GPL24198[RGSE] - GEO DataSets

(Submitter supplied) 3’ untranslated regions (3’UTRs) are critical elements of most messenger RNAs: they contain binding sites for RNA-binding proteins (RBP) and microRNAs that affect various aspects of the RNA life cycle including transcript stability. In response to T cell receptor activation, T cells undergo massive expansion during the effector phase of the immune response and dynamically modify their 3’UTRs. Whether this serves to directly regulate the abundance of specific mRNAs or is a secondary effect of proliferation remains unclear. more...

Organism:: Mus musculus

Type:: Other

Platform:: GPL24198
3 Samples

Download data: GTF

Series

Accession:: GSE209603

ID:: 200209603

PubMed Full text in PMC Similar studies

Select item 2002052113.

RNA catabolism restricts ERV expression and functionalization

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

Organism:: Mus musculus

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

Platforms:: GPL24247 GPL24198 GPL21626
90 Samples

Download data: BW

Series

Accession:: GSE205211

ID:: 200205211

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Select item 2002051754.

RNA catabolism restricts ERV expression and functionalization [Iso-seq]

(Submitter supplied) Endogenous retroviruses (ERVs) are remnants of ancient parasitic viral integrations and comprise a sizable portion of the genome in most organisms. Deregulated expression of ERVs in human is associated with a plethora of disease conditions, such as cancer and neurodegeneration. Epigenetic mechanisms silence most ERVs by generating a local repressive environment (heterochromatin) to prevent their expression. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24198
8 Samples

Download data: GTF

Series

Accession:: GSE205175

ID:: 200205175

Select item 2001885395.

Rapid nuclear deadenylation of mammalian messenger RNA

(Submitter supplied) Poly(A) tails protect RNAs from degradation and deadenylation rates determine RNA stability. Deadenylation has mostly been investigated within the cytoplasm and the dynamics of poly(A) tail length after transcription are not well understood. Combining long-read sequencing with metabolic labeling and cell fractionations, we investigate deadenylation dynamics of newly synthesized poly(A) tails in vitro and in vivo. more...

Organism:: Homo sapiens; Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL26180 GPL24198
60 Samples

Download data: CSV

Series

Accession:: GSE188539

ID:: 200188539

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001667096.

Integrated long- and short-read single-cell RNA-sequencing

(Submitter supplied) Single-cell RNA sequencing analysis has recently provided snapshots of gene expression of specific cell types and enabled cell types classification within an heterogenous population. As well as transcriptional changes, alternative splicing events and modifications of components of splicing machinery actively contributes in shaping cellular phenotype as well as ageing process and diseases occurence. Current high-throughput single-cell RNA sequencing methods may lack information on cell-specific isoform expression, missing key aspects of cell biology. In the present work we introduce a novel approach using the 10X Genomics Chromium to generate short-read (Illumina) and long-read (Pacific Biosciences Sequel II) RNA-sequencing libraries from the same single cells. This approach produced single cell parallel transcriptional and splicing profiling that demonstrates for the first time cell-type specific isoform expression and alterations at transcriptional levels associated with ageing in haematopoietic stem and progenitor cells

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL19057 GPL24198 GPL29177
18 Samples

Download data: GTF, TSV, TXT

Series

Accession:: GSE166709

ID:: 200166709

PubMed Full text in PMC Similar studies

Select item 2002199287.

long read RNA-seq from adrenal gland (ENCSR942UFC)

(Submitter supplied) adrenal gland BL6 male For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24198
2 Samples

Download data: GTF, TSV, TXT

Series

Accession:: GSE219928

ID:: 200219928

PubMed Full text in PMC Similar studies Mouse ENCODE

Select item 2002198138.

long read RNA-seq from C2C12 (ENCSR418ZYU)

(Submitter supplied) Myoblast cell line derived from thigh muscle of C3H mice after crush injury For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24198
2 Samples

Download data: GTF, TSV, TXT

Series

Accession:: GSE219813

ID:: 200219813

PubMed Full text in PMC Similar studies Mouse ENCODE

Select item 2002197709.

long read RNA-seq from forelimb (ENCSR804QMV)

(Submitter supplied) Mus musculus strain B6NCrl embryo (11 days) forelimb tissue For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24198
1 Sample

Download data: GTF, TSV, TXT

Series

Accession:: GSE219770

ID:: 200219770

PubMed Full text in PMC Similar studies Mouse ENCODE

Select item 20021971510.

long read RNA-seq from left cerebral cortex (ENCSR340GWV)

(Submitter supplied) Cortex1 from 6 mo C57BL/6 male For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24198
2 Samples

Download data: GTF, TSV, TXT

Series

Accession:: GSE219715

ID:: 200219715

PubMed Full text in PMC Similar studies Mouse ENCODE

Select item 20021967711.

long read RNA-seq from adrenal gland (ENCSR735IBE)

(Submitter supplied) adrenal gland BL6 female For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24198
2 Samples

Download data: GTF, TSV, TXT

Series

Accession:: GSE219677

ID:: 200219677

PubMed Full text in PMC Similar studies Mouse ENCODE

Select item 20021958912.

long read RNA-seq from layer of hippocampus (ENCSR214HSG)

(Submitter supplied) Hippocampus1 from 6 mo C57BL/6 male For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24198
2 Samples

Download data: GTF, TSV, TXT

Series

Accession:: GSE219589

ID:: 200219589

PubMed Full text in PMC Similar studies Mouse ENCODE

Select item 20021943813.

long read RNA-seq from forelimb (ENCSR082JMB)

(Submitter supplied) Mus musculus strain B6NCrl embryo (13 days) forelimb tissue For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24198
1 Sample

Download data: GTF, TSV, TXT

Series

Accession:: GSE219438

ID:: 200219438

PubMed Full text in PMC Similar studies Mouse ENCODE

Select item 20017601814.

Hybrid sequencing characterizes expression and function of mouse pseudogenes

(Submitter supplied) Pseudogenes are defined as regions of the genome that resemble functional genes but contain disabling mutations and lack regulatory elements needed for transcription or translation. They are excellent markers for genome evolution and are emerging as crucial regulators of the development and disease, especially cancer. However, systematic functional characterization and evolution of pseudogene remain largely unexplored. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24247 GPL24198
35 Samples

Download data: GTF, TXT

Series

Accession:: GSE176018

ID:: 200176018

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015929015.

A comparison of alternative mRNA splicing in the CD4 and CD8 T cell lineages

(Submitter supplied) We consturcted a full-length transcript reference of CD4SP and CD8SP T cells using TGS (PacBio) data. We then used SGS (Illumina) CD4SP and CD8SP data to quantify isoform expressions and study alternative splicing patterns against the full-length transcript reference between CD4SP and CD8SP cells.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24198 GPL19057
10 Samples

Download data: GTF, TXT

Series

Accession:: GSE159290

ID:: 200159290

PubMed Similar studies SRA Run Selector

Select item 20016039016.

PEZIC_STAG1_Pluripotency

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

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL17021 GPL24198 GPL21493
33 Samples

Download data: BAI, BAM, TXT

Series

Accession:: GSE160390

ID:: 200160390

PubMed Full text in PMC Similar studies

Select item 20016038717.

STAG proteins mediate heterochromatin organization to support translation and cell identity [Iso-Seq]

(Submitter supplied) Abstract to add later

Organism:: Mus musculus

Type:: Other

Platform:: GPL24198
1 Sample

Download data: BAI, BAM

Series

Accession:: GSE160387

ID:: 200160387

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015866818.

De novo assembly of macaque gene models

(Submitter supplied) We reported an atlas of de novo-defined, full-length macaque gene models on the basis of single molecule long-read transcriptome sequencing (Iso-seq).

Organism:: Mus musculus; Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24198 GPL26751
14 Samples

Download data: BW

Series

Accession:: GSE158668

ID:: 200158668

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20014420519.

Co-transcriptional splicing regulates 3' end cleavage during mammalian erythropoiesis

(Submitter supplied) Pre-mRNA processing steps are tightly coordinated with transcription in many organisms. To determine how co-transcriptional splicing is integrated with transcription elongation and 3' end formation in mammalian cells, we performed long read sequencing of individual nascent RNAs and PRO-seq during mouse erythropoiesis. Splicing was not accompanied by transcriptional pausing and was detected when RNA polymerase II (Pol II) was within 75-300 nucleotides of 3' splice sites (3'SSs), often during transcription of the downstream exon. more...