GEO DataSets

(Submitter supplied) We assessed whether human transcripts expressed in an aneuploid mouse that carries human chromosome 21 (HsChr21) are spliced in a human-specific or mouse-specific fashion. In almost all cases, human-specific alternative splicing is maintained in the mouse nucleus. Species-specific splicing therefore appears to be primarily directed by cis-acting elements, rather than changes in the levels or activities of trans-acting factors.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9052 GPL9185

6 Samples

Download data: BOWTIE

(Submitter supplied) How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. more...

Organism:

Anolis carolinensis; Xenopus tropicalis; Gallus gallus; Mus musculus; Tetraodon nigroviridis

Type:

Expression profiling by high throughput sequencing

5 related Platforms

21 Samples

Download data: BW, TXT

(Submitter supplied) Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific. more...

Organism:

Bos taurus; Mus musculus; Rattus norvegicus; Macaca mulatta; Gallus gallus

Type:

Expression profiling by high throughput sequencing

7 related Platforms

134 Samples

Download data: GTF

(Submitter supplied) Thousands of human genes contain introns ending in NAGNAG motifs (N any nucleotide), where both NAGs can function as 3' splice sites, yielding isoforms differing by inclusion/exclusion of just three bases. However, the functional importance of NAGNAG alternative splicing is highly controversial. Using very deep RNA-Seq data from sixteen human and eight mouse tissues, we found that approximately half of alternatively spliced NAGNAGs undergo tissue-specific regulation and that regulated events have been selectively retained: alternative splicing of strongly tissue-specific NAGNAGs was ten times as likely to be conserved between species as for non-tissue-specific events. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL13112 GPL11002

48 Samples

Download data: GFF, TXT

(Submitter supplied) Alternative splicing (AS) generates extensive transcriptomic and proteomic complexity. However, the functions of species- and lineage-specific splice variants are largely unknown. Here, we show that mammalian-specific skipping of exon 9 of PTBP1 alters its splicing regulatory activities and affects the inclusion levels of numerous exons. During neurogenesis, skipping of exon 9 reduces PTBP1 repressive activity so as to facilitate activation of a brain-specific AS program. more...

Organism:

Gallus gallus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL19005

14 Samples

Download data: TAB

(Submitter supplied) 22 Normal adult mouse tissues on custom alternative transcript sensitive Affymetrix microarray used to address differeneces in tissue specific alternative splicing. Abstract: Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2720

64 Samples

Download data

(Submitter supplied) Affymetrix Standard Protocol

Organism:

Mus musculus

1 Series

57 Samples

Download data: CDF

(Submitter supplied) Transposable elements (TEs) have been active in the mammalian genome for hundreds of millions of years and each TE has had a distinct period of transpositional activity, followed by inactivation. Mice carrying reporter transgenes can be used to model transcriptional silencing at TEs. A mutagenesis screen for modifiers of epigenetic gene silencing produced a line with a null mutation in Trim33. Heterozygous mutants displayed increased expression of the reporter transgene. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112

9 Samples

Download data: BW, TXT

(Submitter supplied) The PIWI protein MIWI2 and its associated PIWI-interacting RNAs (piRNAs) instruct DNA methylation of young active transposable elements (TEs) in the male germline. Here we show that MIWI2 associates with TEX15 in foetal gonocytes. TEX15 is predominantly a nuclear protein that is not required for piRNA biogenesis but is essential for piRNA-directed TE de novo methylation and silencing. In summary, TEX15 is an essential executor of mammalian piRNA-directed DNA methylation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19057 GPL21103 GPL17021

15 Samples

Download data: TXT

(Submitter supplied) Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation. In lower vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. more...

Organism:

Xenopus tropicalis; Homo sapiens; Mus musculus; Anolis carolinensis; Danio rerio; Gallus gallus; Ornithorhynchus anatinus

Type:

Methylation profiling by high throughput sequencing

10 related Platforms

24 Samples

Download data: BED

(Submitter supplied) Neuromodulatory cells transduce environmental information into long lasting behavioral responses. However, the mechanisms governing how defined neuronal cell types influence behavioral plasticity are difficult to characterize. Here we adapted the Translating Ribosome Affinity Purification (TRAP) approach in C. elegans to profile ribosome-associated mRNAs from three major tissues and the neuromodulatory dopaminergic and serotonergic cells. more...

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL13657

20 Samples

Download data: XLSX

(Submitter supplied) Alternative splicing is a molecular process that contributes greatly to the diversification of proteome and to gene functions. Understanding the mechanisms of stage-specific alternative splicing can provide a better understanding of the development of eukaryotes and the functions of different genes. Schistosoma japonicum is an infectious blood-dwelling trematode with a complex lifecycle that causes the tropical disease schistosomiasis. more...

Organism:

Schistosoma japonicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20772

1 Sample

Download data: FASTA, XLS

(Submitter supplied) We studied the evolution of alternative splicing in the early stages of species divergence in the house mouse.

Organism:

Mus musculus castaneus; Mus spretus; Mus musculus domesticus; Mus musculus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

7 Samples

Download data: SAM

(Submitter supplied) KRAB-zinc finger proteins (KZFPs) represent one of the largest families of DNA binding proteins in vertebrate genomes and appear to have evolved to silence transposable elements (TEs) including endogenous retroviruses through sequence-specific targeting of repressive chromatin states. However, one member, ZFP57, is required to maintain the post-fertilization DNA methylation memory of parental-origin at genomic imprints. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21103 GPL13112

26 Samples

Download data: BED, BW, TXT

(Submitter supplied) In multicellular organisms, histone posttranslational modifications plays roles in transitions associated with the cell cycle, development, germline specification, gametogenesis and inheritance. Here we defined adaptations of an epigenome in tunicates, sister group to vertebrates, to strong secondary genome compaction in the larvacean, Oikopleura dioica, that has separate sexes and male heterogamy. We profiled 19 histone post-translational modifications in homogeneous ovary and testis samples and used the combinatorics of these marks to define chromatin states. We supplemented these with profiles of RNA polymerase II, CTCF and p300 binding sites and integrated existing annotation and expression data to characterize distinct epigenomic landscapes of the ovary and testis.

Organism:

Oikopleura dioica

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL15837

116 Samples

Download data: BEDGRAPH, PAIR

(Submitter supplied) Cytosine methylation (5mC) plays a key role in maintaining progenitor cell self-renewal and differentiation. Here, we analyzed the role of 5mC in kidney development by genome-wide methylation and expression profiling and by systematic genetic targeting of DNA methyltransferases (Dnmt) and Tet eleven hydroxylases (Tet). In mice, nephrons differentiate from Six2+ progenitor cells, therefore we created animals with genetic deletion of Dnmt 1, 3a, 3b, Tet1, or Tet2 in the Six2+ population (Six2Cre/Dnmt1flox/flox, Six2Cre/Dnmt3aflox/flox, Six2Cre/Dnmt3bflox/flox, Six2Cre/Tet2flox/flox or Tet1-/-). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL17021

15 Samples

Download data: TXT

(Submitter supplied) Epigenetic profiling of DNA methylation, histone H3 lysine 4 trimethylation and histone H3 lysine 9 trimethylation at imprinted gene clusters in the mouse.

Organism:

Mus musculus

Type:

Methylation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8714

18 Samples

Download data: TXT

(Submitter supplied) We recently identified a novel protein, Rearranged L-myc fusion (Rlf), that is required for DNA hypomethylation (and transcriptional activity) at certain regions of the mouse genome known to be sensitive to epigenetic gene silencing. Here we report the analysis of 12 whole genome bisulphite sequencing datasets across three different embryonic tissues/stages from mice with and without Rlf. We find that its absence has effects at thousands of differentially methylated regions.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112

22 Samples

Download data: BW, TAB

(Submitter supplied) The goal of the experiment – genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters Keywords: DNA methylation, Methylated CpG island amplification coupled with promoter arrays, normal tissue

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

4 related Platforms

4 Samples

Download data

(Submitter supplied) To assess variation and inheritance of genome-wide patterns of DNA methylation simultaneously in humans, we applied reduced representation bisulfite sequencing (RRBS) to somatic DNA from six members of a three-generation family.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL10999

8 Samples

Download data: TXT