and the extracellular space and to demonstrate preferential selection of transcription complexity for translation in vitro. Finally, the impact of this newly defined transcriptional complexity on known gene-centric network models such as the Plurinet and the cell surface signalling machinery in human ES cells revealed a significant expansion of protein coding components at play, many of which alternative actions based on altered domain content. Human ES cells fractionated for mRNA, cytosolic polysome, membrane polysome

2011-07-01 | E-GEOD-25842 | biostudies-arrayexpress

ChIP-seq from A549 (ENCSR356YXW)

Project description:HES2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2017-01-10 | GSE91250 | GEO

Uncovering obsessive-compulsive disorder risk genes in a pediatric cohort by high-resolution analysis of copy number variation.

Project description:The Affymetrix CytoScan HD 2.5M and Illumina HumanOmni2.5 arrays are high resolution SNP platform for studying copy number variations in the human genome. Both platforms have widely being used in both clinical and research settings for identifying causative variants as well as interrogating the genome for benign variants. We employed both platforms to investigate the risk factor CNVs in trios diagnosed with OCD. We genotyped 307 unrelated probands (including 174 complete parent-child trios; mean age of probands 7.9±3.5 years) and compared their genotypes to those of 3,861 population controls, in order to identify rare CNVs (<0.5% frequency) of at least 15 kb in size that might contribute to OCD. We uncovered de novo CNVs and Decipher Syndromes in probands. We have identified additional potentially risk factor CNVs impacting the coding sequencing of genes involved in brain functions.

2016-12-11 | GSE76436 | GEO

Uncovering obsessive-compulsive disorder risk genes in a pediatric cohort by high-resolution analysis of copy number variation.

2016-12-11 | GSE76437 | GEO

Transcription profiling of mouse embryonic stem cells expressing VE-cadherin (CD144) during endothelial differentiation

Project description:Endothelial differentiation occurs during normal vascular development in the developing embryo. Mouse embryonic stem (ES) cells were used to further define the molecular mechanisms of endothelial differentiation. By flow cytometry a population of VEGF-R2 positive cells was identified as early as 2.5 days after differentiation of ES cells, and a subset of VEGF-R2 + cells, that were CD41+ positive at 3.5 days. A separate population of VEGF-R2+ stem cells expressing the endothelial-specific marker CD144 (VE-cadherin) was also identified at this same time point. Microarray analysis of >45,000 transcripts was performed on RNA obtained from cells expressing VEGF-R2, CD41, and CD144. Experiment Overall Design: We identified four populations of cells; cells expressing VEGF-R2 (day 2.5), CD41 expressing cells (day 3.5), cells expressing CD144 (VE-Cadherin, day 3.5), and cells expressing CD144 (day 6.5). In addition to this, we have also obtained the negative control cells at each time such as VEGF-R2 (day 2.5) negative, CD41 negative (day 3.5), CD144 negative (VE-Cadherin, day 3.5), and negative CD144 (day 6.5). RNA for the microarray experiments were obtained in duplicate from two separately conducted experiments using the murine embryonic stem cells..

2008-10-20 | E-GEOD-10210 | biostudies-arrayexpress

Identification and characterization of extrachromosomal circular DNA in patients with high myopia and cataract

Project description:To explore the presence of extrachromosomal circular DNA (eccDNA) in the anterior capsule of the lens in the eyes of patients with cataract and with high myopia. Circle-Seq was performed to identify differences in the eccDNA and gene expression between the anterior capsule of the lens of patients with simple nuclear cataract (C, n = 6) and patients with nuclear cataract along with high myopia (HM, n = 6). The expression of eccDNA was confirmed using routine quantitative polymerase chain reaction. The eccDNA ranked in C and HM ranged in length from 0.017 kb – 9.9 Mb with two distinctive peaks detected at 0.2 kb and 0.5 kb, while eccDNA that were differentially expressed (up- and down-regulated) ranged in size from 0.05 kb – 57.8 kb with two distinctive peaks observed at 0.1 kb and 0.5 kb. Only 2.5 % of the eccDNA in C and 2 % in HM were > 25 kb in size. The gene-rich chromosomes contributed to more number of eccDNA/Mb, while several well-known high myopia candidate genes, including catenin delta 2 (CTNND2), ubiquitin-like with PHD and ring finger domains 1 binding protein 1 like (UHRF1BP1L) , exhibited significantly increased levels of eccDNA in the anterior capsule of the lens in patients with high myopia. This study highlighted the topologic analysis of the anterior capsule of eyes with high myopia, which is an emerging direction for research and clinical applications. These findings suggested that eccDNA was commonly detected in eyes with high myopia and cataracts, and the candidate genes for high myopia identified in previous studies were also observed in the eccDNA.

2023-04-13 | GSE207646 | GEO

Nascent-seq data from DRB-treated/untreated human U2OS cell line

Project description:Confluent U2OS cells were released to serum-free medium, and continued to grow for 36 h (Per2-dLuc peak) or 48 h (Per2-dLuc trough), then added DRB (10uM) treatment for 0.5, 1.5, 3.5 h, then added BrU (250uM) for 0.5 h, harvested total RNA, captured with anti-BrU antibody, and conduced hi-seq.

2020-10-23 | GSE105815 | GEO

TGF-β specifies TFH versus TH17 cell fates in murine CD4+ T cells through c-Maf (Seq04, scRNA-seq)

Project description:Naive murine CD4+ T cells were cultured under different polarizing conditions in 96-well plates coated with anti-CD3/anti-CD28 for 0, 0.5, 1.5, 3.5 days, sorted by flow cytometry, and subjected to single-cell RNA-seq.

2024-03-01 | GSE197842 | GEO

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