Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq after KD or OE of circRNAs or linear gene

ABSTRACT: RNA-seq after KD or OE of circRNAs or linear gene

PROVIDER: PRJNA510354 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8329170_1.fastq.gz	Fastqsanger.gz
	SRR8329170_2.fastq.gz	Fastqsanger.gz
	SRR8329180_1.fastq.gz	Fastqsanger.gz
	SRR8329180_2.fastq.gz	Fastqsanger.gz
	SRR8329171_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

RNA-seq after KD or OE of circRNAs or linear gene

Project description:The cancer transcriptome is remarkably complex, including low-abundance transcripts, many not polyadenylated. To fully characterize the transcriptome of localized prostate cancer, we performed ultra-deep total RNA-Seq on 144 tumours with rich clinical annotation. This revealed a linear transcriptomic subtype associated with the aggressive intraductal carcinoma sub-histology and a fusion profile that differentiates localized from metastatic disease. Analysis of back-splicing events showed widespread RNA circularization, with the average tumour expressing 7,232 circular RNAs (circRNAs). The degree of circRNA production was correlated to disease progression in multiple patient cohorts. Loss of function screening identified 11.3% of highly-abundant circRNAs as essential for cell proliferation; for ~90% of these, their parental linear transcripts were not essential for cell proliferation. Individual circRNAs can have distinct functions, with circCSNK1G3 promoting cell growth by interacting with miR-181. These data advocate for adoption of ultra-deep RNA-Seq without poly-A selection to interrogate both the linear and circular transcriptome.

2019-02-07 | GSE123940 | GEO

CircRNAs in Arabidopsis thaliana across the lifespan

Project description:To explore the overall circRNAs involved in growth and development of Arabidopsis thaliana across the lifespan, we deeply sequenced samples of whole plants from different developmental stages (cotyledons emergence, rosette leavesï¹¥1 mm, rosette growth complete, first flower open, flourishing florescence, first silique shattered, senescence). The total RNA was purified by rRNA-depletion and linear RNA removal with RNAseR, and sequenced by the Illumina HiSeq2500 platform. We obtained 31 Gb raw data and identified 1217 circRNAs with expression quantity. We annotated these circRNAs and predicted their targeted microRNA. The circRNAs involved in growth and development of Arabidopsis thaliana across lifespan were identified and analyzed using the Illumina HiSeq2500 platform.

2016-09-01 | E-GEOD-77672 | biostudies-arrayexpress

Chromatin ImmunoPrecipitation DNA-Sequencing after H19 OE and KD

Project description:Chromatin ImmunoPrecipitation DNA-Sequencing after H19 OE and KD

| PRJNA642159 | ENA

Next Generation Sequencing Analysis of CircRNAs/linear RNA in Isolated Renal Proximal Tubule tissues from Acute kidney injury mice

Project description:The goal of this study was to find the differentially expressed circRNAs/linear RNA in AKI mice model compared to normal mice. We established cisplatin-induced AKI mice models and then extracted RNAs from isolated renal tubular tissues for Next Generation Sequencing(NGS) at different time points during early stage of AKI. CircRNA library was constructed by NEB Next®Ultra™ small RNA Sample Library Prep Kit for Illumina®. NGS was performed by using Illumina HiSeq 2500 Genome Sequencers.The original image data file was transformed into Raw Data by Base Calling. Clean Data was obtained by removing reads that containing joints and more than 5% N (undetermined base information). Mapped Reads were obtained by sequence alignment between Clean Reads and reference genome sequenced using BWA software package. CIRI software was used to predict circRNAs. Finally, we identified 2162 circRNAs and our study represents the first detailed analysis of AKI mice circRNA transcriptomes, which provide a framework for investigations of circRNAs expression profiles in AKI

2020-02-01 | GSE130814 | GEO

Total RNA-Seq of KHSRP knockdown (KD) and control samples in HepG2 and K562

Project description:We profile the expression of circular RNAs (circRNAs) upon KHSRP KD in HepG2 and K562 cells

2020-11-11 | GSE145984 | GEO

Effect of FTO-KD or FTO-OE on gene expression in GH3 cell line

Project description:Effect of FTO-KD or FTO-OE on gene expression in GH3 cell line

| PRJNA1120007 | ENA

circRNAs in the mouse striatum of HuD ovreexpressing OE mice and wildtype mice

Project description:circRNAs in the mouse striatum of HuD ovreexpressing OE mice and wildtype mice

| PRJNA642214 | ENA

RNA-seq for HCT116 cells with TTC22-OE or kockdown

Project description:object:compare the genes influenced by TTC22 overexpression or knockdown Methods: For whole-genome transcriptome profiling, four libraries were generated from total RNA samples extracted from Flag-TTC22-OE, empty vector control, scramble RNA control, and TTC22-KD (siTTC#1&2&3) HCT116 cells using TruSeq® RNA Sample Preparation Kit (Illumina Inc.) according to the manufacturer’s protocol, and sequenced on the Illumina HiSeq PE150 platform (Genminix, Shanghai, China) using the 150–base pair single-end sequencing module. Hisat2 (version:2.0.4) was used to map the cleaned reads to the human hg38 reference genome. Results: The mRNA data obtained from transcriptome sequencing, subjected to T-test statistics and corrected by the RVM model. Significant differential mRNA (TwoClassDif) between TTC22-OE and vector control cells or between TTC22-KD and scramble RNA control cells was yielded. Up-regulated and down-regulated genes (fold change>1.5, calculated through Ballgown algorithm) were performed to find significant functions and significant signaling pathways based on the Gene Ontology database (GO-Analysis) or KEGG database.(Pathway-Analysis). Conclusion:The results suggested that TTC22 could affect the RNA metabolism pathway that controls the progression and metastasis of CC.

2024-12-01 | GSE189892 | GEO

Comparative gene expression in adult SVZ-neurospheres differentiated under standard conditions and upon manipulations of Pax6 (OE) and/or Pbx1 (KD/OE)

Project description:Comparative gene expression in adult SVZ-neurospheres differentiated under standard conditions and upon manipulations of Pax6 (OE) and/or Pbx1 (KD/OE)

| PRJNA723324 | ENA

circRNAs in the mouse striatum of HuD ovreexpressing OE mice and wildtype mice

Project description:This study explores the expression circRNAs in the striatum

2020-06-27 | GSE153394 | GEO