Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Purification-sequencing of RNA super-assemblies.

ABSTRACT: Purification-sequencing of RNA super-assemblies.

PROVIDER: PRJNA879772 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR21536791_1.fastq.gz	Fastqsanger.gz
	SRR21536791_2.fastq.gz	Fastqsanger.gz
	SRR21536792_1.fastq.gz	Fastqsanger.gz
	SRR21536792_2.fastq.gz	Fastqsanger.gz
	SRR21536793_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

Purification-sequencing of RNA super-assemblies.

Project description:C. elegans oogenesis arrest offers a unique and biologically relevant opportunity to investigate how condensation reorganizes the transcriptome in the context of cellular adaptation to quiescence. To investigate how RNA self-organization into condensates controls mRNA cytosolic stoichiometries depending on sequence identity and translational activity, we adapted a new Fluorescent Activated Particle Sorting (FAPS) method to selectively sort germline P-bodies from C. elegans oocytes. Fluorescently labelled in oocytes, GFP:CAR-1 P-bodies were formaldehyde fixed and FAPS sorted from whole animal extracts by their size and fluorescence. We then performed gene expression profiling analysis using data obtained from RNA-seq of oocyte P-bodies, dissected oocytes and whole animal extracts.

2023-09-12 | GSE213222 | GEO

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals S. aureus RsaG sRNA targetome

Project description:MS2-affinity purification coupled with RNA sequencing (MAPS) reveals S. aureus RsaG sRNA targetome. Affinity purification of in vivo regulatory complexes coupled with high throughput RNA sequencing methodology or MAPS standing for “MS2 affinity purification coupled to RNA".

2024-06-01 | GSE176028 | GEO

The Extracellular RNA Quality Control (exRNAQC) study: RNA Exome sequencing of RNA purification kit study (exRNAQC004)

2021-05-10 | E-MTAB-10504 | biostudies-arrayexpress

The Extracellular RNA Quality Control (exRNAQC) study: Small RNA sequencing of RNA purification kit study (exRNAQC011)

Project description:To evaluate the impact of the RNA purification method on extracellular RNA (exRNA) sequencing, 8 different RNA purification kits were compared by applying Small RNA sequencing (Illumina) to exRNA from human healthy donor plasma. Minimum and maximum plasma input volumes recommended by the manufacturers were tested in triplicate. Due to donor privacy concerns the raw data for this study have been submitted to the controlled-access archive EGA under the accession EGAS00001005263.

2021-06-10 | E-MTAB-10505 | biostudies-arrayexpress

MS2-affinity purification coupled with RNA sequencing (MAPS) revealed MicF sRNA targetome.

Project description:In this study, we performed MAPS (MS2-affinity purification coupled with RNA sequencing) to draw the interacting map of MicF small regulatory RNA in vivo.

2023-03-05 | GSE113584 | GEO

Discordant genome assemblies drastically alter the interpretation of single cell RNA sequencing data which can be mitigated by a novel integration method

Project description:Advances in sequencing and assembly technology has led to the creation of genome assemblies for a wide variety of non-model organisms. The rapid production and proliferation of updated, novel assembly versions can create create vexing problems for researchers when multiple genome as-sembly versions are available at once, requiring researchers to work with more than one reference genome. Multiple genome assemblies are especially problematic for researchers studying the genetic makeup of individual cells as single cell RNA sequencing (scRNAseq) requires sequenced reads to be mapped and aligned to a single reference genome. Using the Astyanax mexicanus this study highlights how the interpretation of a single cell dataset from the same sample changes when aligned to its two different available genome assemblies. We found that the number of cells and expressed genes detected were drastically different when aligning to the different assemblies. When the genome assemblies were used in isolation with their respective annotation, cell type identification was confounded as some classic cell type markers were assembly-specific, whilst other genes showed differential patterns of expression between the two assemblies. To overcome the problems posed by multiple genome assemblies, we propose that researchers align to each available assembly and then integrate the resultant datasets to produce a final dataset in which all genome alignments can be used simultaneously. We found this approach increased the accuracy of cell type identification and maximised the amount of data that could be extracted from our single cell sample by capturing all possible cells and transcripts. As scRNAseq becomes more widely available, it is imperative that the single cell community is aware how genome assembly alignment can alter single cell data and its interpretation, especially when reviewing studies on non-model organisms.

2022-02-10 | GSE194093 | GEO

Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes

Project description:We provide a method for high quality RNA purification out of a small number (5000 - 100,000) of FACS sorted zebrafish cells followed by RNA sequencing

2019-03-11 | GSE121917 | GEO

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RprA sRNA targetome.

Project description:Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. Using this technology, we already revealed the targetome of RyhB, RybB and DsrA, three well-characterized sRNAs in Escherichia coli. In this study, we perform MAPS with RprA sRNA.

2018-01-03 | GSE80020 | GEO

MS2-affinity purification coupled to RNA-sequencing (MAPS) reveals targetomes of Z. mobilis sRNAs Zms4 and Zms6

Project description:The MS2-affinity purification coupled to RNA-sequencing (MAPS) approach was used to identify RNA targets that physically associate in vivo with Zymomonas mobilis small RNAs Zms4 and Zms6.

2020-03-24 | GSE107192 | GEO

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals GcvB sRNA targetome.

2018-12-06 | GSE80019 | GEO