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Multiplexed engineering and analysis of endogenous enhancer activity in single cells: Human/mouse mixing Drop-Seq experiments for K562 and MEFs

ABSTRACT: Multiplexed engineering and analysis of endogenous enhancer activity in single cells: Human/mouse mixing Drop-Seq experiments for K562 and MEFs

OTHER RELATED OMICS DATASETS IN: GSE81848GSE81884

PROVIDER: PRJNA322842 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3586780_1.fastq.gz	Fastqsanger.gz
	SRR3586780_2.fastq.gz	Fastqsanger.gz
	SRR3586781_1.fastq.gz	Fastqsanger.gz
	SRR3586781_2.fastq.gz	Fastqsanger.gz
	SRR3586782_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Multiplexed engineering and analysis of endogenous enhancer activity in single cells: Human/mouse mixing Drop-Seq experiments for K562 and MEFs

Project description:Transcriptional enhancers orchestrate cell-type specific gene expression programs critical to eukaryotic development, physiology, and disease. However, despite the large number of enhancers now identified, only a small number have been functionally assessed. Here, we develop MOsaic Single-cell Analysis by Indexed CRISPR Sequencing (Mosaic-seq), a method that measures one direct phenotype of enhancer repression: change of the transcriptome, at the single cell level. Using dCas9-KRAB to suppress enhancer function, we first implement a multiplexed system to allow the simultaneous measurement of the transcriptome and detection of sgRNAs by single cell RNA sequencing. We validate this approach by targeting the HS2 enhancer in the well-studied beta-globin locus. Next, through computational simulation, we demonstrate strategies to robustly detect changes in gene expression in these single cell measurements. Finally, we use Mosaic-seq to target 71 hypersensitive regions belonging to 15 super-enhancers in K562 cells by utilizing a lentiviral library containing 241 unique-barcoded sgRNAs. Our results demonstrate that Mosaic-seq is a reliable approach to study enhancer function in single cells in a high-throughput manner.

2017-04-13 | GSE81848 | GEO

Mixing experiment

Project description:Baltic Sea mixing experiment

| PRJEB25460 | ENA

Induction of inverted morphology in brain organoids by vertical-mixing bioreactors

Project description:Organoid technology provides an opportunity to generate brain-like structures by recapitulating developmental steps in the manner of self-organization. We examined the vertical-mixing effect on brain organoid structures using bioreactors and established inverted brain organoids. The organoids generated by vertical mixing showed neurons that migrated from the outer periphery to the inner core of organoids, in contrast to orbital mixing. To uncover the mechanisms of the inverted structure, we investigated the direction of primary cilia, a cellular mechanosensor. Primary cilia of neural progenitors by vertical mixing were aligned in a multidirectional manner, and those by orbital mixing in a bidirectional manner. Single-cell RNA sequencing revealed that neurons of inverted brain organoids presented a GABAergic character of the ventral forebrain.

2021-10-27 | GSE184409 | GEO

Mouse Human Purity mixing studies

Project description:Mouse Human Purity mixing studies

| PRJNA902363 | ENA

Mus musculus strain:mouse embryonic fibroblasts (MEFs) | isolate:MEFs | breed:MEFs | cultivar:Mus musculus

Project description:Mus musculus strain:mouse embryonic fibroblasts (MEFs) | isolate:MEFs | breed:MEFs | cultivar:Mus musculus Raw sequence reads

| PRJNA591794 | ENA

Mus musculus strain:mouse embryonic fibroblasts (MEFs) | isolate:MEFs | breed:MEFs | cultivar:Mus musculus

Project description:Mus musculus strain:mouse embryonic fibroblasts (MEFs) | isolate:MEFs | breed:MEFs | cultivar:Mus musculus Raw sequence reads

| PRJNA591721 | ENA

Drop-Seq analysis of P14 mouse retina single-cell suspension

Project description:A cell suspension was prepared from wild-type P14 mouse retinas, and single-cell mRNAseq libraries were generated with Drop-Seq. Drop-Seq was performed on four separate days using the same age (P14) and strain (C57BL/6). On day 1, replicate 1 was obtained. On day 2, replicates 2 and 3 were obtained. On day 3, replicates 4-6 were obtained. On day 4, replicate 7 was obtained.

2015-05-20 | E-GEOD-63472 | biostudies-arrayexpress

WT MEFs or IRE1α-/- MEFs treated with 1μM thapsigargin vs control

Project description:Transcriptional profiling of WT MEFs or IRE1α-/- MEFs treated with 1μM thapsigargin for 12hrs compared with their corresponding non-treated cells.

2014-12-22 | GSE17151 | GEO

Expression data in MEFs

Project description:Expression data in MEFs

| PRJNA448757 | ENA

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 An estimated 84 beads were selected for amplification.

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

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