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Items: 1 to 20 of 10296

1.

High-throughput single-cell transcriptomes of the brain of the nudibranch Berghia stephanieae

(Submitter supplied) Previously, transcriptomics data for mollusc has been obtained by whole-brain bulk RNA-seq and low-throughput scRNA-seq. We want to construct the first molluscan high-throughput single-neuron transcriptomes for Berghia stephanieae. Around 129,000 cells were collected from 20 brains and the libraries were constructed using the 10X Genomics' Chromium platform. The brains were separated into two samples: the main brain (i.e., the cerebropleural, pedal, buccal ganglion) and the rhinophore ganglion sample. more...
Organism:
Berghia stephanieae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29686
2 Samples
Download data: MAT, MTX, TXT
Series
Accession:
GSE165967
ID:
200165967
2.

Non-canonical base modifications of bacterial origin in a eukaryotic genome

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Adineta vaga
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL27729 GPL27727 GPL27728
17 Samples
Download data: BED, BW
Series
Accession:
GSE140052
ID:
200140052
3.

Non-canonical base modifications of bacterial origin in a eukaryotic genome [RNA-seq]

(Submitter supplied) Methylation of cytosines at the 5th carbon position of the aromatic ring has long been regarded as the predominant type of DNA base modification in eukaryotes. Often called “the fifth base”, C5-methylcytosine (5mC) plays an important role in genome defense against mobile genetic elements, and is mostly associated with transcriptional silencing, establishment of the closed chromatin configuration, and repressive histone modifications. more...
Organism:
Adineta vaga
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL27729 GPL27727
5 Samples
Download data: FASTA, GFF3, TXT
Series
Accession:
GSE140051
ID:
200140051
4.

Non-canonical base modifications of bacterial origin in a eukaryotic genome [MeDIP-seq]

(Submitter supplied) Methylation of cytosines at the 5th carbon position of the aromatic ring has long been regarded as the predominant type of DNA base modification in eukaryotes. Often called “the fifth base”, C5-methylcytosine (5mC) plays an important role in genome defense against mobile genetic elements, and is mostly associated with transcriptional silencing, establishment of the closed chromatin configuration, and repressive histone modifications. more...
Organism:
Adineta vaga
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL27728
4 Samples
Download data: BED, BW
Series
Accession:
GSE140050
ID:
200140050
5.

Non-canonical base modifications of bacterial origin in a eukaryotic genome [ChIP-seq]

(Submitter supplied) Methylation of cytosines at the 5th carbon position of the aromatic ring has long been regarded as the predominant type of DNA base modification in eukaryotes. Often called “the fifth base”, C5-methylcytosine (5mC) plays an important role in genome defense against mobile genetic elements, and is mostly associated with transcriptional silencing, establishment of the closed chromatin configuration, and repressive histone modifications. more...
Organism:
Adineta vaga
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL27727
8 Samples
Download data: BED
Series
Accession:
GSE140049
ID:
200140049
6.

Single-cell RNA sequencing atlas from a bivalve larva enhances classical cell lineage studies

(Submitter supplied) Here, we report on the gene expression profile of individual cells of the trochophore larva of the invasive freshwater bivalve Dreissena rostriformis as inferred from single cell RNA sequencing. We generated transcriptomes of 632 individual cells and identified seven transcriptionally distinct cell populations. Developmental trajectory analyses identify cell populations that, for example, share an ectodermal origin such as the nervous system, the shell field, and the prototroch. more...
Organism:
Dreissena rostriformis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL31147
1 Sample
Download data: FASTA, MTX, TSV
Series
Accession:
GSE192624
ID:
200192624
7.

Rhesus macaques self-curing from a schistosome infection can display complete immunity to challenge

(Submitter supplied) The rhesus macaque provides a unique model of acquired immunity against schistosomes, which afflict >200 million people worldwide. By monitoring bloodstream levels of parasite-gut derived antigen, we show that from week 10 onwards an established infection with Schistosoma mansoni was cleared in an exponential manner, eliciting resistance to reinfection. Secondary challenge at week 42 demonstrated that protection was strong in all animals and complete in some. more...
Organism:
Schistosoma mansoni
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30536
12 Samples
Download data: TXT
Series
Accession:
GSE182594
ID:
200182594
8.

High-throughput transcriptomics reveals mechanisms of nanopesticides – nanoformulation vs conventional pesticides and active ingredient – a case study with Enchytraeus crypticus

(Submitter supplied) Nanoformulations are developed to offer controlled release of active ingredients (a.i.) and thus aim to keep functionality while having a smaller environmental footprint. However, the toxic effects of nanoformulations, particularly to non-target organisms, is poorly known, and even more so at the mechanistic level. The aim of the present study was to investigate the mechanisms of toxicity of atrazine when delivered as a nanoformulation of atrazine (nano_ATZ), a commercial atrazine-based formulation (Gesaprim), and the pure a.i. more...
Organism:
Enchytraeus crypticus
Type:
Expression profiling by array
Platform:
GPL20310
48 Samples
Download data: TXT
Series
Accession:
GSE176125
ID:
200176125
9.

A non-ribosomal peptide pheromone controls male-induced female sexual development in Schistosoma mansoni II

(Submitter supplied) βAlanyl-tryptamine (BATT) is a peptide secreted by male S. mansoni upon pairing with a female parasite. Treatment of synthetic BATT on virgin females wihtout any pairing is sufficient to induce sexual development and egg depostiion.
Organism:
Schistosoma mansoni
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28252
6 Samples
Download data: CSV
Series
Accession:
GSE191062
ID:
200191062
10.

Characterization of small RNAs in the different developmental stages of carcinogenic parasite-Clonorchis sinensis

(Submitter supplied) Clonorchiasis is a foodborne zoonotic disease caused by Clonorchis sinensis which belongs to trematodes with a complex lifecycle, there are increasing evidences that small RNAs including microRNAs and PIWI-interacting RNAs can participate in regulation of embryonic development. However, there is little information about the small RNAs in the different developmental stages of C. sinensis. In the present study, we investigated profiles of miRNAs and piRNAs in the different developmental stages including eggs, metacercaria and adults of C. more...
Organism:
Clonorchis sinensis
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL27485
4 Samples
Download data: TXT, XLSX
Series
Accession:
GSE137695
ID:
200137695
11.

The Schistosoma mansoni nuclear receptor FTZ-F1 maintains esophageal gland function via direct transcriptional regulation of meg-8.3

(Submitter supplied) The schistosome homolog of ftz-f1 is a nuclear receptor. In order to understand the function of Smftz-f1, we performed RNAseq with samples taken on two days, Day 5 and Day 9, on either control (RNAi) or Smftz-f1 (RNAi) parasites to see the transcriptional consequences of Smftz-f1 RNAi and to find potential transcriptional targets.
Organism:
Schistosoma mansoni
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28252
12 Samples
Download data: XLSX
Series
Accession:
GSE188736
ID:
200188736
12.

Diagnosis of Taenia solium infections based on “mail order” RNA-sequencing of single tapeworm egg isolates from stool samples

(Submitter supplied) Combined community health programs aiming at health education, preventive antiparasitic chemotherapy, and vaccination of pigs have proven their potential to regionally reduce and even eliminate Taenia solium infections that are associated with a high risk of neurological disease through ingestion of T. solium eggs. Yet it remains challenging to target T. solium endemic regions precisely or to make exact diagnoses in individual patients. more...
Organism:
Taenia solium
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL30204 GPL30205
3 Samples
Download data: BAM, TAB
13.

S-adenosylhomocysteine hydrolase regulates anterior patterning in Dugesia japonica

(Submitter supplied) We report RNA-seq results from planarians of Dugesia japonica species which have developed resistance to a S-adenosyl homocysteine hydrolase inhibitor AdOx after prolonged exposure.
Organism:
Dugesia japonica
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28963
6 Samples
Download data: CSV, FASTA, TXT
Series
Accession:
GSE155645
ID:
200155645
14.

A non-ribosomal peptide pheromone controls male-induced female sexual development in Schistosoma mansoni

(Submitter supplied) gli1 is a gene in the male S. mansoni required for female sexual development. As a putative transcription factor, RNAseq comparing pairs with gli1 knocked-down or control males was performed to look for the genes which are trancriptionally regulated by gli1. sm-nrps was one of the essential candidate discovered in this analysis that has been characterized in the same publication, revealing a pheromone directed novel mechanism of female schistosome sexual development.
Organism:
Schistosoma mansoni
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28252
24 Samples
Download data: CSV
Series
Accession:
GSE184849
ID:
200184849
15.

Application of a Agilent hydatid 4x44k - cDNA microarray for identification of dihydroartemisinin targeting genes in Echinococcus granulosus larval protoscoleces

(Submitter supplied) A cDNA microarray composed of 9306 uniEST probes was constructed andapplied to detect the gene expression profile of protoscoleces of E. granulosus treated with dihydroartemisinin in vitro, respectively. Compared with the untreated protoscoleces, 752 genes were up-regulated and 269 genes were down-regulated in protoscoleces treated with dihydroartemisinin. The differential expression genes in protoscoleces induced by dihydroartemisinin were clustered into molecular metabolic process, cell development and differentiation, anatomical structure morphogenesis and formation, and were enriched in calcium signaling pathway, protein processing in endoplasmic reticulum (ER), molecular metabolism and synthesis, Wnt signaling pathway, MAPK signaling pathway, TGF-beta signaling pathway.
Organism:
Echinococcus granulosus
Type:
Expression profiling by array
Platform:
GPL30676
6 Samples
Download data: TXT, XLSX
Series
Accession:
GSE184908
ID:
200184908
16.

equinox is a planarian wound epidermis gene required for the initiation of regeneration

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Schmidtea mediterranea
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15553
123 Samples
Download data: MTX, TSV
Series
Accession:
GSE179295
ID:
200179295
17.

equinox RNAi gene expression profiling

(Submitter supplied) Regeneration is a widespread phenomenon that often requires formation of a new tissue outgrowth at wounds called a blastema. Identifying the key signals that trigger blastema formation is therefore fundamental for understanding the mechanistic basis of regeneration. We uncovered a role for the wound epidermis in regeneration initiation in planarians. The gene equinox is expressed within hours of injury in the planarian wound epidermis and encodes a secreted protein conserved in many phyla. more...
Organism:
Schmidtea mediterranea
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15553
58 Samples
Download data: TXT, XLSX
Series
Accession:
GSE179293
ID:
200179293
18.

bmp4 RNAi gene expression profiling

(Submitter supplied) Regeneration is a widespread phenomenon that often requires formation of a new tissue outgrowth at wounds called a blastema. Identifying the key signals that trigger blastema formation is therefore fundamental for understanding the mechanistic basis of regeneration. We uncovered a role for the wound epidermis in regeneration initiation in planarians. The gene equinox is expressed within hours of injury in the planarian wound epidermis and encodes a secreted protein conserved in many phyla. more...
Organism:
Schmidtea mediterranea
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15553
60 Samples
Download data: TXT, XLSX
Series
Accession:
GSE179291
ID:
200179291
19.

Single cell gene expression profiling using 10x v3

(Submitter supplied) Regeneration is a widespread phenomenon that often requires formation of a new tissue outgrowth at wounds called a blastema. Identifying the key signals that trigger blastema formation is therefore fundamental for understanding the mechanistic basis of regeneration. We uncovered a role for the wound epidermis in regeneration initiation in planarians. The gene equinox is expressed within hours of injury in the planarian wound epidermis and encodes a secreted protein conserved in many phyla. more...
Organism:
Schmidtea mediterranea
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15553
5 Samples
Download data: MTX, TSV
Series
Accession:
GSE179290
ID:
200179290
20.

RNA Seq analysis following RNAi perturbation of Hox genes in flatworm

(Submitter supplied) Hox genes are highly conserved transcription factors renowned for their roles in the segmental patterning of the embryonic anterior-posterior (A/P) axis1. Emerging evidence for Hox gene expression and function in postnatally derived structures has fueled interest in their additional roles beyond embryogenesis2,3. We report novel functions for Hox genes in A/P directed adult tissue segmentation and transverse fission behavior underlying asexual reproduction in the planaria, Schmidtea mediterranea. more...
Organism:
Schmidtea mediterranea
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21689
24 Samples
Download data: TXT
Series
Accession:
GSE159876
ID:
200159876
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