GEO DataSets

(Submitter supplied) In this study colorectal cancer (CRC) patient-derived cancer-associated fibroblasts (CAFs) and primary monocytes or macrophages were co-cultured in 2D set-up and single-cell transcriptomics was employed to analyze the phenotypic and functional changes of the myeloid cells and CAFs upon their interaction. The results showed that CAFs instruct monocytes to gain a tumor-associated macropages (TAM)-like cells phenotype. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

7 Samples

Download data: MTX, TSV

(Submitter supplied) Concomitant cloning of RNA degradation products is a major issue in standard small RNA-sequencing practices. It not only adds complexity in bona fide sRNA characterization, but also affects experimental replicability and sometimes results in library construction failure. Given that all kinds of canonical plant small RNAs bearing the 3’ end 2’-O-methylation modification, we here developed an sRNA-seq method (named terminal ribose-modified sRNA sequencing, TRM-sRNA-seq).

Organism:

Arabidopsis thaliana; Solanum lycopersicum; Zea mays; Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

54 Samples

Download data: TXT

(Submitter supplied) Cardiovascular disease remains a significant global health concern, yet the cardiotoxic effects of environmental chemicals are largely unexplored. Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-Cardiomyocytes) are well-established as valuable high-throughput cardiotoxicity testing model based on the analysis of various beating parameters; however, additional adverse effects that may not be directly related to ion channel activity are difficult to ascertain from traditional assays. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4558 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24247 GPL17021

52 Samples

Download data: XLSX

(Submitter supplied) Transfer RNAs (tRNAs) play a central and well recognized role in protein synthesis. Recent studies revealed that these molecules can be cleaved to generate tRNA fragments (tRFs) with regulatory functions. Here, we studied the contribution of tRFs to pancreatic β-cell loss during the initial phases of type 1 diabetes (T1D), an autoimmune disorder characterized by the invation of immune cells in the pancreas and progressive loss of insulin-secreting cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: XLSX

(Submitter supplied) Brown adipose tissue plays a crucial role in modulating whole-body energy expenditure through the thermogenic function of its mitochondrial respiratory chain. Pharmacological interventions targeting this function hold significant therapeutic promise. Thus, gaining a comprehensive understanding of the pathophysiological regulation of brown adipose tissue is imperative for future therapeutic applications. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

6 Samples

Download data: TXT

(Submitter supplied) In this study we combined small RNA isolation from post-ribosomal supernatant with RibOxi-seq to identify 2’-O-methylation (Nm) in single nucleotide resolution. Our analysis identified ~49 Nm sites in tRNA, snRNAs, snoRNAs, 7SL RNA and vtRNA.

Organism:

Trypanosoma brucei brucei TREU927

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL30921

4 Samples

Download data: CSV

(Submitter supplied) In this study we used RibOxi-seq to identify 2’-O-methylation (Nm) present on mRNAs in single nucleotide resolution. Our analysis identified hundreds of Nm sites in mRNAs, predominantly in CDS and 3’ UTR.

Organism:

Trypanosoma brucei

Type:

Other

Platform:

GPL20572

3 Samples

Download data: CSV

(Submitter supplied) In this study we report the complete repertoire of 2'-O-methylation sites present in the rRNA of Leishmania amazonensis rRNAs and a subset of small RNAs using RibOxi-seq.

Organism:

Leishmania amazonensis

Type:

Other

Platform:

GPL30917

3 Samples

Download data: TXT

(Submitter supplied) In this study we profiled the complete repertoire of 2'-O-methylation sites present in the rRNA and a subset of small RNAs of Leishmania major rRNA using RibOxi-seq.

Organism:

Leishmania major

Type:

Other

Platform:

GPL21434

3 Samples

Download data: TXT

(Submitter supplied) In this study we used RibOxi-seq to identify 2’-O-methylation (Nm) present on rRNAs in single nucleotide resolution.

Organism:

Leishmania donovani

Type:

Other

Platform:

GPL30916

3 Samples

Download data: TXT

(Submitter supplied) We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species, except mouse. We found endo-siRNAs resulted from the truncated Dicer isoform were mouse-specific, and os-piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2’-3’-O-methylation. The sequences of many highly expressed piRNA clusters are fast-evolving compared with their syntenic genomic locations, and the TE families distributing in the conserved piRNA clusters are various between species.

Organism:

Canis lupus familiaris

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25760

8 Samples

Download data

(Submitter supplied) We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species, except mouse. We found endo-siRNAs resulted from the truncated Dicer isoform were mouse-specific, and os-piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2’-3’-O-methylation. The sequences of many highly expressed piRNA clusters are fast-evolving compared with their syntenic genomic locations, and the TE families distributing in the conserved piRNA clusters are various between species.

Organism:

Capra hircus; Rattus norvegicus; Danio rerio; Homo sapiens; Canis lupus familiaris; Sus scrofa domesticus; Cavia porcellus; Macaca fascicularis; Oryctolagus cuniculus; Cricetulus griseus; Mesocricetus auratus; Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

12 related Platforms

138 Samples

Download data

(Submitter supplied) Despite the well-established significance of transcription factors (TFs) in pathogenesis, their utilization as pharmacological targets has been limited by the inherent challenges mainly associated with modulating their protein-protein and protein-DNA interactions. The lack of defined small-molecule binding pockets and the nuclear localization of TFs makes neither small molecule inhibitors nor neutral antibodies suitable in blocking TF interactions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TXT

(Submitter supplied) MicroRNA (miRNA) maturation is critically dependent on structural features of primary transcripts (pri-miRNAs). However, the scarcity of determined pri-miRNA structures has limited our understanding of miRNA maturation. Here we employed SHAPE-MaP, a high-throughput RNA structure probing method, to unravel the secondary structures of 476 high-confidence human pri-miRNAs. Our SHAPE-based structures diverge substantially from those inferred solely from computation, particularly in the apical loop and basal segments, underlining the need for experimental data in RNA structure prediction. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL23227

12 Samples

Download data: CSV

(Submitter supplied) In metazoans mitochondrial DNA (mtDNA) or retrotransposon cDNA released to cytoplasm are degraded by nucleases to prevent sterile inflammation. It remains unknown whether degradation of these DNA also prevents nuclear genome instability. We used an amplicon sequencing-based method in yeast enabling analysis of millions of DSB repair products. In non-dividing stationary phase cells, Pol4-mediated non-homologous end-joining increases, resulting in frequent insertions of 1-3 nucleotides, and insertions of mtDNA (NUMTs) or retrotransposon cDNA. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17143

95 Samples

Download data: BED

(Submitter supplied) Oxygen deprivation and excess are both toxic to mammals. Thus, the body’s ability to adapt to varying oxygen tensions is critical for survival. While the transcriptional response to acute hypoxia has been well-studied, the post-translational effects of hypoxia and hyperoxia have been underexplored. In this study, we systematically investigate protein turnover rates in mouse heart, lung, and brain under different inhaled oxygen tensions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

13 Samples

Download data: TXT

(Submitter supplied) Single cell RNA sequencing, 5 week deletion of O-GlcNAc transferase (OGT) in hepatocytes

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: H5

(Submitter supplied) Direct-RNA Sequencing expression data, quantifying both abundance and 3'-processing (cleavage and polyadenylation) site was obtained for two distinct mutations of Pcf11 and matched wildtype w303 samples under both standard growth conditions, as well as under growth in a caffeine-supplemented medium, since these mutations have been shown to increase susceptiblity to caffeine-related phenotypes. The overall goal was quantification of expression and pre-mRNA processing changes in response to these mutations.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23014

8 Samples

Download data: TXT

(Submitter supplied) Tumoroid cultures suppress gene expression programs involved in communication with the TME, and introduction of human monocyte-derived macrophages into tumoroid cultures instructs macrophages to acquire pro-tumorigenic gene expression programs similar to those observed in vivo.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

53 Samples

Download data: CSV, TXT