GEO DataSets

(Submitter supplied) Tissue-resident memory CD8 T cells (TRM) provide protection from infection at barrier sites. In the small intestine, TRM cells are found in at least two distinct subpopulations: one with higher expression of effector molecules and another with greater memory potential. However, the origins of this diversity remain unknown. We proposed that distinct tissue niches drive TRM phenotypic heterogeneity. To test this, we leveraged spatial transcriptomics of human samples, a murine model of acute systemic viral infection, and a newly established strategy for pooled optically-encoded gene perturbations to profile the location, interaction, and transcriptome of pathogen-specific TRM differentiation at single-transcript resolution. more...

Organism:

Mus musculus; Homo sapiens; synthetic construct

Type:

Other

Platforms:

GPL31217 GPL33896 GPL33762

17 Samples

Download data: CSV, H5AD, PARQUET

(Submitter supplied) We describe an effort (“Codebook”) to determine the sequence specificity of 332 putative and largely uncharacterized human transcription factors (TFs), as well as 61 control TFs. Nearly 5,000 independent experiments, including in vitro and in vivo assays, produced motifs for most of the uncharacterized TFs analyzed (180, or 53%), the vast majority of which are unique to a single TF. The data highlight the extensive contribution of transposable elements to TF evolution, both in cis and trans, and identify tens of thousands of conserved, base-level binding sites in the human genome. more...

Organism:

Homo sapiens; synthetic construct

Type:

Other

Platform:

GPL11260

462 Samples

Download data: TXT

(Submitter supplied) Pseudouridine is considered as the most abundant modified nucleotides in RNA, playing an indispensable role in various life processes. The identification of pseudouridine sites provides the basis for the study of their function. Here, we proposed a new method for the identification of pseudouridine sites with a higher signal-to-noise ratio, combining CMC-specific labeling of pseudouridine sites and exonuclease-assisted strategy. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL26526

21 Samples

Download data: TXT

(Submitter supplied) Background: Ulcerative colitis (UC) and irritable bowel syndrome (IBS) are both chronic bowel diseases involving stress. To identify genes differentially expressed in UC and IBS, and to determine whether psychological stress can influence those gene expressions, we conducted this pilot study. Methods: Patients of UC, irritable bowel syndrome (IBS) and normal controls (NC) (n=5 in each group) were recruited. more...

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL21572

15 Samples

Download data: CEL

(Submitter supplied) N6-methyladenosine (m6A) has been one of the most abundant and well-known modifications in mRNA since its discovery in 1970s. Recent studies have demonstrated that m6A gets involved in various biological processes such as alternative splicing and RNA degradation, playing an important role in all kinds of diseases. To better understand the role of m6A, transcriptome-wide m6A profiling data is indispensable. more...

Organism:

synthetic construct

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25738

3 Samples

Download data: FA, TSV

(Submitter supplied) Epigenetic modifications, including the role of miRs in various diseases, are key regulators of gene expression. In this study we aimed to explore whether epigenetic alterations could play a role in the TRPV4-mediated regulation of miR-146a. Here we report that there is no significant differences in the methylation status of the examined 10 CpG sites on miR146a promoter between WT and TRPV4 KO cells under LPS treatment, indicating that the regulation of miR-146a by TRPV4 may not be mediated by methylation changes at these specific sites.

Organism:

synthetic construct; Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL34670 GPL25723

11 Samples

Download data: CSV

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

Organism:

synthetic construct

Type:

Other

Platform:

GPL26526

38 Samples

Download data

(Submitter supplied) Pluripotent stem cells are a hallmark of animal multicellularity. Sox and POU family transcription factors are pivotal for stemness and were believed to be animal innovations as they were reported absent from the genomes of their unicellular relatives. Here we describe new unicellular holozoan orthologues to Sox and POU families, indicating that they emerged before the appearance of animals. We show that choanoflagellate and filasterean Sox genes have DNA binding specificity similar to Sox2. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL26526

4 Samples

Download data

(Submitter supplied) Pluripotent stem cells are a hallmark of animal multicellularity. Sox and POU family transcription factors are pivotal for stemness and were believed to be animal innovations as they were reported absent from the genomes of their unicellular relatives. Here we describe new unicellular holozoan orthologues to Sox and POU families, indicating that they emerged before the appearance of animals. We show that choanoflagellate and filasterean Sox genes have DNA binding specificity similar to Sox2. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL26526

34 Samples

Download data: CSV

(Submitter supplied) Enhancer of zeste homolog 2 (EZH2) is highly expressed in small-cell lung cancer (SCLC). Epigenetic modifications through EZH2 induce epithelial-mesenchymal transition (EMT). MicroRNAs (miRNAs) are small non-coding RNAs that modulate EMT to determine tumor phenotypes. miRNA expression profiles were compared between EZH2 siRNA-transfected SCLC cells and negative control-transfected SCLC cells, using miRNA array analysis. more...

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL21572

4 Samples

Download data: CEL

(Submitter supplied) We used microarrays to analyze the global programme of miRNA expression in extracellular vesicles from different types of tissue of 8-week male C57BL/6 mice.

Organism:

synthetic construct; Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL19117

9 Samples

Download data: CEL

(Submitter supplied) The functional effects of an RNA can arise from complex three-dimensional folds known as tertiary structures. However, predicting the tertiary structure of an RNA and whether an RNA adopts distinct tertiary conformations remains challenging. To address this, we developed BASH MaP, a single-molecule dimethyl sulfate (DMS) footprinting method and DAGGER, a computational pipeline, to identify alternative tertiary structures adopted by different molecules of RNA. more...

Organism:

Homo sapiens; synthetic construct

Type:

Other

4 related Platforms

26 Samples

Download data: TXT, XLSX

(Submitter supplied) Cellular transcription enables cells to adapt to various stimuli and maintain homeostasis. Transcription factors bind to transcription response elements (TREs) in gene promoters, initiating transcription. Synthetic promoters, derived from natural TREs, can be engineered to control exogenous gene expression using endogenous transcription machinery. This technology has found extensive use in biological research for applications including reporter gene assays, biomarker development, and programming synthetic circuits in living cells. more...

Organism:

Mus musculus; Homo sapiens; Mesocricetus auratus; synthetic construct

Type:

Expression profiling by high throughput sequencing

5 related Platforms

65 Samples

Download data: CSV

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

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array; Expression profiling by array

Platforms:

GPL31001 GPL21572 GPL23159

176 Samples

Download data: CEL, RCC

(Submitter supplied) Gene expression profile of platelets have been explored due to their stability and abundance in plasma. In this study, we try to address the knowledge gap regarding liquid biopsy markers for early detection of non-small cell lung cancer (NSCLC). For that blood samples were collected in two time points, in the presence and absence of NSCLC. Platelets were isolated and miRNA expression evaluated by microarray technique.

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL21572

19 Samples

Download data: CEL

(Submitter supplied) CRISPR tiling screens have advanced the identification and characterization of regulatory sequences but are limited by low resolution arising from the indirect readout of editing via guide RNA sequencing. This study introduces CRISPR-CLEAR, an end-to-end experimental assay and computational pipeline, which leverages targeted sequencing of CRISPR-introduced alleles at the endogenous target locus following dense base-editing mutagenesis. more...

Organism:

synthetic construct; Homo sapiens

Type:

Other

Platforms:

GPL26526 GPL24676 GPL15520

49 Samples

Download data: CSV, TSV

(Submitter supplied) Roquin proteins target specific RNA stem-loop motifs with their unique ROQ domain for mRNA degradation. The cellular levels of mRNAs are controlled by these post-transcriptional cis-regulatory stem-loop elements in the 3'-untranslated region (3'-UTR). Here, we first provide an RBNS (RNA Bind-n-Seq) experiment using pre-structured RNA libraries as input. This sRBNS (structured RBNS) was used to map Roquin's RNA binding preferences at nucleotide resolution, revealing preferences for loop sizes and consensus motifs for CDEs and ADEs.

Organism:

synthetic construct

Type:

Other

Platform:

GPL27484

10 Samples

Download data: XLSX

(Submitter supplied) Given that the striatum is a large, multifunctional nucleus, we next aimed to understand where astrocyte subtypes exist in the striatum at a single-cell resolution using MERFISH. We reproducibly identified the seven astrocyte subtypes, some of which were dorsal (A1, A7), medial (A3, A6) or ventral dominant (A4).

Organism:

Mus musculus; synthetic construct

Type:

Other

Platform:

GPL31217

4 Samples

Download data: CSV, TXT

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

Organism:

synthetic construct; Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL20795 GPL26697 GPL21273

27 Samples

Download data

(Submitter supplied) RNA binding proteins can modulate RNA secondary structures, thus participating in post-transcriptional regulation. The DEAH-box helicase 36 (DHX36) has a remarkable ability to bind and unwind RNA G-quadruplex (rG4) and duplex. However, the transcriptome-wide RNA structure dynamic induced by DHX36 and how structure change subsequently influences RNA fate remain poorly understood. Here, we first identify the endogenous binding sites and specificity of DHX36 based on binding profiles. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL26697

11 Samples

Download data: TSV