Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: PARE of DXO and Rai1

PROVIDER: PRJNA1103799 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28782500.fastq.gz	Fastqsanger.gz
	SRR28781573.fastq.gz	Fastqsanger.gz
	SRR28781574.fastq.gz	Fastqsanger.gz
	SRR28782497.fastq.gz	Fastqsanger.gz
	SRR28782498.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Genome-wide maps of Rai1 binding sites in mouse cortex

Project description:By generating knockin mice with an epitope tag on the C terminus of endogenous Rai1, we were able to perform in vivo ChIP-seq. Rai1 peaks co-localize with H3K4me3, Pol2, and Zfx peaks. Our data suggest that Rai1 is a transcription factor that interacts with chromatin, specifically in the promoter and enhancer regions.

2017-01-03 | GSE81204 | GEO

RNA-Sequencing to identify the transcriptional targets of Rai1

Project description:The goals of this study are to harvest adult-onset Rai1-deficient mouse brains from hypothalamus and compare the transcriptome with their wild-type littermates. Methods: mRNA profiles from Rai1 conditional knockouts and wild-type mice were generated by deep sequencing, in duplicate using Illumina system. Conclusions: Our study suggests that Rai1 preferentially regulate genes involved in cell communication

2022-01-05 | GSE149952 | GEO

RNA-Sequencing to identify the transcriptional targets of Rai1

Project description:The goals of this study are to harvest Rai1-deficient mouse brains from multiple tissues and timepoints and compare the transcriptome with their wild-type littermates. Methods: mRNA profiles from Rai1 conditional knockouts and wild-type mice were generated by deep sequencing, in duplicate using Illumina system. Conclusions: Our study suggests that Rai1 preferentially regulate genes involved in cell adhesion and neural projection.

2017-01-03 | GSE81206 | GEO

Altered activity-dependent nascent transcription in Rai1-knockdown mature mouse cortical cultures

Project description:We performed the nascent RNA-seq technique, Bru-Seq, and chromatin immunoprecipitation sequencing (ChIP-seq) for Retinoic acid induced 1 (RAI1) using a custom antibody, on mouse neuronal cultures treated with control or Rai1-targeted shRNA, with 4 hour treatment of vehicle, tetrodoxin (TTX) or bicuculline (BIC) and 20 minute labeling of bromouridine.

2020-06-20 | GSE121749 | GEO

Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics and 3D genomics

Project description:Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances and stereotypic behaviors. We investigated a cohort of 15 individuals with a clinical suspicion of SMS, who showed neither deletion in the SMS critical region nor damaging variants in RAI1. Potentially deleterious variants were identified in nine of these subjects using whole-exome sequencing. Eight of these changes affect KMT2D, ZEB2, MAP2K2, GLDC, CASK, MECP2, KDM5C and POGZ, known to be associated with Kabuki syndrome 1, Mowat-Wilson syndrome, cardiofaciocutaneous syndrome, glycine encephalopathy, mental retardation and microcephaly with pontine and cerebellar hypoplasia, X-linked mental retardation 13, X-linked mental retardation Claes-Jensen type and White-Sutton syndrome, respectively. The ninth individual carries a de novo variant in JAKMIP1, a regulator of neuronal translation that was recently found deleted in a patient with autism spectrum disorder. Analyses of coexpression and biomedical text mining suggest that these pathologies and SMS are part of the same disease network. Further support for this hypothesis was obtained from transcriptome profiling that showed that the expression levels of both Zeb2 and Map2k2 are perturbed in Rai1-/- mice. As an orthogonal approach to potentially contributory disease gene variants, we used chromatin conformation capture to reveal chromatin contacts between RAI1 and the loci flanking ZEB2 and GLDC, as well as between RAI1 and human orthologs of the genes that show perturbed expression in our Rai1-/- mouse model. These holistic studies of RAI1 and its interactions allow insights into SMS and other disorders associated with intellectual disability and behavioral abnormalities. Our findings support a pan-genomic approach to the molecular diagnosis of a distinctive disorder.

2017-02-12 | GSE83420 | GEO

mRNA-seq of Rai1 ex 4 KO and wild-type control lines in mESC-differentiated NPCs and neurons

Project description:Mouse 129-B13 ESCs were genetically modified using CRISPR-Cas9 with two guides to remove exon 4 of Rai1, single-cell sorted and expanded to establish modified cell lines. Additionally, cell lines derived from unsuccessfully modified lines were used as "wild-type" controls. 3 lines of each group were used as biological replicates. Samples were differentiated from mouse ESCs (Day 0) to neural progenitor cells (Day 8) and glutamatergic neurons (Day 12). NEBNext Poly(A) mRNA Magnetic Isolation Module was used to enrich mRNA. Nonsense-mediated decay was not observed in Rai1 ex 4 KOs.

2023-01-31 | E-MTAB-10490 | biostudies-arrayexpress

PARE libraries for the identification of miRNA target genes in Norway spruce

Project description:We constructed four PARE libraries for the identification of miRNA target genes in Norway spruce. PARE libraries were constructed from four different tissues

2015-09-02 | E-GEOD-65248 | biostudies-arrayexpress

PARE libraries for the identification of miRNA target genes in Norway spruce

Project description:We constructed four PARE libraries for the identification of miRNA target genes in Norway spruce.

2015-09-02 | GSE65248 | GEO

MicroRNA-guided regulation of heat stress response in wheat

Project description:Sequencing of 24 small RNA libraries produced 55.2M reads while 404M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. Heat stress responsive miRNA targeted superoxide dismutases and an array of homeobox leucine-zipper proteins, F-box proteins and protein kinases. Query of miRNA targets to interactome databases revealed a predominant association of stress responses such as signalling, antioxidant activity and ubiquitination to superoxide dismutases, F-box proteins, pentatricopeptide repeat-containing proteins and mitochondrial transcription termination factor-like proteins.

2019-05-08 | GSE113357 | GEO

Sorghum bicolor and Setaria viridis PARE-seq

Project description:Parallel Analysis of RNA Ends (PARE) sequencing reads were generated to validate putative microRNAs and identify cleavage sites in Sorghum bicolor and Setaria viridis.

2020-05-19 | GSE150798 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data