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SRP062950
Homo sapiens
8 Downloadable Samples
IlluminaHiSeq2000
Description
Despite many years of study of inversions, very little is known about their functional consequences, especially in humans. A common hypothesis is that the selective value of inversions stems in part from their effects on nearby genes, although evidences of this in natural populations are almost nonexistent. Here we present a global analysis of a new 415-kb polymorphic inversion that is among the longest ones found in humans and is the first with clear position effects. This inversion is located in chromosome 19 and has been generated by non-homologous end joining between blocks of transposable elements with low identity. PCR genotyping in 541 individuals from eight different human populations allowed the detection of tag SNPs and inversion genotyping in multiple worldwide populations, showing that the inverted allele is mainly found in East-Asia with an average frequency of 4.7%. Interestingly, one of the breakpoints disrupts the transcription factor gene ZNF257, causing a significant reduction in the total expression level of this gene in lymphoblastoid cell lines. RNA-Seq analysis of the effects of this expression change in standard homozygotes and inversion heterozygotes revealed distinct expression patterns that were validated by quantitative RT-PCR. Moreover, we have found a new fusion transcript that is generated exclusively from inverted chromosomes around one of the breakpoints. Finally, by the analysis of the associated nucleotide variation, we have estimated that the inversion was generated approximately 43,450 years ago and, while a neutral evolution cannot be ruled out, its current frequencies are more consistent with those expected for a deleterious variant, although no significant association with phenotypic traits has been found so far.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 14 Downloadable Samples
- IlluminaHiSeq1000
Description
RNA-seq data from control and MCT8 morphant zebrafish embryos at 25hpf
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 109 Downloadable Samples
- Illumina HiSeq 2500
Description
No description.
Publication Title
No associated publication
Alternate Accession IDs
None
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
Alternate Accession IDs
None
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
Alternate Accession IDs
None
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
Alternate Accession IDs
None
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
Alternate Accession IDs
None
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
Alternate Accession IDs
None
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.
Alternate Accession IDs
None
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
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples