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

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

PROVIDER: PRJNA644383 | ENA |

REPOSITORIES: ENA

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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

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

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ERCC TAC-seq

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

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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

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

ERCC TAC-seq

Project description:ERCC TAC-seq

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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

RNA-Seq on libraries made from ERCC external RNA controls, and a mixture of D. melanogaster S2 cell mRNA and ERCC mRNAs

Project description:RNA-Seq on libraries made from External RNA Controls Consortium (ERCC) external RNA controls, and a mixture of mRNA from Drosophila melanogaster S2 cell and ERCC mRNAs. We evaluated performance of RNA-Seq on known synthetic PolyA+ mRNAs from the External RNA Controls Consortium (ERCC) alone and in mixtures with PolyA+ mRNA from Drosophila S2 cells. ERCC mRNAs were obtained under Phase V testing from the National Institutes of Standards and Technology (NIST). The ERCC pool contained 96 species of mRNA of various lengths and GC content covering a 2^20 concentration range. Libraries were constructed using 100ng S2 mRNA with 5ng, 2.5ng, or 1ng ERCC mRNAs, and using 50ng ERCC mRNA without S2 cell mRNA. Our data shows an outstanding linear fit between RNA-Seq read density and known input amounts. We made libraries with 100ng S2 mRNA with 5ng, 2.5ng or 1ng ERCC mRNAs and with 50ng ERCC mRNAs only. For each library, one lane was sequenced for a 36bp run and around 15 million reads were obtained for each lane.

2010-04-19 | E-GEOD-20579 | biostudies-arrayexpress

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

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