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) The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening on animal cells is a powerful tool to reveal the expression patterns of viral entry genes for different hosts. But such exploration for SARS-CoV-2 remained limited. Here, we presented the broadest pan-species single-nucleus RNA sequencing study to date, covering 11 representative species in pets (cat, dog, hamster, lizard), livestock (goat, rabbit), poultry (duck, pigeon) and wildlife (pangolin, tiger, deer), from which we investigated the co-expression of ACE2 and TMPRSS2. more...

Organism:

Columba livia; Felis catus; Oryctolagus cuniculus; Mesocricetus auratus; Capra aegagrus; Manis javanica; Cervus nippon taiouanus; Anas platyrhynchos; Canis lupus familiaris; Anolis carolinensis; Panthera tigris altaica

Type:

Expression profiling by high throughput sequencing

11 related Platforms

29 Samples

Download data: TXT

(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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Anolis carolinensis

Type:

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

Platforms:

GPL15001 GPL19057

21 Samples

Download data: BW

(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) In order to rule out the presence of imprinted X inactivation in A. carolinensis females we generated RNA-seq data from brain, heart, kidney, liver, ovary and genome sequence data from kidney.

Organism:

Anolis carolinensis

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL23252 GPL15001

15 Samples

Download data: VCF

(Submitter supplied) In order to rule out the presence of random X inactivation in A. carolinensis females we generated scRNA-Seq from liver cells and genome sequence data from liver.

Organism:

Anolis carolinensis

Type:

Genome variation profiling by high throughput sequencing

Platforms:

GPL23678 GPL15001

7 Samples

Download data: VCF

(Submitter supplied) In order to study the green anole dosage compensation mechanism we generated strand-specific RNA-seq libraries for a total of 186 samples from the green anole and other representative amniotes (human, mouse, opossum, platypus, chicken and xenopus). Moreover, in order to understand the dosage compensation mechanism of A. carolinensis, we generated ChIP-Seq data for the histone modification H4K16ac and compared levels of acetylation between males and females. more...

Organism:

Xenopus tropicalis; Gallus gallus; Ornithorhynchus anatinus; Mus musculus; Homo sapiens; Anolis carolinensis; Monodelphis domestica

Type:

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

8 related Platforms

197 Samples

Download data: BW, TXT

(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:

Anolis carolinensis; Mus musculus

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:

Mus musculus; Anolis carolinensis

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:

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

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:

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

Type:

Expression profiling by high throughput sequencing

5 related Platforms

21 Samples

Download data: BW, TXT

(Submitter supplied) Anolis carolinensis embryos were collected 0-1 days post egg laying, and total RNA was extracted for RNA-Seq analysis (Illumina Hi-Seq2000). Transcriptome sequence from these stages in the green anole, equivalent to mouse 9.5-10.5 dpc embryos, will help to improve gene annotations in A. carolinensis and provide expression level information for key organogenesis and patterning processes.

Organism:

Anolis carolinensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15001

2 Samples

Download data: TXT