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Mus musculus
1 Downloadable Sample
Illumina HiSeq 2000
Description
Open chromatin is induced locally during the repair of DNA double strand breaks, when a cascade of protein recruitments and modifications is triggered. This "ATM cascade" includes components like the Mrn complex, ATM kinase, phosphorylated histon variant ?H2AX, MDC1, E3 ligases RNF 8 and RNF8, 53BP1, and Rif1. Recent investigations have shown that also the Mad2l2 protein is a downstream effector of the ATM cascade during DNA repair. It was first described as an accessory subunit during translesion DNA repair, and more recently as a key factor inhibiting the resection of DNA 5`ends, thus promoting non-homologous end joining, and repressing homologous recombination.Naive embryonic stem cells (ESCs) have a globally open chromatin. A preliminary study from this laboratory has demonstrated that ESCs require the presence of the Mad2l2 protein for the maintenance of their transcriptional and epigenetic profiles, and thus for the stability of pluripotency (Pirouz et al., Cell Cycle 14, 1596, 2015). The aim of the present study was to correlate Mad2l2 with the ATM cascade and the chromatin status in ESCs.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
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- Arabidopsis thaliana
- 1 Downloadable Sample
- Illumina HiSeq 2000
Description
RNA-SEQ of Arabidopsis thaliana leaf tissues under normal and low CO2
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part
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SRP105671- Homo sapiens
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
Gene expression of human liver cells at different developmental stages.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- 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- Caenorhabditis elegans
- 186 Downloadable Samples
- Illumina HiSeq 2000
Description
To investigate the effect of local genetic variation on heritable traits, we developed a new recombinant inbred line (RIL) population derived from four wild isolates. The wild isolates were collected from two closely located sites in France: Orsay and Santeuil. By crossing these four genetically diverse parental isolates a population of 200 RILs was constructed. RNA-seq was used to obtain sequence polymorphisms
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Arabidopsis thaliana
- 35 Downloadable Samples
- Illumina HiSeq 2500
Description
No description.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 30 Downloadable Samples
- Illumina HiSeq 2500
Description
No description.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples- Mus musculus
- 16 Downloadable Samples
- Illumina HiSeq 2000
Description
In mice, zygotic activation mainly occurs on a wide variety of genes mainly at the 2-cell stage. Long noncoding RNAs (lncRNAs) are increasingly being recognized as molecules that modulate gene expression. In this study, we performed the directional RNA-seq of MII oocytes and 2-cell embryos to identify the long noncoding RNAs activated during ZGA.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples SRP045624- Homo sapiens
- 6 Downloadable Samples
- IlluminaHiSeq2000
Description
VHL inactivation is a major component of renal cancer. In this study we re-engineered RCC4 cells to re-express VHL and performed mRNA-sequencing on triplicates to analyse gene and transcript expression changes specific to VHL inactivation.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples