GEO DataSets

(Submitter supplied) Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

6 Samples

Download data: TXT

(Submitter supplied) Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

6 Samples

Download data: TXT

(Submitter supplied) Transcriptomic analysis of suspended and flocculated (with the fungi) Synechocystis cells suggested that the EM-mediated co-flocculation was a result of down-regulation of the minor pilin genes and up-regulation of several genes including the chaperone gene for pilin regulation, the S-layer protein genes, the exopolysaccharide-polymerization gene, and the genes for signaling proteins involved in cell attachment and abiotic-stress responses. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28944

6 Samples

Download data: TXT

(Submitter supplied) We performed V(D)J scRNA sequencing to find transcriptional and B cell receptor repertoire differences in the germinal center of the draining lymph node of mice born to mothers chronically infected with Schistosoma mansoni. Cite-seq was used to help identify antigen specific cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24247

12 Samples

Download data: CSV, H5

(Submitter supplied) Hepatocellular carcinoma (HCC) is one of the most common gastrointestinal (GI) malignancies and a major cause of death worldwide, with limited therapeutic options. Although Mixed Lineage Kinase 3 (MLK3), a MAPKKK, has emerged as a key regulator of acute liver injury, inflammation, and non-alcoholic steatohepatitis (NASH), its role in HCC remains unclear. TCGA databases suggest an elevated expression of MAP3K11 (gene of MLK3) and TMA studies show higher MLK3 activation in human HCCs compared to the normal livers. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

10 Samples

Download data: TXT

(Submitter supplied) We have conducted RNA-seq analysis on Group B Streptococcus (GBS) when interacting with human stem-cell (hSC) derived BECs. The study contains a control group for GBS and a control group for BECs each with three biological replicates. The last group contains GBS infection BECs and also has three replicates.

Organism:

Homo sapiens; Streptococcus sp. 'group B'

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL31998 GPL31999

9 Samples

Download data: CSV

(Submitter supplied) Transposon-encoded tnpB and iscB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination. These widespread gene families were repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas12. We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas. more...

Organism:

Enterobacter cloacae; Escherichia coli; Enterobacter sp. BIDMC93

Type:

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

4 related Platforms

51 Samples

Download data: BED, BW, XLSX

(Submitter supplied) This study aimed to investigate the survival of an environmental isolate under salt stress and to identify the various genes involved in stress protection following RNA sequencing analysis. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to salt stress.

Organism:

Bacillus sp. (in: firmicutes)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34384

4 Samples

Download data: TXT

(Submitter supplied) Background Bleomycin (BLM)-induced lung injury is characterized by the mixed histopathologic changes with inflammation and fibrosis. These changes are also observed in human patients with bronchopulmonary dysplasia, idiopathic pulmonary fibrosis, and chronic obstructive pulmonary disease. Although no curative therapies for these lung vsdiseases exist, stem cell therapy has emerged as a potential therapeutic option. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: TXT

(Submitter supplied) Mutation in the alveolar epithelial type 2 cell Surfactant Protein-C gene [SP-CI73T] is associated with pulmonary fibrosis (PF). We have previously demonstrated that inducible expression of the most common PF-linked mutation in the SP-C gene triggers inflammatory exacerbations of lung injury, progressing to fibrosis. We used single-cell sequencing to define the phenotype of epithelial, endothelial, immune and stromal cells accumulating in the lung at a time coordinated with peak injury (14 d post induction) and fibrotic remodeling (42 d post induction). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

19 Samples

Download data

(Submitter supplied) Adult inflammatory bowel disease is incompletely understood. We combine unbiased single-cell RNA sequencing (gene expression profiling, CITE-seq derived cell surface protein data, TCR and BCR sequence data) with unbiased spatial transcriptomics to interrogate changes across immune and non-immune populations in colitis and health, across tissue and blood. We compare idiopathic ulcerative colitis with hitherto under-studied immune checkpoint therapy induced colitis, utilizing non-inflamed disease states as additional controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

62 Samples

Download data

(Submitter supplied) Adult inflammatory bowel disease is incompletely understood. We combine unbiased single-cell RNA sequencing (gene expression profiling, CITE-seq derived cell surface protein data, TCR and BCR sequence data) with unbiased spatial transcriptomics to interrogate changes across immune and non-immune populations in colitis and health, across tissue and blood. We compare idiopathic ulcerative colitis with hitherto under-studied immune checkpoint therapy induced colitis, utilizing non-inflamed disease states as additional controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL18573

15 Samples

Download data

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL24676

117 Samples

Download data: ZIP

(Submitter supplied) Adult inflammatory bowel disease is incompletely understood. We combine unbiased single-cell RNA sequencing (gene expression profiling, CITE-seq derived cell surface protein data, TCR and BCR sequence data) with unbiased spatial transcriptomics to interrogate changes across immune and non-immune populations in colitis and health, across tissue and blood. We compare idiopathic ulcerative colitis with hitherto under-studied immune checkpoint therapy induced colitis, utilizing non-inflamed disease states as additional controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

16 Samples

Download data: ZIP

(Submitter supplied) Protein complexes of aegerolysins pleurotolysin A2 (PlyA2) and pleurotolysin B (PlyB) from oyster mushrooms Pleurotus sp. display targeted toxicity against Colorado potato beetle (CPB; Leptinotarsa decemlineata) larvae. This selective toxicity is achieved through aegerolysins' interaction with insect-specific membrane sphingolipids. This study explores the potential adaptive response of CPB larvae to the aegerolysin complex.

Organism:

Leptinotarsa decemlineata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33587

16 Samples

Download data: TXT, XLSX

(Submitter supplied) Root exudates contain specialised metabolites that affect the plant’s root microbiome. How host-specific microbes cope with these bioactive compounds, and how this ability shapes root microbiomes, remains largely unknown. We investigated how maize root bacteria metabolise benzoxazinoids, the main specialised metabolites of maize. Diverse and abundant bacteria metabolised the major compound in the maize rhizosphere MBOA and formed AMPO. more...

Organism:

Microbacterium sp. LMB2-1.2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34376

10 Samples

Download data: TXT

(Submitter supplied) Here we developed BreakTag, a versatile, highly parallel and scissile-aware methodology for the profiling of Cas9-induced DNA double strand break (DSBs), to identify molecular determinants influencing Cas9 incisions

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

4 Samples

Download data: TXT

(Submitter supplied) Here we developed BreakTag, a versatile, highly parallel and scissile-aware methodology for the profiling of Cas9-induced DNA double strand break (DSBs), to identify molecular determinants influencing Cas9 incisions

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

48 Samples

Download data: BED

(Submitter supplied) East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. more...

Organism:

Haplochromis burtoni; Oreochromis niloticus; Maylandia zebra; Astatotilapia calliptera; Tropheops sp. 'mauve'; Pundamilia nyererei

Type:

Expression profiling by high throughput sequencing

6 related Platforms

40 Samples

Download data: TXT

(Submitter supplied) East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. more...

Organism:

Astatotilapia calliptera; Pundamilia nyererei; Oreochromis niloticus; Haplochromis burtoni; Maylandia zebra; Tropheops sp. 'mauve'

Type:

Non-coding RNA profiling by high throughput sequencing

6 related Platforms

31 Samples

Download data: TXT