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Chimeric RNA profiling demonstrates an association of alveolar rhabdomyosarcoma with specific stages of normal myogenesis

ABSTRACT: Total RNA extracted from differentiated mesenchymal stem cells at four time points (T1,T2,T3,T4) and sequenced using Illumina Hi-seq 2000 platform to generate RNA sequencing with 101bp in read length. Nearly 50 million raw reads were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and SOAPfuse software to detect fusion transcripts.

ORGANISM(S): Homo sapiens

PROVIDER: GSE64032 | GEO | 2016/02/09

SECONDARY ACCESSION(S): PRJNA269918

REPOSITORIES: GEO

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Chimeric RNA profiling demonstrates an association of alveolar rhabdomyosarcoma with specific stages of normal myogenesis

Project description:Total RNA extracted from differentiated mesenchymal stem cells at four time points (T1,T2,T3,T4) and sequenced using Illumina Hi-seq 2000 platform to generate RNA sequencing with 101bp in read length. Nearly 50 million raw reads were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and SOAPfuse software to detect fusion transcripts. Discovering fusion genes from muscle differentiated mesenchymal stem cells

2016-02-09 | E-GEOD-64032 | biostudies-arrayexpress

Discovery of cis-spliced chimeric RNAs between adjacent genes in human prostate cells

Project description:Total RNA extracted from prostate cancer LNCaP cells transfected with siRNA against CTCF(siCTCF), or negative control siRNA (si-)were processed, and sequenced by two different companies using Illumina Hi-seq 2000 platform to generate RNA sequencing with two output sequences: paired-end 50bp and 101bp in read length. Nearly 100 million and 50 million raw reads were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and SOAPfuse software to detect fusion transcripts. Discovering fusion genes from siCTCF and si- in LNCaP cells.

2015-02-09 | E-GEOD-63487 | biostudies-arrayexpress

Discovery of cis-spliced chimeric RNAs between adjacent genes in human prostate cells

2015-02-09 | GSE63487 | GEO

sRNA sequencing of mature and developing gonads during protandrous changes in the Asian seabass

Project description:Purpose: sRNA-sequencing of mature and intermediate gonadal tissue in order to identify the differential expression of miRNAs during male to female (i.e. protandrous) sex transition Methods: Total RNA was extracted and sRNA was purified. cDNA libraries were constructed using a high definition adapter protocol (Xu et al. 2015). 50 bp sequencing was performed on Illumina's HiSeq 2500 at the Earlham Institute, Norwich, UK. Sequenced data was trimmed for adapters and filtered to remove very short and low complexity sequences. miRBase animal miRNA precursor sequences were mapped against the Asian seabass genome in order to generate a set of putative miRNA precursors. Putative precursor molecules with aligning mature miRBase miRNA(s) and forming a valid pre-miRNA hairpin structure were annotated as valid precursor miRNAs. Novel precursor and mature miRNAs were annotated using a combination of published algorithms and manual checking to ensure consistency with canonical miRNA biogenesis criteria. The alignment of sequenced reads against a non-redundant miRNA precursor set was used to determine raw read counts of mature miRNAs. Differential expression analysis was performed in order to identify differentially expressed mature miRNAs between conditions. Results: We detect 156, 71, 122, 151, 171 and 155 differentially expressed miRNA for the testis -> T1/T2, T1/T2 -> T3/T4, T3/T4 -> ovary, testis -> T3/T4, T1/T2 -> ovary and the testis->ovary comparisons respectively Conclusions: There is substantial differential expression of miRNAs at every stage of gonadal change in the Asian seabass during the sex transition process

2022-10-20 | GSE122720 | GEO

Liver Chromatin accessibility landscapes during onset of salmon maturation

Project description:We sequenced 12 ATAC-Seq lbraries from four biological replicates before (T1) and after the onset of maturation (T2, T3, T4) from liver. To characterise changes in chromatin state following long light initiation, we defined differentially accessible regions (DARs) where mapping counts differed significantly between T1 and other time points. This revealed a strong early remodelling in the chromatin state landscape, as most DARs were observed at T2 (n=1501) before decreasing in stepwise fashion at T3 (n=477) and T4. The majority of DARs (n=1036 or 57%) exhibit reduced accessibility at T2 compared with T1 and subsequently remained unchanged at later time points (Fig. 5a; Supplementary Figure S14). Similarly, regions that gained accessibility at T2 (n=696 or 38%) also remained unchanged at later timepoints. This left less than 10% of DARs (n=99) that displayed an oscillating pattern following the onset of the maturation. Together, this revealed the ATAC-seq signatures were predominantly stable chromatin state changes.

2020-08-28 | GSE156998 | GEO

Gene expression in glycerol-grown Yarrowia lipolytica Af4 (DHA producing strain) and Yarrowia lipolytica Po1h (non-producing stain) in different growth phases and different medium conditions

Project description:mRNA was sampled during exponential growth phase (T1), beginning of stationary/production phase (T2), middle of production phase (T3-T4) and end of production phase (T5-T6) strains: Y. lipolytica Af4 - DHA producer (Gemperlein et al., 2019) and Y. lipolytica Po1h - wild type

2024-01-01 | GSE224529 | GEO

Synthetic apomixis transfers stably over multiple generations in hybrid rice

Project description:we reproduced the clonal plants of Fix (Fixation of rice heterozygosity) to T4 generation with 1.9~3.2% clonal seeds rate of Fix-T01th, T12th, T23th and T34th. The descendant clonal plants Fix-T0, T1, T2, T3 and T4 exhibited no discernible differences on plant morphology, clonal seeds rate (3.7~4.3%), genome, methylome and transcriptome. Unexpectedly, few aneuploids were identified in each generation. The visible morphology changes of aneuploids might be caused by chromosome segments elimination. Together, the synthetic apomixis was heritable through multiple generations and few aneuploids were induced when using the synthetic apomixis system.

2022-09-28 | GSE214179 | GEO

Time-series transcriptome analysis of peripheral blood mononuclear cells obtained from individuals who received the SARS-CoV-2 mRNA vaccine

Project description:Messenger ribonucleic acid (mRNA) vaccination against coronavirus disease 2019 (COVID-19) is an effective prevention strategy, despite a limited understanding of the molecular mechanisms underlying the host immune system and individual heterogeneity of the variable effects of mRNA vaccination. We assessed the time-series changes in the comprehensive gene expression profiles of 200 vaccinated healthcare workers by performing bulk transcriptome and bioinformatics analyses, including dimensionality reduction utilizing the uniform manifold approximation and projection (UMAP) technique. For these analyses, blood samples, including peripheral blood mononuclear cells (PBMCs), were collected from 214 vaccine recipients before vaccination (T1) and on Days 22 (T2, after second dose), 90, 180 (T3, before a booster dose), and 360 (T4, after a booster dose) after receiving the first dose of BNT162b2 vaccine (UMIN000043851). UMAP successfully visualized the main cluster of gene expression at each time point in PBMC samples (T1–T4). Through differentially expressed gene (DEG) analysis, we identified genes that showed fluctuating expression levels and gradual increases in expression levels from T1 to T4, as well as genes with increased expression levels at T4 alone. We also succeeded in dividing these cases into five types based on the changes in gene expression levels. High-throughput and temporal bulk RNA-based transcriptome analysis is a useful approach for inclusive, diverse, and cost-effective large-scale clinical studies.

2023-06-27 | GSE220682 | GEO

Bifidobacterium bifidum PRL2010 actively changes the expression profiles of human cell lines

Project description:We studied the global transcription profiling of human cell lines upon colonization with Bifidobacterium bifidum PRL2010 by using DNA microarrays. We decided to use HT29 monolayer as an in vitro model to investigate the molecular impact of B. bifidum PRL2010 on human intestinal transcriptome. HT29 monolayers cultivated at 15 days of post confluence were placed in contact with PRL2010 cells for a range of time spanning from 0 h, 1 h (T1), 2 h (T2) to 4 h (T4).

2013-11-19 | E-GEOD-48494 | biostudies-arrayexpress

All Tumor Sector Experiments (T1-T20)

Project description:This SuperSeries is composed of the following subset Series: GSE16598: Tumor T1 Sectors GSE16599: Tumor T2 Sectors GSE16600: Tumor T3 Sectors GSE16601: Tumor T4 Sectors GSE16602: Tumor T5 Sectors GSE16603: Tumor T6 Sectors GSE16604: Tumor T7 Sectors GSE16605: Tumor T8 Sectors GSE16606: Tumor T9 Sectors GSE16607: Tumor T10 Sectors GSE16608: Tumor T11 Sectors GSE16609: Tumor T12 Sectors GSE16610: Tumor T13 Sectors GSE16611: Tumor T14 Sectors GSE16663: Tumor T15 Sectors GSE16664: Tumor T16 Sectors GSE16665: Tumor T17 Sectors GSE16667: Tumor T18 Sectors GSE16668: Tumor T19 Sectors GSE16669: Tumor T20 Sectors ROMA CGH experiments were conducted on four to six dissected sectors (S1-S6) from single primary ductal carcinomas (T1-T20). T1-T4 were analyzed by sectoring and analysis by ROMA. T5-T20 were analyzed using the Sector-Ploidy-Profiling (SPP) Approach. SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations. The genomic DNA from each tumor was labeled with Cy5 and a reference fibroblast genome was labeled with Cy3 and cohybridized to a ROMA microarray (85K or 390K). Experiments were performed in color-reversal by dye-swapping samples and hybridizing the labeled DNA to a second microarray for T1-T15 experiments, but not for T16-T20 experiments.

2009-07-10 | E-GEOD-16672 | biostudies-arrayexpress

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