GEO DataSets

(Submitter supplied) To investigate the effects of Dnmt1 Knockout in Sst expressing interneurons on celltype distribution in the embryonic brain, Sst-Cre/tdTomato/Dnmt1 loxp2 knockout mice and Sst-Cre/tdTomato control mice were analysed. 10 µm coronal sections of E16.5 brains were prepared for the Merscope platform using the commercially available Pan Neuro panel (Vizgen), covering 500 distinct transcripts.

Organism:

Mus musculus; synthetic construct

Type:

Other

Platform:

GPL31217

2 Samples

Download data: CSV, PARQUET

(Submitter supplied) Plasmablastic lymphoma has been scarcely studied because of its rarity. Transcriptomic studies are crucial to unveil the biology of this lymphoma. In particular, miRNA expression will help to understand the lymphomagenesis of plasmablastic lymphoma. We used microarrays to depict the miRNA expression landscape of plasmablastic lymphoma and to identify miRNAs differentially expressed compared to a control group.

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL21572

80 Samples

Download data: CEL, CHP

(Submitter supplied) DICER-LIKE1 (DCL1), a plant-specific RNase III enzyme, is fundamental to post-transcriptional gene regulation mediated by microRNAs (miRNAs). DCL1 processes precursor miRNAs into mature miRNAs, typically 20–22 nucleotides in length. Despite its crucial role, the RNA elements that guide DCL1's cleavage site selection have remained largely uncharacterized. In this study, we employed a high-throughput sequencing approach to analyze Arabidopsis thaliana DCL1 cleavage patterns on over 46,000 short-hairpin RNA (shRNA) sequences previously studied with human DICER. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL26526

2 Samples

Download data: TXT

(Submitter supplied) Defining viral proteomes is crucial to understanding viral life cycles and immune recognition but the landscape of translated regions remains unknown for most viruses. We have developed massively parallel ribosome profiling (MPRP) to determine open reading frames (ORFs) across tens of thousands of designed oligonucleotides. MPRP identified 4208 unannotated ORFs in 679 human-associated viral genomes. more...

Organism:

synthetic construct; Homo sapiens

Type:

Other

Platforms:

GPL34710 GPL34711

7 Samples

Download data: TXT

(Submitter supplied) We used Sequence-Scope (Seq-Scope), which can generate ultra-high definition images of sequence-based molecular signatures resolved at a submicrometer scale, for profiling spatial transcriptome associated with abdominal aortic aneurysm Experimental Methods: Seq-Scope experiment is divided into two consecutive sequencing steps: 1st-Seq and 2nd-Seq. 1st-Seq of Seq-Scope starts with the solid-phase amplification of a single-stranded synthetic oligonucleotide library using an Illumina sequencing-by-synthesis (SBS) platform. more...

Organism:

Mus musculus; synthetic construct

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19604 GPL21273

3 Samples

Download data: MTX, TSV

(Submitter supplied) Downregulation of BLID in breast cancer has been correlated with poor disease-free survival and overall survival. We used miRNA arrays to study the effects of BLID knockdown on miRNA expression profiles in breast cancer cells.

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL16384

18 Samples

Download data: CEL

(Submitter supplied) Although RNA-binding proteins (RBPs) are key regulators of gene expression, their RNA-binding specificities, i.e., motifs, have not been comprehensively determined. Here, we introduce EuPRI (Eukaryotic Protein-RNA Interactions), a freely available resource of RNA motifs for 34,746 RBPs from 690 eukaryotes. EuPRI includes in vitro binding data for 504 RBPs, including newly collected RNAcompete data for 174 RBPs, along with thousands of predicted motifs. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL16119

174 Samples

Download data

(Submitter supplied) The prognosis for colorectal cancer (CRC) patients with liver metastasis remains poor, and the molecular mechanisms driving CRC liver metastasis are still not fully understood. Hypoxia-induced extracellular vesicles (H-EVs) derived from tumors have emerged as key players in inducing angiogenesis by transferring non-coding RNAs. However, the specific role of CRC-derived hypoxic EVs (H-EVs) in regulating the formation of the pre-metastatic microenvironment (PMN) by inducing angiogenesis remains unclear. more...

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL21572

6 Samples

Download data: CEL

(Submitter supplied) Transcriptional enhancers are non-coding DNA elements that regulate gene transcription in a temporal and tissue-specific manner. Despite advances in computational and experimental methods, identifying enhancers and their target genes essential for specific biological processes remains challenging. Determining target genes for enhancers is also complex and often relies on indirect, low-resolution, and/or assumptive methodologies. more...

Organism:

synthetic construct; Homo sapiens

Type:

Other

Platforms:

GPL18573 GPL19424

15 Samples

Download data: TXT

(Submitter supplied) Immune molecules, including cytokines, chemokines, and their cognate receptors, are developmentally regulated in the brain and dynamically expressed in the context of neurodevelopmental and neuropsychiatric disease. Here, we employed highly multiplexed in situ spatial transcriptomics to map the expression of major immune ligands and receptors in the developing mouse brain during mid and late gestation. more...

Organism:

synthetic construct; Mus musculus

Type:

Other

Platform:

GPL31217

35 Samples

Download data: CSV

(Submitter supplied) Recognition of specific DNA sequences by transcription factors (TFs) is a key step in transcriptional control of gene expression. While most forkhead (FH) TFs bind either an FKH (RYAAAYA) or an FHL (GACGC) recognition motif, some FHs can bind both motifs. Mechanisms that control whether a FH is monospecific versus bispecific have remained unknown. Screening a library of 12 reference FH proteins, 61 naturally occurring missense variants including clinical variants, and 22 designed mutant FHs for DNA binding activity using universal (“all 10-mer”) protein binding microarrays (PBMs) revealed non-DNA-contacting residues that control mono- versus bispecificity. more...

Organism:

Homo sapiens; synthetic construct

Type:

Genome binding/occupancy profiling by array

Platform:

GPL33450

260 Samples

Download data: GPR, TXT

(Submitter supplied) Dysregulated gut lipid handling contributes to atherogenic dyslipidemia, a cardiovascular disease risk factor for patients with diabetes. The gut hormone glucagon-like peptide-2 (GLP-2) plays significant roles in intestinal lipid handling. In post-absorptive state, GLP-2 mobilizes pre-formed chylomicrons that are stored in the intestine from previous meals, the mechanisms of which are not fully understood. more...

Organism:

Rattus; synthetic construct

Type:

Other

Platforms:

GPL26526 GPL32253

31 Samples

Download data: DCC, PKC

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

Organism:

synthetic construct; Mus musculus

Type:

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

6 related Platforms

244 Samples

Download data: BW

(Submitter supplied) Developmental genes are controlled by several cis-acting regulatory elements (REs), which in turn respond to multiple trans-acting transcription factors (TFs). Understanding this regulatory complexity has remained a challenge. Here, we combine pooled CRISPR screens with different phenotypic readouts to dissect how a cis-regulatory landscape integrates information from a large number of TFs. We apply our approach to the murine X-inactivation center, which harbors the Xist gene. more...

Organism:

Mus musculus; synthetic construct

Type:

Other

4 related Platforms

20 Samples

Download data: TXT

(Submitter supplied) To generate a test data to facilitate development of toolkit for off-target nomination data analysis, a library consisting >81K in silico predicted on- and off-target regions for an EMX1 gRNA are synthesized and cleaved in vitro with SpCas9. The cleaved products are used to build NGS library followed by sequencing leading to >13 million reads. About 99% of examined regions are covered by 10 or more valid UMIs. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL17769

1 Sample

Download data: TXT

(Submitter supplied) Gene therapy products, such as rAAV, are typically produced by DNA plasmid transfected to mammalian cell lines. Host cell DNA and plasmid DNA can be inadvertently packaged inside the rAAV capsids during production. It is important to characterize these residual DNA impurities in gene therapy products due to the theoretical risk of immunogenicity, infectivity, and oncogenicity. Previous studies showed the level of residual DNA impurity is around 1-2% of the expected rAAV genome. more...

Organism:

synthetic construct

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34723

1 Sample

Download data: BED, TXT

(Submitter supplied) The CRISPR/Cas9 technology has revolutionized genotype-to-phenotype assignments through large-scale loss-of-function (LOF) screens. However, limitations like editing inefficiencies and unperturbed genes cause significant noise in data collection. To address this, we introduce CRISPR Gene and Epigenome Engineering (CRISPRgenee), which uses two specific sgRNAs to simultaneously repress and cleave the target gene within the same cell, increasing LOF efficiencies and reproducibility. more...

Organism:

synthetic construct; Homo sapiens

Type:

Other

Platforms:

GPL24676 GPL32628 GPL30173

19 Samples

Download data: TXT, XLSX

(Submitter supplied) Typical mammalian overexpression systems test protein sequence variants with little control over expression levels and steady-state protein abundances, hindering interpretations of how protein sequence and expression converge to yield phenotypic outcomes. We explored the translation initiation sequence, commonly referred to as the Kozak sequence, as a means to modulate protein steady-state abundance and cellular function. more...

Organism:

synthetic construct

Type:

Other

Platforms:

GPL17769 GPL27609

87 Samples

Download data: CSV

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

Organism:

synthetic construct

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL21616

276 Samples

Download data: TAR, TXT

(Submitter supplied) Cell fates are controlled by ‘pioneers’, sequence-specific transcription factors (TFs) that bind recognition motifs on nucleosomes (‘pioneer binding’). Pioneers occupy a minority of their recognition sequences in the genome, suggesting that the sequence context regulates their binding. Here, we developed PIONEAR-seq, a high-throughput biochemical assay to characterize pioneer binding to nucleosomes. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL21616

268 Samples

Download data: TXT