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Items: 1 to 20 of 4414

1.

Optimized design of antisense oligomers for targeted RNA depletion

(Submitter supplied) RNA sequencing (RNA-seq) has become a standard method for quantifying gene expression transcriptome-wide. Due to the extremely high proportion of ribosomal RNA (rRNA) in total RNA, sequencing libraries usually incorporate messenger RNA (mRNA) enrichment. Although polyadenylate (poly(A)) tail selection is widely used, many applications require alternate approaches such as rRNA depletion. Recently, selective rRNA digestion, using RNaseH and antisense DNA oligomers that tile the length of target RNAs, has emerged as an easy, cost-effective alternative to commercial rRNA depletion kits. more...
Organism:
Xenopus laevis; Danio rerio
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL20828 GPL21248
10 Samples
Download data: TSV
Series
Accession:
GSE152902
ID:
200152902
2.

Identification and characterization of centromeric sequences in Xenopus laevis

(Submitter supplied) Centromeres play an essential role in cell division by specifying the site of kinetochore formation on each chromosome so that chromosomes can attach to the mitotic spindle for segregation. Centromeres are defined epigenetically by the histone  H3 variant CEntromere Protein A (CENP-A). Dividing cells maintain the centromere  by depositing new CENP-A each cell cycle to replenish CENP-A diluted by replication. more...
Organism:
Xenopus laevis
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL22393 GPL22426
15 Samples
Download data: BW
Series
Accession:
GSE153058
ID:
200153058
3.

Neurodevelopmental disorder risk gene DYRK1A is required for ciliogenesis and brain size in Xenopus embryos

(Submitter supplied) DYRK1A (dual specificity tyrosine-(Y)-phosphorylation-regulated kinase 1 A) is a high confidence autism risk gene that encodes a conserved kinase. In addition to autism, patients with putative loss of function variants in DYRK1A exhibit microcephaly, intellectual disability, developmental delay, and congenital anomalies of the kidney and urinary tract. DYRK1A is also located within the critical region for Down syndrome; therefore, understanding the role of DYRK1A in brain development is crucial for understanding the pathobiology of multiple developmental disorders. more...
Organism:
Xenopus tropicalis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23182
6 Samples
Download data: CSV
Series
Accession:
GSE149538
ID:
200149538
4.

Epigenetic homogeneity underlies sperm programming for embryonic transcription

(Submitter supplied) Epigenetic homogeneity underlies sperm programming for embryonic transcription single-ended ChIP-Seq libraries from sperm, egg extract (-geminin) treated sperm, egg extract (+geminin) treated sperm, and St 7 embryos with antibody for H3Kme3, H3K27me3, 3 replicates for each histone modification pull-down
Organism:
Homo sapiens; Xenopus laevis
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL21046 GPL18460
36 Samples
Download data: BED, BROADPEAK, NARROWPEAK
Series
Accession:
GSE125982
ID:
200125982
5.

Specification of embryonic mesoderm by Pinhead signaling

(Submitter supplied) Among the three embryonic germ layers, mesoderm plays a central role in the establishment of the vertebrate body plan. Mesoderm is specified by secreted signaling proteins from the FGF, Nodal, BMP and Wnt families. No new classes of extracellular mesoderm-inducing factors have been identified in more than two decades. Here we show that the Xenopus pinhead (pnhd) gene encodes a novel secreted protein that activates specific mesodermal markers in presumptive ectoderm. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17682
8 Samples
Download data: XLSX
Series
Accession:
GSE143795
ID:
200143795
6.

Targets of Sf3b4 during neural crest development

(Submitter supplied) Mutations in Sf3b4, a component of the spliceosome, have been linked to craniofacial dismorphology known as Nager syndrome. To understand the role Sf3b4 in this condition, we knockdown Sf3b4 in Xenopus laevis embryos, and found that in these embryos the formation of neural crest-derived craniofacial skeletal structures was compromised. We performed RNA-Seq to identify the repertoire of genes affected by Sf3b4 splicing activity.
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18936
30 Samples
Download data: CSV
Series
Accession:
GSE143395
ID:
200143395
7.

Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Xenopus tropicalis
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL24884
33 Samples
Download data: MTX, TSV
Series
Accession:
GSE146837
ID:
200146837
8.

Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors

(Submitter supplied) Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable the growth and differentiation of new tissue, a process executed over multiple days and across dozens of cell types. The heterogeneity of tissues and temporally-sensitive fate decisions involved has made it difficult to articulate the gene regulatory programs enabling regeneration of individual cell types. more...
Organism:
Xenopus tropicalis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24884
2 Samples
Download data: MTX, TSV, TXT
Series
Accession:
GSE146836
ID:
200146836
9.

Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors

(Submitter supplied) Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable the growth and differentiation of new tissue, a process executed over multiple days and across dozens of cell types. The heterogeneity of tissues and temporally-sensitive fate decisions involved has made it difficult to articulate the gene regulatory programs enabling regeneration of individual cell types. more...
Organism:
Xenopus tropicalis
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24884
31 Samples
Download data: BED, TXT
Series
Accession:
GSE146830
ID:
200146830
10.

ATAC-seq identifies accessible chromatin domains in gastrula stage Xenopus laevis

(Submitter supplied) In the embryo, inductive cues are interpreted by competent tissues in a spatially and temporally restricted manner, and the mechanisms for the loss of responsiveness are not well understood. To test the hypothesis that loss of competence is associated with changes in chromatin accessibility, we adapted the assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) for use in Xenopus laevis to evaluate genome-wide changes in chromatin accessibility in early and late gastrula stages. more...
Organism:
Xenopus laevis
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL22393
6 Samples
Download data: BED
Series
Accession:
GSE138905
ID:
200138905
11.

Axonal precursor miRNAs hitchhike on endosomes and locally regulate the development of neural circuits

(Submitter supplied) Various species of non-coding RNAs (ncRNAs) are enriched in subcellular compartments but the mechanisms orchestrating their localization and their local functions remain largely unknown. We investigated both aspects using the elongating retinal ganglion cell axon and its tip, the growth cone, as models. We reveal that specific endogenous precursor microRNAs (pre-miRNAs) are actively trafficked to distal axons by hitchhiking primarily on late endosomes / lysosomes. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21248
1 Sample
Download data: TXT
Series
Accession:
GSE124168
ID:
200124168
12.

Identification of genes regulated by Erythroferrone (ERFE) in Xenopus embryos at tadpole stages.

(Submitter supplied) RNA-seq was employed to analyze differential gene expression upon ERFE knockdown in Xenopus laevis embryos at three different developmental stages using two non-overlapping translation blocking morpholino oligonucleotides. Only a small number of genes was affected by both morpholinos and at more than one of the developmentel stages analyzed, among them gja4, the gene coding for Gap junction junction protein Alpha 4.
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22393
45 Samples
Download data: TXT
Series
Accession:
GSE126058
ID:
200126058
13.

Profiling of alternative transcription start sites and alternative polyadenylation sites in Xenopus tropicalis

(Submitter supplied) We have developed both WTSS-seq (whole transcriptome start site sequencing) and WTTS-seq (whole transcriptome termini site sequencing) methods to capture either 5’- or 3’-ends of transcripts. HATT-seq (head and tail tag sequencing) is still under development, which can be used to capture both 5’- and 3’ ends of each transcript simultaneously. Iso-seq was used to produce full-length transcripts, which can be used to validate both alternative transcription start sites and alternative polyadenylation sites. more...
Organism:
Xenopus tropicalis
Type:
Expression profiling by high throughput sequencing; Other
4 related Platforms
30 Samples
Download data: TXT
Series
Accession:
GSE110063
ID:
200110063
14.

ATAC-Seq of Xenopus tail regeneration

(Submitter supplied) Mammals possess limited regeneration capabilities, where the few examples of scarless healing tend to be restricted to early development. In light of this, it is of great interest to study animals that can faithfully regrow complete appendages, and uncover the biological properties that facilitate this process. Xenopus tropicalis tadpoles are excellent vertebrate models of regeneration, as they rapidly recover lost tails within just one week post amputation. more...
Organism:
Xenopus tropicalis
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL21874 GPL24884
18 Samples
Download data: BW
Series
Accession:
GSE138303
ID:
200138303
15.

Genome-wide analysis of mRNA polyadenylation and translation during vertebrate oocyte maturation

(Submitter supplied) Changes in gene expression are required to orchestrate changes in cell state during development. Most cells change patterns of gene expression through transcriptional regulation. In contrast, oocytes are transcriptionally silent and use changes in mRNA poly-A tail length to control protein production. Recent technical advances have enabled genome-wide measurement of poly-A tail length. Poly-A tail lengthening is correlated with translational activation and poly-A tail shortening is correlated with translational repression at a global level during early development. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL18936 GPL17682
32 Samples
Download data: TXT
Series
Accession:
GSE134537
ID:
200134537
16.

RNA-seq based identification of potential RARgamma target genes in Xenopus laevis

(Submitter supplied) The development of massively parallel sequencing technologies has revolutionized transcriptome analysis. Sequencing of total cDNA (RNA-Seq) can determine the expression levels of known and novel transcripts with high sensitivity from various developmental stages or conditions. Here we report a robust method for RNA-Seq in Xenopus laevis and apply it to understanding how modulation of retinoic acid signaling alters the transcriptome in early Xenopus laevis development. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21377
15 Samples
Download data: FA, TXT
Series
Accession:
GSE77281
ID:
200077281
17.

Regulated local synthesis of ribosomal proteins maintains ribosome function in axons

(Submitter supplied) Ribosome assembly occurs mainly in the nucleolus yet recent studies have revealed robust enrichment and translation of mRNAs encoding many ribosomal proteins (RPs) in axons, far away from neuronal cell bodies. Here, we report a physical and functional interaction between locally synthesized RPs and ribosomes in the axon. We show that axonal RP translation is regulated through a novel sequence motif, CUIC, that forms an RNA-loop structure in the region immediately upstream of the initiation codon. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21248
2 Samples
Download data: TXT
Series
Accession:
GSE135502
ID:
200135502
18.

DNA methylation dynamics underlie metamorphic gene regulation programs in Xenopus tadpole brain [RNA-seq]

(Submitter supplied) Changes in gene expression in the preoptic area/hypothalamus/thalamus of Xenopus tropicalis tadpoles were analyzed using RNAseq at four stages of metamorphosis.
Organism:
Xenopus tropicalis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21874
12 Samples
Download data: FA, MATRIX, TXT
Series
Accession:
GSE140120
ID:
200140120
19.

DNA methylation dynamics underlie metamorphic gene regulation programs in Xenopus tadpole brain

(Submitter supplied) Changes in DNA methylation in the preoptic area/hypothalamus/thalamus of Xenopus tropicalis tadpoles were analyzed using Methylated DNA Capture sequencing (MethlCap-seq) at four stages of metamorphosis.
Organism:
Xenopus tropicalis
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL21874
15 Samples
Download data: BED
Series
Accession:
GSE139267
ID:
200139267
20.

Gene expression in dorsal halves of Apcdd1-depleted Xenopus laevis embryos

(Submitter supplied) apcdd1, a gene mutated in hereditary hypotrychosis simplex, is a maternally expressed gene in Xenopus embryos, required for correct formation of anterior and dorsal structures. Initial data suggested Apcdd1 functions as zyogtic Wnt inhibitor. Here we indentify genes regulated by Apcdd1 in the organizer area of early gastrula stage embryos
Organism:
Xenopus laevis
Type:
Expression profiling by array
Platform:
GPL10756
6 Samples
Download data: CEL
Series
Accession:
GSE138834
ID:
200138834
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