GEO DataSets

(Submitter supplied) Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related death, primarily due to limited therapeutic targets and the emergence of drug resistance. In this study, we conducted CRISPR knockout screens to identify the pre-mRNA processing factor 19 (PRPF19) as a potential therapeutic target for NSCLC. Our findings revealed that PRPF19 is highly expressed in NSCLC, and its expression is negatively correlated with the clinical outcomes. more...

Organism:

Musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34247

9 Samples

Download data: CSV

(Submitter supplied) We used scRNA-seq to examine serotonergic function in asexual planarians. We profiled 47,292 single cell transcriptomes of planarian of 3 different RNAi categories: gfp(RNAi), lhx1/5-1(RNAi) and pitx(RNAi). We detected changes in cell type frequency and gene expression patterns in planarian of different knock-down conditions, capturing regulatory programs of distinct cell types in response to loss of serotonergic function.

Organism:

Schmidtea mediterranea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29967

5 Samples

Download data: MTX, TSV

(Submitter supplied) The innate immune response is the first line of defense for all animals to not only detect invading microbes and toxins but also sense and interface with the environment. One such environment that can significantly affect innate immunity is spaceflight. In this study, we explored the impact of microgravity stress on key elements of the NFκB innate immune pathway. The symbiosis between the bobtail squid Euprymna scolopes and its beneficial symbiont Vibrio fischeri was used as a model system under a simulated microgravity environment. more...

Organism:

Euprymna scolopes

Type:

Expression profiling by array

Platform:

GPL33929

96 Samples

Download data: RCC

(Submitter supplied) The assay for transposase-accessible chromatin using sequencing (ATAC-seq) at single-cell level can provide different perspectives of regulatory patterns based on cell type-specific accessible regions. While human genomic elements have been well studied, understanding how nuclear acid sequence regulates the expression of target genes in a genome-wide level in other organisms remains a major challenge. more...

Organism:

Eisenia andrei

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30479

2 Samples

Download data: BED

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

Organism:

Drosophila melanogaster; Eisenia andrei; Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30277 GPL30479 GPL32518

13 Samples

Download data: BED

(Submitter supplied) The assay for transposase-accessible chromatin using sequencing (ATAC-seq) at single-cell level can provide different perspectives of regulatory patterns based on cell type-specific accessible regions. While human genomic elements have been well studied, understanding how nuclear acid sequence regulates the expression of target genes in a genome-wide level in other organisms remains a major challenge. more...

Organism:

Eisenia andrei

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30479

1 Sample

Download data: BED

(Submitter supplied) Transcriptome profiling of whole proboscis and body wall of the marine Polychaeta Glycera alba, adults, wild population (sex undiscriminated), collected from the muddy-sandy intertidal flats at W Portugal (2020). Transcriptome profiling of glandular and muscular regions of proboscis of the marine Polychaeta Hediste diversicolor, adults, wild population (sex undiscriminated), collected from the muddy-sandy intertidal flats at W Portugal (2019).

Organism:

Hediste diversicolor; Glycera alba

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL31948 GPL31947

12 Samples

Download data: FASTA, XLSX

(Submitter supplied) We used scRNA-seq to examine cell type allometry in asexual planarians. We profiled 28,738 single cell transcriptomes of planarian of 3 different sizes categories: small (S), medium (M) and large (L). We detected changes in cell type frequency and gene expression patterns in planarian of different sizes, capturing regulatory programs of distinct cell types in response to allometric scaling.

Organism:

Schmidtea mediterranea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29967

2 Samples

Download data: MTX, TSV

(Submitter supplied) Nrf2 plays a pivotal role in regulating oxidative stress, and in mollusks, understanding how Nrf2 governs the expression of new target genes is crucial in the context of oxidative stress. In this study, we have identified solute carrier family 35 member E2 (SLC35E2) as a novel Nrf2 target gene that counteracts the oxidative stress response induced by Bap.Initially, we confirmed the Nrf2-SLC35E2 interaction through dual luciferase and qRT-PCR assays, demonstrating that Nrf2 both targeted and inhibited SLC35E2 expression. more...

Organism:

Mytilus coruscus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33732

2 Samples

Download data: TXT

(Submitter supplied) Time-course RNA-Seq of X-ray irradiated planarians Dugesia japonica.

Organism:

Dugesia japonica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30183

18 Samples

Download data: CSV

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

Organism:

Dugesia japonica

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32771 GPL30183

19 Samples

Download data: CSV

(Submitter supplied) A single cell RNA-Seq analysis of Dugesia japonica intact animals by TAS-Seq (Shichino et al, 2022)

Organism:

Dugesia japonica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32771

1 Sample

Download data: CSV

(Submitter supplied) The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical models or comparative studies of already old sex chromosomes. more...

Organism:

Macrostomum lignano

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33731

24 Samples

Download data: SF

(Submitter supplied) We accomplished de novo transcriptome assembly for planarian Dugesia japonica.

Organism:

Dugesia japonica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32771

18 Samples

Download data: FASTA, XLSX

(Submitter supplied) We accomplished the m6A landscapes at single-base resolution with multiple time-points during AP axis regeneration for planarian Dugesia japonica.

Organism:

Dugesia japonica

Type:

Other

Platform:

GPL32771

19 Samples

Download data: FASTA, XLSX

(Submitter supplied) Background: The establishment of the anterior-posterior (A-P) axis is a crucial step during tissue repair and regeneration. Despite the association reported recently of N6-methyladenosine (m6A) with regeneration, the mechanism underlying the regulation of m6A in A-P axis specification during regeneration remains unknown. Herein, we deciphered the m6A landscape at a single-base resolution at multiple time points during A-P axis regeneration and constructed the de novo transcriptome assembly of the Dugesia japonica planarian.

Organism:

Dugesia japonica

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL32771

37 Samples

Download data

(Submitter supplied) To investigate the role of alx-3 in activating wound-induced transciptional programs during anterior regneneraiton, control(RNAi) and alx-3(RNAi) planarians were amputated below the pharynx and were allowed to regenerate for 0.5 hours post-amputation (HPA), 6HPA, 24HPA, 48HPA and 72HPA. Intact animals were are also included.Tissue from tail fragments and intact animals was collected at each time point for RNA extraction and cDNA synthesis. more...

Organism:

Schmidtea mediterranea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29967

36 Samples

Download data: XLSX

(Submitter supplied) The complexity of cell types and states revealed by scRNAseq cell atlases presents a challenge for the systematic analysis of fate determinants using traditional screening methodologies. Differentiation in the planarian Schmidtea mediterranea exemplifies this problem, as these animals continuously produce over 100 differentiated cell types for homeostasis and regeneration using adult pluripotent stem cells termed neoblasts. more...

Organism:

Schmidtea mediterranea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21689

75 Samples

Download data: XLSX

(Submitter supplied) Single-cell transcriptomics (scRNA-seq) has revolutionized our understanding of cell types and states in various contexts, such as development and disease. Most methodology relies on poly(A) enrichment to selectively capture protein-coding polyadenylated transcripts, intending to exclude ribosomal transcripts that constitute >80% of the transcriptome. However, it is common for ribosomal transcripts to sneak into the library, which can add significant background by flooding libraries with irrelevant sequences. more...

Organism:

Schmidtea mediterranea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33372

9 Samples

Download data: MTX, TSV

(Submitter supplied) Sample dataset for the described bioinformatic pipeline (piRNAnalyzer) comprising epidermal piRNA libraries of Schmidtea mediterranea

Organism:

Schmidtea mediterranea

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21689

3 Samples

Download data: BW