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Transcriptome of Dp1Tyb and wild-type mouse embryonic fibroblasts [ERCC spike-ins]

ABSTRACT: Transcriptome of Dp1Tyb and wild-type mouse embryonic fibroblasts [ERCC spike-ins]

PROVIDER: PRJNA508970 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8308720_1.fastq.gz	Fastqsanger.gz
	SRR8308720_2.fastq.gz	Fastqsanger.gz
	SRR8308721_1.fastq.gz	Fastqsanger.gz
	SRR8308721_2.fastq.gz	Fastqsanger.gz
	SRR8308714_1.fastq.gz	Fastqsanger.gz

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Transcriptome of Dp1Tyb and wild-type mouse embryonic fibroblasts [ERCC spike-ins]

Project description:Purpose: to identify the effects of the Dp1Tyb mutation on the transcriptome of mouse embryonic fibroblasts

2019-03-29 | GSE123514 | GEO

Drop-Seq analysis of ERCC spike in capture

Project description:A bead supsension and a solution of ERCC spike-ins at a concentration of ~100,000 molecules per droplet was used in Drop-Seq, a novel technology for high-throughput single cell mRNAseq

2015-05-20 | GSE66694 | GEO

Drop-Seq analysis of ERCC spike in capture

2015-05-20 | E-GEOD-66694 | biostudies-arrayexpress

MAQC-III/SEQC Main Study ABCD titration experiment, ERCC spike-in profiles and gene-level estimates for a selected test set

Project description:Comparison to RNA-Seq showed different strengths and weaknesses for different regimes of expression strength. At sufficient read-depth, both platforms seemed comparable for gene-level expression profiling. Comparison to RNA-Seq showed comparable accuracy and precision with microarrays for ERCC spike-ins at medium to high expression levels. At low expression levels, the array showed signal attenuation but better precision, while RNA-Seq maintained accuracy albeit with highly inflated variance. In summary, both platforms can be meaningfully applied in a similar range of expression strength. Assessment of (precision, accuracy, reproducibility, mutual information, titration order consistency, and known mixing ratio recovery) by measurement of known-ratio mixtures of two RNA reference samples. The array probes 776 complex genes representative of the AceView gene model annotation, as well as 92 ERCC spike-in controls.

2015-04-03 | E-GEOD-48016 | biostudies-arrayexpress

Evaluation of RNA-Seq with External RNA Control Consortium (ERCC) spike-ins

Project description:This SuperSeries is composed of the following subset Series: GSE20555: RNA-Seq on libraries made from serial dilutions of Drosophila melanogaster S2 cell mRNA and ERCC external RNA controls GSE20579: RNA-Seq on libraries made from ERCC external RNA controls, and a mixture of D. melanogaster S2 cell mRNA and ERCC mRNAs Refer to individual Series

2010-04-18 | E-GEOD-20580 | biostudies-arrayexpress

Transcriptome of Dp1Tyb and wild-type mouse embryonic fibroblasts

Project description:Purpose: to identify the effects of the Dp1Tyb mutation on the transcriptome of mouse embryonic fibroblasts

2019-03-29 | GSE109293 | GEO

MAQC-III/SEQC Main Study ABCD titration experiment, ERCC spike-in profiles and gene-level estimates for a selected test set

2015-04-03 | GSE48016 | GEO

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (RNA-seq with ERCC spike-in) [RNA-Seq]

Project description:We report the ERCC spike-in controlled RNA-seq in human hippocampus subject to normal aging and Alzheimer's disease.

2020-07-07 | GSE153873 | GEO

ERCC TAC-seq

Project description:Targeted assay to detect 22 selected ERCC spike-in mRNA molecules for method sensitivity testing purposes

2018-03-01 | GSE108759 | GEO

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data

Project description:This study aims to assess the reliability of spike-in normalization for analyzing single-cell RNA sequencing data. This is done by performing mixture experiments where two different sets of spike-in RNA (ERCC and SIRV) are added separately to a single mouse cell (416B or trophoblast stem cells (TSCs)), followed by generation of sequencing libraries using a modified version of the Smart-seq2 protocol. The aim is to measure the variance of the log-ratio of the total counts between the two spike-in sets. This will quantify how precisely the spike-in RNA was added to each well. As a control, addition was also performed with a premixed solution of both spike-ins, to quantify the variability in the log-ratios due to the experimental protocol. The same data can also be used to measure the well-to-well variability in the differences in behaviour between the two spike-in sets. The data contain four batches of libraries (block), using different batches of cells that were processed and sequenced separately. Each batch contains libraries with all three types of spike-in addition (ERCC+SIRV, SIRV+ERCC or Premixed). The 416B cells also contain a CBFB-MYH11 oncogene, which is expressed in half of the cells (Induced) and silent in the other half (Control).

2017-05-31 | E-MTAB-5522 | biostudies-arrayexpress

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