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Items: 1 to 20 of 64

1.

SRSF7-mediated Alternative Splicing of USO1 Promotes Hepatocellular Carcinoma by Activating the MAPK/ERK1-ELK1 Pathway

(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
Series
Accession:
GSE262667
ID:
200262667
2.

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape.

(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:
GPL16791 GPL17021 GPL21311
170 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE226003
ID:
200226003
3.

Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [Long read sequencing]

(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
Series
Accession:
GSE225992
ID:
200225992
4.

Novel, abundant Drosha isoforms are deficient in miRNA processing in cancer cells

(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
Series
Accession:
GSE143169
ID:
200143169
5.

Multi-contact 3C data reveal that the human genome is largely unentangled

(Submitter supplied) Setup Pacbio sequencing in combination with 3C
Organism:
Homo sapiens
Type:
Other
Platform:
GPL21311
2 Samples
Download data: TXT
Series
Accession:
GSE146945
ID:
200146945
6.

Long-TUC-seq is a robust method for quantification of metabolically labeled full-length isoforms

(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:
GPL21311 GPL18573
7 Samples
Download data: TXT
Series
Accession:
GSE149551
ID:
200149551
7.

Octameric nucleosomes are present within the inner kinetochore of human centromeres

(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
Series
Accession:
GSE129351
ID:
200129351
8.

High-Throughput Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation

(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:
GPL21311 GPL24462 GPL20301
8 Samples
Download data: BIGWIG, GFF
Series
Accession:
GSE130726
ID:
200130726
9.

PacBio sequencing of Cp/Wp-driven transcripts from B95-8 LCLs

(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
Series
Accession:
GSE102102
ID:
200102102
10.

Ribothrypsis, a novel process of canonical mRNA decay, mediates ribosome-phased mRNA endonucleolysis.

(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
11.

Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify

(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
12.

High-throughput manual-quality annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS)

(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
Series
Accession:
GSE93848
ID:
200093848
13.

Global transcript structure resolution of high gene density genomes through multi-platform data integration

(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
Series
Accession:
GSE79337
ID:
200079337
14.

Global transcript structure resolution of high gene density genomes through multi-platform data integration: Iso-Seq

(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
Series
Accession:
GSE79335
ID:
200079335
15.

Multiplex enhancer-reporter assays uncover unsophisticated p53 enhancer logic

(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
Series
Accession:
GSE76657
ID:
200076657
16.

Multiplex enhancer-reporter assays uncover unsophisticated p53 enhancer logic [CHEQ-seq]

(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
Series
Accession:
GSE76653
ID:
200076653
17.

Capturing pairwise and multi-way chromosomal conformations using C-walks

(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:
Homo sapiens; Mus musculus
Type:
Other
8 related Platforms
20 Samples
Download data: TXT
Series
Accession:
GSE77553
ID:
200077553
18.

PacBio RS II (Homo sapiens)

Organism:
Homo sapiens
17 Series
46 Samples
Download data
Platform
Accession:
GPL21311
ID:
100021311
19.

Tumor

Organism:
Homo sapiens
Source name:
Tumor
Platform:
GPL21311
Series:
GSE262667
Download data
Sample
Accession:
GSM8173317
ID:
308173317
20.

HepG2, cells, ASO-E15

Organism:
Homo sapiens
Source name:
HepG2, cells, ASO-E15
Platform:
GPL21311
Series:
GSE262667
Download data
Sample
Accession:
GSM8173316
ID:
308173316
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