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ERP003460
Homo sapiens
12 Downloadable Samples
IlluminaHiSeq2000
Description
Background: Gene expression analysis by RNA sequencing is now widely used in a number of applications surveying the whole transcriptomes of cells and tissues. The recent introduction of ribosomal RNA depletion protocols, such as RiboZero, has extended the view of the polyadenylated transcriptome to the poly(A)- fraction of the RNA. However, substantial amounts of intronic transcriptional activity has been reported in RiboZero protocols, raising issues regarding their potential nuclear origin and the impact on the actual sequence depth in exonic regions. Method: Using HEK293 human cells as source material, we assessed here the impact of the two commonly used RNA extraction methods and of the library construction protocols (rRNA depletion versus mRNA) on 1) the relative abundance of intronic reads and 2) on the estimation of gene expression values. Results: We benchmarked the rRNA depletion-based sequencing with a specific analysis of the cytoplasmic and nuclear transcriptome fractions, suggesting that the large majority of the intronic reads correspond to unprocessed nuclear transcripts rather than to independent transcriptional units. We show that Qiagen or TRIzol extraction methods retain differentially nuclear RNA species, and that consequently, rRNA depletion-based RNA sequencing protocols are particularly sensitive to the extraction methods. Conclusions: We could show that the combination of Trizol-based RNA extraction with rRNA depletion sequencing protocols led to the largest fraction of intronic reads, after the sequencing of the nuclear transcriptome. We discuss here the impact of the various strategies on gene expression and alternative splicing estimation measures. Further, we propose guidelines and a double selection strategy for minimizing the expression biases, without loss of information.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 5 Downloadable Samples
- Illumina HiSeq 2500
Description
To comprehensively identify AS events regulated by Nova2 in endothelium, we performed high-throughput RNA sequencing (RNA-Seq) of two biological replicates of Nova2 knockdown and control ECs.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Mus musculus
- 109 Downloadable Samples
- Illumina HiSeq 2500
Description
No description.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Mus musculus
- 35 Downloadable Samples
- Illumina HiSeq 2500
Description
RNAseq of YAC128 mice treated with pridopidine
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment
View Samples- Zea mays
- 31 Downloadable Samples
- NextSeq 500
Description
FACS RNAseq of transgenic lines pWUS and pYAB
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Caenorhabditis elegans
- 25 Downloadable Samples
- Illumina HiSeq 2000
Description
Raw sequence reads are provided for RNA-seq of parental and transgenerational worms in which the P0 were treated with OP50 (control) or PA14.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Caenorhabditis elegans
- 23 Downloadable Samples
- Illumina HiSeq 2000
Description
Identifying transcriptional changes in adults, whose biology and behavior differsubstantially from developing animals, is important when evaluating adult phenotypes.Moreover, cell- and tissue-specific information is critical for understanding the biologyof multicellular animals. We used adult cell-specific isolation to identify thetranscriptomes of C. elegans'' major adult tissues (muscle, intestine, epidermis, andneurons).
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
We evaluated the therapeutic activity of the modified U1 particles in a mouse model affected by severe spinal muscular atrophy. ExSpeU1 introduced by germline transgenesis efficiently rescued the phenotype increasing SMN2 exon 7 splicing, SMN protein production and radically extending the life span.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- IlluminaGenomeAnalyzerII
Description
Regulatory T-cells (Treg) play an essential role in the negative regulation of immune answers by developing an attenuated cytokine response that allows suppressing proliferation and effector function of T-cells (CD4+ Th). The transcription factor FoxP3 is responsible for the regulation of many genes involved in the Treg gene signature. Its ablation leads to severe immune deficiencies in human and mice. Recent developments in sequencing technologies have revolutionized the possibilities to gain insights into transcription factor binding by ChiP-Seq and into transcriptome analysis by mRNA-Seq. We combine FoxP3 ChiP-Seq and mRNA-Seq in order to understand the transcriptional differences between primary human CD4+ T helper and regulatory T-cells, as well as to study the role of FoxP3 in generating those differences. We show, that mRNA-Seq allows analyzing the transcriptomal landscape of T-cells including the expression of specific splice variants at much greater depth than previous approaches, whereas 50% of transcriptional regulation events have not been described before by using diverse array technologies.
Publication Title
Next-generation insights into regulatory T cells: expression profiling and FoxP3 occupancy in Human.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 180 Downloadable Samples
- Illumina HiSeq 2500
Description
Mice carrying embryos that were either Pax6fl/fl;Emx1CreER (experimental group) or Pax6fl/+;Emx1CreER (control group) were given tamoxifen on embryonic day 9.5 (E9.5) to induce Pax6 deletion. Embryos were harvested on E13.5, the cerebral cortices were removed and divided into rostral and caudal halves, and total RNA was extracted. Samples from littermates of the same genotype were pooled. Poly-A mRNA was purified and TruSeq RNA-Seq libraries were prepared and sequenced (100 base paired-end; Illumina, HiSeq v3).
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
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