Similar studies for GEO DataSets (Select 200147895) - GEO DataSets

Select item 2001478951.

Photoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of the RNA-binding protein (RBP) RBM4 in KBM-7 derived near-haploid human cell line, HAP1.

(Submitter supplied) We hypothesized that RBM4 regulates HERVs by directly binding to their transcripts. To test this possibility, we performed photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP). We performed four independent PAR-CLIP replicates of our own using HAP1 cells stably expressing a FLAG-tagged RBM4 (FLAG-RBM4) transgene under control of a doxycycline-inducible promoter. Following metabolic labeling with 4-thiouridine (4SU) and crosslinking with ultraviolet light (UV) of 312 nm wavelength, we isolated RNA covalently linked to FLAG-RBM4. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL16791
8 Samples

Download data: TSV

Series

Accession:: GSE147895

ID:: 200147895

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Select item 2001478972.

Post-transcriptional regulation of human endogenous retroviruses by RNA-Binding Motif Protein 4, RBM4

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

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL18573 GPL26180 GPL16791
20 Samples

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Series

Accession:: GSE147897

ID:: 200147897

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Select item 2001478963.

PacBio long-read RNA-sequencing to identify differentially expressed genes and repetitive elements between Wild Type RBM4 KO HAP1 cell line samples

(Submitter supplied) Since short reads from Illumina RNA-seq data are challenging to map to repetitive elements , we wanted to confirm the bulk RNA-seq findings using an orthogonal method, namely, using the long read technology of Pacific Biosciences (PacBio) full-length transcriptome sequencing. This dataset provided around 1.1 (WT) and 1.3 (RBM4 KO) million sequence reads of 2.6 kb average length mapping to the human genome.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26180
2 Samples

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Series

Accession:: GSE147896

ID:: 200147896

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Select item 2001478934.

RNA-sequencing experiments to identify differentially expressed genes between Wild Type and RBM4 KO HAP1 cell line samples

(Submitter supplied) Here, we implemented a computational pipeline to determine the correlation of expression between individual RBPs and ERVs from single-cell or bulk RNA sequencing data. One of our top candidates for an RBP negatively regulating ERV expression was RNA-Binding Motif Protein 4 (RBM4). This set of bulk RNA-sequencing experiments was performed to identify differentially expressed genes and repetitive elements, particularly HERVs, between independent Wild Type and RBM4 KO clones in the KBM-7 derived, near-haploid human cell line, HAP1

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
10 Samples

Download data: TSV

Series

Accession:: GSE147893

ID:: 200147893

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Select item 2001224595.

SLE PBMC RNA-seq

(Submitter supplied) RNA sequencing of systemic lupus erythematosus (SLE) and healthy PBMCs to measure transcriptional changes in gene and endogenous retrovirus expression

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL18573 GPL16791
26 Samples

Download data: XLSX

Series

Accession:: GSE122459

ID:: 200122459

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Select item 2002296536.

Optimized Infra-red photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells

(Submitter supplied) We report the PAR-CLIP data for endogenous IGF2BP3 protein in colorectal carcinoma cell line (HCT116). In this study, we established an immunoprecipitation protocol to obtain highly pure endogenous IGF2BP3-RNA complexes and compared RNase cleavage conditions. The PAR-CLIP protocol was modified to use single adapter circular ligation approach to increase the efficiency in library preparation and reduce sequence bias. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL24676
6 Samples

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Series

Accession:: GSE229653

ID:: 200229653

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Select item 2000612387.

Tranposable elements modulate human mRNAs and lncRNAs via specific RNA-protein interactions.

(Submitter supplied) Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. Here, studied a collection of CLIP-Seq (CrossLinked ImmunoPrecipitation) experiments mapping the RNA binding sites for a diverse set of 46 human proteins across 68 experiments to explore the role of TEs in post-transcriptional regulation genome-wide via RNA-protein interactions. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: DIFF

Series

Accession:: GSE61238

ID:: 200061238

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Select item 2000299438.

Unstressed HeLa cells and ELAVL1/HuR knock down conditions: polyA RNA-Seq, small RNA-Seq, and PAR-CLIP

(Submitter supplied) Post-transcriptional gene regulation relies on hundreds of RNA binding proteins (RBPs) but the function of most RBPs is unknown. The human RBP HuR/ELAVL1 is a conserved mRNA stability regulator. We used PAR-CLIP, a method based on RNA-protein crosslinking, to identify transcriptome wide ~26,000 HuR binding sites. These sites were on average highly conserved, enriched for HuR binding motifs and mainly located in 3' untranslated regions. more...

Organism:: Homo sapiens

Type:: Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:: GPL11154 GPL9115
9 Samples

Download data: BED, TXT, WIG

Series

Accession:: GSE29943

ID:: 200029943

Select item 2001516669.

RNA sequencing of pre-treatment primary cervical cancer

(Submitter supplied) Investigate the transcriptomic differences between HPV-positive and HPV-negative primary cervical tumors.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21290
68 Samples

Download data: TSV

Series

Accession:: GSE151666

ID:: 200151666

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Select item 20023401010.

Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives

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

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium

Type:: Other; Expression profiling by high throughput sequencing

Platforms:: GPL21220 GPL17070
132 Samples

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Series

Accession:: GSE234010

ID:: 200234010

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Select item 20023400911.

Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [RIF-seq]

(Submitter supplied) RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in post-transcriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. more...

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17070
120 Samples

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Series

Accession:: GSE234009

ID:: 200234009

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Select item 20023400712.

Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [CLIP-seq]

(Submitter supplied) RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in post-transcriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. more...

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium

Type:: Other

Platform:: GPL21220
12 Samples

Download data: CSV, GFF

Series

Accession:: GSE234007

ID:: 200234007

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Select item 20013778213.

Endogenous retroviruses are associated with hippocampus-based memory impairment

(Submitter supplied) Retrotransposons comprise a staggering 40% of the mammalian genome. Among them, endogenous retroviruses (ERV) represent sequences that closely resemble the proviruses created after exogenous retroviral infection. ERVs make up 8–10% of human and mouse genomes and range from evolutionarily ancient sequences to recent acquisitions. Studies in Drosophila have provided a causal link between genomic retroviral elements and cognitive decline. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL17021 GPL19057
25 Samples

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Series

Accession:: GSE137782

ID:: 200137782

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Select item 20015993614.

Morc3 silences endogenous retroviruses by enabling Daxx-mediated H3.3 incorporation

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

Organism:: Mus musculus

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

Platform:: GPL18480
76 Samples

Download data: BIGWIG, TAB

Series

Accession:: GSE159936

ID:: 200159936

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Select item 20015993515.

Morc3 silences endogenous retroviruses by enabling Daxx-mediated H3.3 incorporation [RNA-seq_res]

(Submitter supplied) Endogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes. Although, specific ERV loci feature regulatory roles for host gene expression, most ERV integrations are transcriptionally repressed by Setdb1 mediated H3K9me3 and DNA methylation. However, the protein network which regulates deposition of these chromatin modifications is still incompletely understood. Here, we performed a genome-wide sgRNA screen for genes involved in ERV silencing and identified the GHKL ATPase protein Morc3 as top scoring hit. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18480
4 Samples

Download data: TAB

Series

Accession:: GSE159935

ID:: 200159935

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Select item 20015993416.

Morc3 silences endogenous retroviruses by enabling Daxx-mediated H3.3 incorporation [RNA-seq_wt/ko]

(Submitter supplied) Endogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes. Although, specific ERV loci feature regulatory roles for host gene expression, most ERV integrations are transcriptionally repressed by Setdb1 mediated H3K9me3 and DNA methylation. However, the protein network which regulates deposition of these chromatin modifications is still incompletely understood. Here, we performed a genome-wide sgRNA screen for genes involved in ERV silencing and identified the GHKL ATPase protein Morc3 as top scoring hit. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18480
6 Samples

Download data: TAB

Series

Accession:: GSE159934

ID:: 200159934

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Select item 20015993317.

Morc3 silences endogenous retroviruses by enabling Daxx-mediated H3.3 incorporation [ChIP-seq]

(Submitter supplied) Endogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes. Although, specific ERV loci feature regulatory roles for host gene expression, most ERV integrations are transcriptionally repressed by Setdb1 mediated H3K9me3 and DNA methylation. However, the protein network which regulates deposition of these chromatin modifications is still incompletely understood. Here, we performed a genome-wide sgRNA screen for genes involved in ERV silencing and identified the GHKL ATPase protein Morc3 as top scoring hit. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL18480
47 Samples

Download data: BIGWIG

Series

Accession:: GSE159933

ID:: 200159933

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Select item 20015993218.

Morc3 silences endogenous retroviruses by enabling Daxx-mediated H3.3 incorporation [ATAC-seq]

(Submitter supplied) Endogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes. Although, specific ERV loci feature regulatory roles for host gene expression, most ERV integrations are transcriptionally repressed by Setdb1 mediated H3K9me3 and DNA methylation. However, the protein network which regulates deposition of these chromatin modifications is still incompletely understood. Here, we performed a genome-wide sgRNA screen for genes involved in ERV silencing and identified the GHKL ATPase protein Morc3 as top scoring hit. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL18480
19 Samples

Download data: BIGWIG

Series

Accession:: GSE159932

ID:: 200159932

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Select item 20011499819.

KAP1 regulates ERVs in differentiated human cells and contributes to innate immune control

(Submitter supplied) Endogenous retroviruses (ERVs) have accumulated in vertebrate genomes and contribute to the complexity of gene regulation. KAP1 represses ERVs during development by its recruitment to their repetitive sequences through KRAB-zinc finger proteins (KZNFs), but little is known about the regulation of ERVs in differentiated cells. We observed that KAP1 repression of HERVK14C was conserved in differentiated human cells and performed KAP1 knockout to obtain an overview of KAP1 function. more...