GEO DataSets

(Submitter supplied) Lizards cannot naturally regenerate limbs but are the closest known relatives of mammals capable of epimorphic tail regrowth. However, the mechanisms regulating lizard blastema derivation and chondrogenesis remain unclear. We utilized single-cell RNA sequencing analyses of regenerating lizard tails throughout the course of regeneration to assess diversity and heterogeneity in regeneating tail cell populations.

Organism:

Anolis carolinensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23678

10 Samples

Download data: MTX, TSV

(Submitter supplied) PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs essential for fertility. In adult mouse testes, most piRNAs are derived from long single-stranded RNAs lacking annotated open reading frames (ORFs). The mechanisms underlying how piRNA sequences are defined during the cleavages of piRNA precursors remain elusive. Here, we show that 80S ribosomes translate the 5′-proximal short ORFs (uORFs) of piRNA precursors. more...

Organism:

Mus musculus; Anolis carolinensis

Type:

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

Platforms:

GPL13112 GPL15001

61 Samples

Download data: BED2, TXT

(Submitter supplied) In crown group tetrapods, individual digits are homologized in relation to a pentadactyl ground plan. However, testing hypotheses of digit homology is challenging because it is unclear whether digits develop with distinct and conserved gene regulatory states. Here we show dramatic evolutionary dynamism in the gene expression profiles of digits, challenging the notion that five digit identities are conserved across amniotes. more...

Organism:

Anolis carolinensis; Alligator mississippiensis; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24412 GPL15001 GPL13112

59 Samples

Download data: TXT

(Submitter supplied) The PITX1 transcription factor is expressed during hindlimb development, where it plays a critical role in directing hindlimb growth and the specification of hindlimb morphology. While it is known that PITX1 regulates hindlimb formation, in part, through activation of the Tbx4 gene, other transcriptional targets remain to be elucidated. We have used a combination of ChIP-seq and RNA-seq to investigate enhancer regions and target genes that are directly regulated by PITX1 in embryonic mouse hindlimbs. more...

Organism:

Anolis carolinensis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15001

3 Samples

Download data: BW

(Submitter supplied) The MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) gene encodes a non-coding RNA that is processed into a long nuclear retained transcript (MALAT1) and a small cytoplasmic tRNA-like transcript (mascRNA). Using a RNA sequence- and structure-based covariance model, we identified more than 130 genomic loci in vertebrate genomes containing the MALAT1 3’-end triple helix structure and its immediate downstream tRNA-like structure, including 44 in the green lizard Anolis carolinensis. more...

Organism:

Anolis carolinensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23260

4 Samples

Download data: BEDGRAPH

(Submitter supplied) The morphologies of the amniote phallus and limbs differ dramatically, but these structures share signaling pathways and patterns of gene expression in early development. Thus far, the extent to which genital and limb transcriptional networks share cis-regulatory elements has remained unexplored. Using chromatin immunoprecipitation with an antibody against the histone modification mark H3K27ac followed by Illumina high-throughput sequencing, we identify thousands of active enhancers in developing limbs, genital tubercle, and additional embryonic tissues of the mouse and green anole lizard (Anolis carolinensis). more...

Organism:

Mus musculus; Anolis carolinensis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL15001

21 Samples

Download data: BED, BW

(Submitter supplied) Comparative RNA-seq profiling of mouse and anole lizard developing limbs and external genitalia, to assess evolutionary and develomental relationships, between the two tissue types based on transcriptomic data

Organism:

Anolis carolinensis; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL15001

24 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) 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