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Items: 1 to 20 of 69

1.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.
Organism:
Saccharomyces cerevisiae; Drosophila melanogaster; Gallus gallus; Hypsibius dujardini; Lethenteron camtschaticum; Triticum aestivum; Caenorhabditis elegans; Aplysia californica; Aedes aegypti; Culex quinquefasciatus; Homo sapiens; Muntiacus reevesi; Muntiacus muntjak; Arachis hypogaea; Agaricus bisporus; Branchiostoma lanceolatum; Xenopus laevis; Notamacropus eugenii; Pygocentrus nattereri; Cristatella mucedo; Clonorchis sinensis; Chiloscyllium punctatum; Strongylocentrotus purpuratus; Ciona intestinalis; Pleurobrachia bachei; Acropora millepora; Python bivittatus
Type:
Other
30 related Platforms
32 Samples
Download data: BEDPE, FASTA, HIC, VCF, WIG
Series
Accession:
GSE169088
ID:
200169088
2.

circRNA-sequencing of Chiloscyllium plagiosum liver

(Submitter supplied) circRNA sequencing for 1 samples..
Organism:
Chiloscyllium plagiosum
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL29086
1 Sample
Download data: FA, XLSX
Series
Accession:
GSE157160
ID:
200157160
3.

A comparison of evolutionary changes and constraints on gene regulation between fin and limb development

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus; Chiloscyllium punctatum
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL21273 GPL27153 GPL18480
43 Samples
Download data: BW
Series
Accession:
GSE136445
ID:
200136445
4.

A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [RNA-seq]

(Submitter supplied) We report time-series transcriptome of developing bamboo shark fin buds and mouse forelimb buds, and open chromatin regions of developing mouse forelimb buds. The major contributions of this study are 1) transcriptomic data with an accurate orthology map for a systematic comparison between the two species; 2) high quality chromatin accessibility data for mouse limb development; 3) discovery of mass heterochronic genes between fins and limbs; 4) hourglass-shaped conservation between fins and limbs, providing insights into a general trend of gene regulatory evolution.
Organism:
Chiloscyllium punctatum; Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL27153 GPL18480
30 Samples
Download data: TXT
Series
Accession:
GSE136437
ID:
200136437
5.

The synarcual of the little skate: Novel development among the vertebrates

(Submitter supplied) The synarcual is a specialized adaptation of the anterior axial skeleton comprising a putatively fused array of vertebral elements characteristic of jawed vertebrate (gnathostome) clades such as batoid and chimaeroid chondrichthyans, as well as a fossil group known as the placoderms. Placoderms represent the phylogenetically most basal jawed vertebrates and the presence of a synarcual in these and chondrichthyans may suggest a conserved vertebral type for jawed vertebrates, predating the divergence of stem and crown gnathostomes. more...
Organism:
Leucoraja erinacea
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25704
4 Samples
Download data: FASTA, MATRIX, TXT
Series
Accession:
GSE121572
ID:
200121572
6.

RNA-seq of Scyliorhinus retifer electroreceptors

(Submitter supplied) Transcriptional profiling from adult Scyliorhinus retifer from electrosensory cells of the ampullae of Lorenzini, forebrain, skin, and skeletal muscle shows differential gene expression of voltage-activated ion channels related to sensory transduction.
Organism:
Scyliorhinus retifer
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24026
4 Samples
Download data: TXT
Series
Accession:
GSE103977
ID:
200103977
7.

Genomewide screening for pectoral fin MN specific markers

(Submitter supplied) The goal of this study is to find skate pectoral fin motor neuron markers. Total RNA was extracted from manually sorted pectoral fin MNs, which were retrogradely labeled and tail spinal cord cells. By comparing RNA expression profiles of pectoral fin MNs and tail spinal cord neurons, we could identity general MN, MN columnar, and subset MN pool markers for fin MNs.
Organism:
Leucoraja erinacea
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24146
6 Samples
Download data: FASTA, XLSX
Series
Accession:
GSE105156
ID:
200105156
8.

RNASeq of molecular basis of ancestral vertebrate electroreception

(Submitter supplied) Elasmobranch fishes, including sharks, rays, and skates, use specialized electrosensory organs called Ampullae of Lorenzini to detect extremely small changes in environmental electric fields. Electrosensory cells within these ampullae are able to discriminate and respond to minute changes in environmental voltage gradients through an as-yet unknown mechanism. Here we show that the voltage-gated calcium channel CaV1.3 and big conductance calcium-activated potassium (BK) channel are preferentially expressed by electrosensory cells in little skate (Leucoraja erinacea) and functionally couple to mediate electrosensory cell membrane voltage oscillations, which are important in the detection of specific, weak electrical signals. more...
Organism:
Leucoraja erinacea
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22922
4 Samples
Download data: FASTA, TXT
Series
Accession:
GSE93582
ID:
200093582
9.

microRNA expression profiling of the normal and regenerating liver of Chiloscyllium plagiosum

(Submitter supplied) This study aimed to improve our understanding of the mechanisms of liver regeneration in sharks and to identify the microRNAs that participate in liver regeneration and other liver-related diseases. To this end, normal and regenerating liver tissues from C. plagiosum were harvested 0, 3, 6, 12 and 24 h after partial hepatectomy (PH) and were sequenced using the Illumina/Solexa platform. In total, 309 known microRNAs and 590 novel microRNAs were identified in C. more...
Organism:
Chiloscyllium plagiosum
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL20847
5 Samples
Download data: XLSX
Series
Accession:
GSE72339
ID:
200072339
10.

Late-stage embryonic gene expression in three cartilaginous fishes

(Submitter supplied) Gene expression profiling of pooled late stage embryos from Leucoraja erinacea, Scyliorhinus canicula and Callorhinchus milii show that HOXC cluster genes are not expressed in the two elasmobranch fishes, L. erinacea and S. canicula. This finding supports the observations that these genes are not found in whole genome shotgun sequencing of L. erinacea or genomic clones from S. canicula.
Organism:
Leucoraja erinacea; Scyliorhinus canicula; Callorhinchus milii
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL11347 GPL11349 GPL11348
3 Samples
Download data: CSV, FA
Series
Accession:
GSE26235
ID:
200026235
11.

HiSeq X Ten (Leucoraja erinacea)

Organism:
Leucoraja erinacea
Download data
Platform
Accession:
GPL31065
ID:
100031065
12.

Illumina NovaSeq 6000 (Leucoraja erinacea)

Organism:
Leucoraja erinacea
Download data
Platform
Accession:
GPL31064
ID:
100031064
13.

Illumina HiSeq 2000 (Scyliorhinus canicula)

Organism:
Scyliorhinus canicula
Download data
Platform
Accession:
GPL31019
ID:
100031019
14.

DNBSEQ-G400 (Leucoraja erinacea)

Organism:
Leucoraja erinacea
Download data
Platform
Accession:
GPL30966
ID:
100030966
15.

Illumina NovaSeq 6000 (Chiloscyllium punctatum)

Organism:
Chiloscyllium punctatum
1 Series
1 Sample
Download data
Platform
Accession:
GPL29868
ID:
100029868
16.

Illumina HiSeq 4000 (Chiloscyllium plagiosum)

Organism:
Chiloscyllium plagiosum
1 Series
1 Sample
Download data
Platform
Accession:
GPL29086
ID:
100029086
17.

Illumina HiSeq 1500 (Chiloscyllium punctatum)

Organism:
Chiloscyllium punctatum
2 Series
18 Samples
Download data
Platform
Accession:
GPL27153
ID:
100027153
18.

Illumina HiSeq 2000 (Leucoraja erinacea)

Organism:
Leucoraja erinacea
1 Series
4 Samples
Download data
Platform
Accession:
GPL25704
ID:
100025704
19.

Illumina HiSeq 2500 (Leucoraja erinacea)

Organism:
Leucoraja erinacea
1 Series
6 Samples
Download data
Platform
Accession:
GPL24146
ID:
100024146
20.

Illumina HiSeq 4000 (Scyliorhinus retifer)

Organism:
Scyliorhinus retifer
1 Series
4 Samples
Download data
Platform
Accession:
GPL24026
ID:
100024026
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