Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SCRB-seq comparison with TruSeq on bulk RNA-seq human LCL (DMSO) and BAY treated LCL (BAY)

ABSTRACT: Here, we validate a novel protocol, Bulk RNA Barcoding and sequencing (BRB-seq), that combines the multiplexing-driven cost-effectiveness of a single-cell RNA-seq protocol with the efficiency of a bulk RNA-seq procedure. For this we first gauge the applicability of the SCRB-seq protocol on bulk DMSO and BAY treated human LCL, and compare its effectiveness as compared to TruSeq.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Vincent Gardeux

PROVIDER: E-MTAB-6984 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing.

Alpern Daniel D Gardeux Vincent V Russeil Julie J Mangeat Bastien B Meireles-Filho Antonio C A ACA Breysse Romane R Hacker David D Deplancke Bart B

Genome biology 20190419 1

Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3' cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time. BRB-seq has a comparable performance to the standard TruSeq approach while showing greater tolerance for lower RNA quality and being up to 25 times cheaper. We anticipate that BRB-seq will transform ...[more]

PMID: 30999927

Similar Datasets

Bulk RNA Barcoding and sequencing (BRB-seq) protocol for RNA-seq of 60 human LCL from the 1000G project

2018-12-17 | E-MTAB-7524 | biostudies-arrayexpress

Bulk RNA Barcoding and sequencing (BRB-seq) protocol for RNA-seq of human pre-adipocytes and differentiated adipocytes

Project description:Here, we validate a novel protocol, Bulk RNA Barcoding and sequencing (BRB-seq), that combines the multiplexing-driven cost-effectiveness of a single-cell RNA-seq protocol with the efficiency of a bulk RNA-seq procedure. For this we use BRB-seq protocol on human pre-adipocytes and differentiated adipocytes, and compare its effectiveness as compared to TruSeq. Indeed, one of the principal limitations of bulk RNA-seq is the time and costs of library preparation, which makes it difficult to profile many samples simultaneously. Here, BRB-seq produces 3’ libraries that exhibit similar gene expression quantification to TruSeq and maintain this quality even with low quality RNA samples.

2018-02-06 | E-MTAB-6469 | biostudies-arrayexpress

Bulk RNA Barcoding and sequencing (BRB-seq) of Mock, ICV, and IDV infected airway epithelial cell cultures of human, porcine, and bovine origin at 33°C and 37°C

Project description:For the assessment of host response dynamics to ICV and IDV infections in human, porcine, and bovine airway epithelial cells at ambient temperature corresponding to the upper or lower respiratory tract. We performed a temporal transcriptome analysis on human, porcine, and bovine airway epithelial cell (AEC) cultures infected with ICV and IDV, as well as uninfected hAEC cultures, incubated either at 33°C or 37°C. AEC cultures from the different species were harvested at 24, 48 72, 96 hpi and processed for Bulk RNA Barcoding and sequencing (BRB-seq), which allows a rapid and sensitive genome-wide transcriptomic analysis in a highly multiplexed manner. Transcriptome data from human, procine, and bovine was obtained from a total of 3 biological donors for pairwise comparisons of ICV and IDV virus-infected to unexposed AEC cultures at respective time points and temperatures.

2022-07-13 | E-MTAB-11939 | biostudies-arrayexpress

Whole genome \"TraDIS-Xpress\" assay to determine gene roles during growth of E. coli in different concentrations of the antibiotics trimethoprim and sulfamethoxazole

Project description:To assay every gene in the E. coli genome to identify those that contribute to increased or decreased susceptibility to the antibiotics trimethoprim and sulfamethoxazole. This will help to define more accurately those bacterial cell mechanisms that contribute to these phenomena and provide information that will contribute to the development of new antibiotics, or compounds or known antibiotics that synergise with those already in clinical use. Thus, this set of experiments confirmed that AZT, widely known for its antiviral activity, acts synergistically with trimehoprim.

2020-10-19 | E-MTAB-9305 | biostudies-arrayexpress

Mir142 loss unlocks IDH2R140-dependent leukemogenesis through antagonistic regulation of HOX genes

Project description:Acute myeloid leukaemia (AML) is genetically a genetically heterogeneous condition. It was observed that mutations in the micro RNA mir142 co-occurred with mutations in isocitrate dehdrogenase genes IDH1 and 2. These experiments intend to investigate the interaction between miR142 and IDH in AML.

2020-06-05 | E-MTAB-8042 | biostudies-arrayexpress

RNA-seq to assess the impact of circulation on hematopoietic stem cell differentiation.

Project description:Blood flow promotes hematopoiesis, Definitive hematopoietic stem cells can not be assessed in circulation negative Ncx-/- mice. This study looks at the impact of lack of blood flow on the earliest blood cell precursors, the pro-HSCs. E9.5 was chosen as this is the time point pro-HSCs are normally generated. Cells from the hemogenic endothelium, the endothelium and pro-HSCs were sequenced.

2021-10-01 | E-MTAB-8362 | biostudies-arrayexpress

A long-term feeder-free culture method for human pancreatic progenitors on extra cellular matrix or matrix-free polymers

Project description:The dataset comprises RNA-seq information of human embryonic stem cell derived pancreatic progenitors and their proliferating cells cultured in defined condition. Total RNA of each sample was isolated, labelled, and purified by standard chemistry. Sequencing libraries were prepared from 250ng of purified total mRNA using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). Single-read RNA-sequencing was performed using the NextSeq 500 (Illumina) with 75 High Output Kit (Illumina, FC-404-2005).

2021-12-20 | E-MTAB-9992 | biostudies-arrayexpress

SCRB-seq comparison with TruSeq on bulk RNA-seq human LCL (DMSO) and BAY treated LCL (BAY)

Project description:SCRB-seq comparison with TruSeq on bulk RNA-seq human LCL (DMSO) and BAY treated LCL (BAY)

| PRJEB27652 | ENA

Bulk RNA-seq of paired human brown and white adipocytes

Project description:To identify candidates of interest that were more highly expressed in BAT than WAT, we conducted RNAseq in human primary brown and white adipocytes. Adipose tissue was obtained from the central compartment of the neck, superior to the clavicle and deep to the lateral thyroid lobe either adjacent to the longus colli muscle or to the oesophagus (brown adipose tissue) and more superficially from the subcutaneous neck tissue (white adipose tissue). The stromal vascular fraction was isolated and cultured as described (Ramage, Akyol et al. 2016 doi: 10.1016/j.cmet.2016.06.011). Following differentiation, cells were cultured in serum-stripped medium for 48 hours prior to RNA extraction and subsequent bulk RNA-seq.

2023-05-22 | E-MTAB-10123 | biostudies-arrayexpress

RNA-Seq analysis of resting and activated mouse Tregs

Project description:RNA-Seq was used to compare the gene expression patterns in resting and activated Tregs.

2020-10-23 | E-MTAB-9657 | biostudies-arrayexpress