GEO DataSets

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL18573 GPL15520

63 Samples

Download data: CSV, H5, TSV

(Submitter supplied) In order to get insight in the role of metabolic perturbations during the first steps of cell differentiation, the phenotype, gene expression profile and chromatin accessibility of CD34+ cells were examined using bulk- and single-cell techniques during the initial 96 hours of in vitro differentiation. Specific enzyme inhibitors targeting key steps of the energy metabolism were employed to induce perturbations and assess their effect. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL15520 GPL18573

41 Samples

Download data: CSV, RDS

(Submitter supplied) We performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to profile genome-wide chromatin accessibility in the human H1 embryonic stem cell (ESC) line. We used this data to train a deep learning model called ChromBPNet which can accurately predict base-resolution accessibility profiles as a function of DNA sequence, while accounting for and correcting biases due the sequence preferences of the Tn5 transposase used in ATAC-seq. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15520

2 Samples

Download data: BB, BIGWIG, NARROWPEAK

(Submitter supplied) We identified LAMC1 as a critical NUDT21 target involved in several core glioma-driving signaling pathways. qRT-PCR analysis confirmed that NUDT21-knockdown in GBM cells resulted in the preferred usage of the proximal C/PAS of LAMC1. Furthermore, functional studies revealed that NUDT21-knockdown-induced 3’UTR shortening of LAMC1 was sufficient to induce translational gain, as LAMC1 was upregulated in these cells compared to their respective controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

12 Samples

Download data: BW

(Submitter supplied) The Tousled-like kinases 1 and 2 (TLK1/TLK2) regulate DNA replication, repair and chromatin maintenance. TLK2 variants are associated with ‘Intellectual Disability, Autosomal Dominant 57’ (MRD57), a neurodevelopmental disorder (NDD) characterized by intellectual disability (ID), autism spectrum disorder (ASD) and microcephaly. Several TLK1 variants have been reported in NDDs but their functional significance is unknown. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

4 Samples

Download data: VCF

(Submitter supplied) Fusions involving tyrosine kinases are oncogenic drivers in lung cancer and other solid tumors but also mediate resistance to targeted therapy. Despite gene rearrangements involving tyrosine kinases tending to show recurrent patterns in solid tumors, little is known about their mechanisms of formation and their selection process. To elucidate these mechanisms, we developed a functional high-throughput, genome-wide translocation sequencing (F-HTGTS) approach. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

12 Samples

Download data: BED

(Submitter supplied) Dengue virus (DENV) can hijack non-neutralizing IgG antibodies to facilitate its uptake into target cells expressing Fc gamma receptors (FcgR) - a process known as antibody-dependent enhancement (ADE) of infection. Beyond a requirement for FcgR, host dependency factors for this non-canonical infection route remain unknown. To identify cellular factors exclusively required for ADE, here, we performed CRISPR knockout screens in an in vitro system permissive to infection only in the presence of IgG antibodies. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL18573 GPL15520

12 Samples

Download data: TSV

(Submitter supplied) Stage 3 cells from a suspension environment and adherent culture were compared and evaluated through RNA sequencing. RNA sequencing data in heatmap and volcano plot evaluation of core endocrine genes showed that expression levels in adherent cells were lower than those expressed in 3D environment. Several genes that are essential for insulin transcription such as NEUROD1, MAFA, PPARGC1A and NKX2.2 along with INS were expressed with higher transcript levels in bioreactor samples. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

9 Samples

Download data: TSV

(Submitter supplied) N1-methyl adenosine (m1A) is a wide-spread RNA modification present in tRNA, rRNA and mRNA. m1A modification sites in tRNAs are evolutionary conserved and its formation on tRNA is catalyzed by methyltransferase TRMT61A and TRMT6 complex. m1A promotes translation initiation and elongation. Due to its positive charge under physiological conditions, m1A can notably modulate RNA structure. It also blocks Watson-Crick base pairing and causes mutation and truncation during reverse transcription. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15520

12 Samples

Download data: TXT

(Submitter supplied) Obtaining high-quality omics data at the single-cell level from archived human tissue samples is crucial for gaining insights into cellular heterogeneity and pushing the field of personalized medicine forward. In this technical brief we present a comprehensive methodological framework for the efficient enzyme-free preparation of tissue-derived single cell suspensions and their conversion into single-cell miRNA sequencing libraries. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15520

33 Samples

Download data: TSV

(Submitter supplied) v3-v4 16S rRNA sequencing was used to characterize both gut and oral microbiota composition of RCC (refractory chronic cough) patients and matched healthy controls (HC). The groups are matched in age and gender.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

39 Samples

Download data: FASTA, TSV

(Submitter supplied) Manuscript Name: "Addressing Bioreactor hiPSC Aggregate Stability, Maintenance and Scaleup Challenges Using a Design of Experiment Approach" Evaluation of core pluripotent genes showed that expression levels were similar between samples with a clear indication of a primed phenotype. In addition, we evaluated several well-known oncogenes notable TP53, MYC, NANOGP8, EEF1A2 and KLF4 were expressed with similar transcript levels between samples, though KLF4 had low overall expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

6 Samples

Download data: TXT

(Submitter supplied) Background: The incidence of colorectal cancer (CRC) has been steadily increasing in younger individuals over the past several decades for reasons that are incompletely defined. Identifying differences in gene expression profiles, or transcriptomes, in early-onset colorectal cancer (EOCRC, < 50 years old) patients versus later-onset colorectal cancer (LOCRC, > 50 years old) patients is one approach to understanding molecular and genetic features that distinguish EOCRC. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

44 Samples

Download data: CSV, TXT

(Submitter supplied) Enhancer hijacking, caused by structural alterations, is a common cancer driver event that causes aberrant expression of oncogenes. Unfortunately, enhancer hijacking is difficult to detect due to the complexity of the cancer genome. Here we propose a simple yet robust strategy HAPI (Highly Active Promoter Interactions) to identify and characterize such events by following two rules: 1) oncogenes subject to enhancer hijacking should be potentially highly regulated by enhancers, 2) the hijacked enhancers should contribute an appreciable proportion of an oncogene’s overall enhancer activity. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15520

6 Samples

Download data: BW

(Submitter supplied) We discovered that PCR-mediated template switching poses a significant challenge in ensemble tagged PCR, particularly in the template sequences with high similarities, which we successfully addressed by introducing a dual barcode. Template switching presents in repair sequencing (repair seq) and severely interfere the interpretation of the association between repair outcomes and the sgRNA in the vicinity. more...

Organism:

Escherichia coli; Homo sapiens

Type:

Other

Platforms:

GPL15520 GPL16085 GPL25368

30 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18573 GPL24676 GPL15520

30 Samples

Download data: BEDPE, BW, RESULTS

(Submitter supplied) Uveal melanoma (UM) is the most common cancer of the eye. The loss of chromosome-3 (M3) is associated with high risk of metastases. M3-tumors are more infiltrated by T-lymphocytes than low-risk disomic-3 (D3) tumors, contrasting with other tumor types in which T-cell infiltration correlates with better prognosis. Whether these T-cells represent an anti-tumor response and how these T-cells would be primed in the eye are both unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24676 GPL15520

15 Samples

Download data: CSV, MTX, TSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24676 GPL15520

12 Samples

Download data: FPKM_TRACKING, PAIRS

(Submitter supplied) Aging is associated with a progressive decline in cellular function. To reset the aged cellular phenotype, various reprogramming approaches, including mechanical routes, have been proposed. However, the epigenetic mechanisms underlying cellular rejuvenation are poorly understood. We studied the transcriptional changes in young, aged and mechanically rejuvenated fibroblasts using RNA-seq. The mechanically rejuvenated aged fibroblasts, that had reset their transcription to a younger cell state. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

6 Samples

Download data: FPKM_TRACKING

(Submitter supplied) GBM cells derived from a patient were subjected to CLIP and RNAseq assays to for transcriptome analysis (CLIP and RNAseq).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24676 GPL15520

36 Samples

Download data: BEDGRAPH