GEO DataSets

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21311 GPL20301

156 Samples

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(Submitter supplied) We have developed a panel of isogenic iPSC lines carrying MAPT splice-site mutations S305S, S305I or S305N, derived from four different donors. All three mutations significantly increased the proportion of 4R tau expression in iPSC-neurons and astrocytes, with up to 80% 4R transcripts in S305N neurons from as early as 4 weeks of differentiation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21311

73 Samples

Download data: CSV

(Submitter supplied) We conducted a transcriptome-wide survey to identify novel hepatocellular carcinoma (HCC)-associated genes that have undergone aberrant alternative splicing. We revealed that the vesicle transport factor (USO1) is a major alternatively spliced target in HCC, mainly composed of a long wild-type isoform (USO1-L) and a short truncated isoform lacking exons 5 and 15 (USO1-S). A markedly increased isoform switching from USO1-L to USO1-S occurs in approximately 80% of HCCs and predicts poor clinical outcomes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21311 GPL24676

19 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL17021 GPL16791 GPL21311

170 Samples

Download data: BED, BW, TXT

(Submitter supplied) To understand how SF3B1K700E impacts co-transcriptional splicing, we peformed long read sequencing of RNA (nSRS-seq) in K562 cells (wild type and SF3B1K700E mutant) at 4 days after mutant allele expression We then performed co-transcriptional splicing efficiency analysis using data obtained from Long read sequencing

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21311

4 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a class of small noncoding RNAs about 22-nucleotide (nt) in length that collectively regulate more than 60% of coding genes. Aberrant miRNA expression is associated with numerous diseases, including cancer. miRNA biogenesis is licensed by the ribonuclease (RNase) III enzyme Drosha, the regulation of which is critical in determining miRNA levels. We and others have previously revealed that alternative splicing regulates the subcellular localization of Drosha. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL15520 GPL21311

20 Samples

Download data: FASTA, TXT

(Submitter supplied) Setup Pacbio sequencing in combination with 3C

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21311

2 Samples

Download data: TXT

(Submitter supplied) The steady state expression of each gene is the result of transcriptional rate, dynamic processing, and degradation of RNA. While regular RNA-seq methods only measure steady state expression levels, RNA-seq of metabolically labeled RNA identifies transcripts that were transcribed during the window of metabolic labeling. Whereas short-read RNA sequencing can identify metabolically labeled RNA at the gene level, long-read sequencing results in dramatically improved resolution of isoform-level transcription. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL21311

7 Samples

Download data: TXT

(Submitter supplied) The centromere is a vital locus on each chromosome which seeds the kinetochore, allowing for a physical connection between the chromosome and the mitotic spindle. At the heart of the centromere is the centromere-specific histone H3 variant CENP-A/CENH3. Throughout the cell cycle the constitutive centromere associated network is bound to CENP-A chromatin, but how this protein network modifies CENP-A nucleosome dynamics in vivo is unknown. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21311

4 Samples

Download data: TXT

(Submitter supplied) We have successfully characterized R-loop structures using non-denaturing bisulfite treatment coupled with single-molecule sequencing to reveal that R-loops form defined overlapping molecular clusters around promoter, gene body, and terminal regions of genes. Our results uncovers that R-loop formation is both driven by favorable DNA sequence as well as topological state.

Organism:

Homo sapiens; Escherichia coli

Type:

Other

Platforms:

GPL24462 GPL21311 GPL20301

8 Samples

Download data: BIGWIG, GFF

(Submitter supplied) PacBio sequencing was performed to identify alternative splice patterns of Cp/Wp-driven transcripts. We were particularly interested in splicing from Cp/Wp exons to the HF exon. The HF exon contains pri-miR-BHRF1-2 and 1-3, so splicing to the HF exon would indicate that these pri-miRNAs are capable of regulating the 5' EBNA-LP ORF in cis through excision by Drosha.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21311

2 Samples

Download data: BED, XLSX

(Submitter supplied) By developing Akron-Seq, a novel approach that captures native 3' and 5' ends of capped and polyadenylated RNAs respectively, we show that canonical human mRNAs are subject to repeated, cotranslational, ribosome-phased, endonucleolytic cuts in a process that we term ribothrypsis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL21311

11 Samples

Download data: BW

(Submitter supplied) Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, Splicify, which is able to detect differentially expressed protein isoforms. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21311 GPL16791

16 Samples

Download data: BED, GFF, TXT

(Submitter supplied) Accurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy. As a result, the GENCODE reference collection of long noncoding RNAs remains far from complete: many are fragmentary, while thousands more remain uncatalogued. To accelerate lncRNA annotation, we have developed RNA Capture Long Seq (CLS), combining targeted RNA capture with third generation long-read sequencing. more...

Organism:

Mus musculus; Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

6 related Platforms

36 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:

GPL11154 GPL16791 GPL21311

23 Samples

Download data: BEDGRAPH, WIG

(Submitter supplied) Pacific Biosciences Iso-Seq was used in conjunction with Illumina RNA-Seq and deepCAGE to globally resolve transcript structures in replicating Epstein-Barr virus.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21311

1 Sample

Download data: BEDGRAPH

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL21311

26 Samples

Download data: BW, TXT

(Submitter supplied) Analysis of p53 binding sites using multiplex enhancer reporter assays, ChIP-seq data and RNA-seq data. Transcription factors establish and maintain the specific transcriptome of a cell by binding to genomic regulatory regions, thereby regulating the transcription of their target genes. Like many transcription factors, the DNA sequence-specific binding preferences of p53 are known. However, it remains largely unclear what distinguishes functional enhancers from other bound genomic regions that have no regulatory activity. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL21311 GPL11154

12 Samples

Download data: TXT

(Submitter supplied) Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information. Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs), are highly conserved between cell types and species. Whether pairwise loops synergize to form higher order structures is still unclear. Here we develop a conformation capture approach to study higher order organization using chromosomal walks (C-walks) that link multiple genomic loci together into proximity chains. more...

Organism:

Mus musculus; Homo sapiens

Type:

Other

8 related Platforms

20 Samples

Download data: TXT