GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus; Escherichia coli

Type:

Expression profiling by high throughput sequencing; Other

7 related Platforms

368 Samples

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(Submitter supplied) The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. more...

Organism:

Escherichia coli

Type:

Other

Platforms:

GPL32081 GPL21222 GPL28771

42 Samples

Download data: TXT

(Submitter supplied) The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

48 Samples

Download data: TXT

(Submitter supplied) The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

120 Samples

Download data: TXT

(Submitter supplied) The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30172 GPL19057

12 Samples

Download data: RDS, TXT

(Submitter supplied) The inability to scalably and precisely measure the cell-type-specific activity of developmental enhancers is a bottleneck in genomics. To address this, we developed a “dual RNA”' system that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. Together with RNA barcode circularization, the resulting single-cell quantitative expression reporters (scQers) facilitate the robust detection of which reporter(s) are present in which single cells, thereby providing high contrast readouts analogous to classic in situ assays but entirely from sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

15 Samples

Download data: RDS, TXT

(Submitter supplied) The inability to scalably and precisely measure the cell-type-specific activity of developmental enhancers is a bottleneck in genomics. To address this, we developed a “dual RNA”' system that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. Together with RNA barcode circularization, the resulting single-cell quantitative expression reporters (scQers) facilitate the robust detection of which reporter(s) are present in which single cells, thereby providing high contrast readouts analogous to classic in situ assays but entirely from sequencing. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30172 GPL19057

22 Samples

Download data: RDS, TXT

(Submitter supplied) The inability to scalably and precisely measure the cell-type-specific activity of developmental enhancers is a bottleneck in genomics. To address this, we developed a “dual RNA”' system that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. Together with RNA barcode circularization, the resulting single-cell quantitative expression reporters (scQers) facilitate the robust detection of which reporter(s) are present in which single cells, thereby providing high contrast readouts analogous to classic in situ assays but entirely from sequencing. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

4 Samples

Download data: BW, TXT

(Submitter supplied) The inability to scalably and precisely measure the cell-type-specific activity of developmental enhancers is a bottleneck in genomics. To address this, we developed a “dual RNA”' system that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. Together with RNA barcode circularization, the resulting single-cell quantitative expression reporters (scQers) facilitate the robust detection of which reporter(s) are present in which single cells, thereby providing high contrast readouts analogous to classic in situ assays but entirely from sequencing. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL21222

7 Samples

Download data: TXT

(Submitter supplied) The inability to scalably and precisely measure the cell-type-specific activity of developmental enhancers is a bottleneck in genomics. To address this, we developed a “dual RNA”' system that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. Together with RNA barcode circularization, the resulting single-cell quantitative expression reporters (scQers) facilitate the robust detection of which reporter(s) are present in which single cells, thereby providing high contrast readouts analogous to classic in situ assays but entirely from sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

(Submitter supplied) The inability to scalably and precisely measure the cell-type-specific activity of developmental enhancers is a bottleneck in genomics. To address this, we developed a “dual RNA”' system that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. Together with RNA barcode circularization, the resulting single-cell quantitative expression reporters (scQers) facilitate the robust detection of which reporter(s) are present in which single cells, thereby providing high contrast readouts analogous to classic in situ assays but entirely from sequencing. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL30172

80 Samples

Download data: TXT

(Submitter supplied) The inability to scalably and precisely measure the cell-type-specific activity of developmental enhancers is a bottleneck in genomics. To address this, we developed a “dual RNA”' system that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. Together with RNA barcode circularization, the resulting single-cell quantitative expression reporters (scQers) facilitate the robust detection of which reporter(s) are present in which single cells, thereby providing high contrast readouts analogous to classic in situ assays but entirely from sequencing. more...

Organism:

Homo sapiens; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21222 GPL18573

6 Samples

Download data: TXT

(Submitter supplied) Cis-regulatory elements (CREs) encode the genomic blueprints for coordinating the spatiotemporal regulation of gene transcription programs necessary for highly specialized cellular functions. To identify cis-regulatory elements underlying cell-type specification and developmental transitions, we implemented single-cell sequencing of Assay for Transposase Accessible Chromatin (scATAC-seq) in an atlas of Zea mays tissues and organs. more...

Organism:

Zea mays; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25410 GPL26208

14 Samples

Download data: TXT

(Submitter supplied) Neurodevelopmental disorders (NDDs) result from highly penetrant variation in hundreds of different genes, some of which have not yet been identified. Using the MatchMaker Exchange, we assembled a cohort of 27 individuals with rare, protein-altering variation in the transcriptional coregulator gene ZMYM3, located on the X chromosome. Most (n=24) individuals were males, 17 of which have a maternally inherited variant and four of which have de novo variants. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL21103

22 Samples

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(Submitter supplied) We performed mRNA transcriptional profiling of mouse retina in the wild-type and Nrl-null context to determine Nrl-dependent gene expression We sequenced cDNA libraries made from polyA+ selected RNA from retinas of litter-matched WT and Nrl-/- adult mice at postnatal day 21 (P21) (WT vs Nrl-/-, n=5 and n= 6 resp.)

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

11 Samples

Download data: XLSX

(Submitter supplied) We performed non-coding transcriptional profiling to identify Nrl-dependent ncRNAs by deep sequencing non-polyadenylated RNA from the same control and Nrl-/- retinal samples. non-coding RNA profiling is a robust method for the identification of cell-type specific functional enhancer elements in the mouse retina

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21103

11 Samples

Download data: BW, TXT

(Submitter supplied) Here we describe sci-CAR, a combinatorial indexing strategy to jointly profile chromatin accessibility and mRNA in each of thousands of single cells. As a proof-of-concept, we apply sci-CAR to 4,825 cells comprising a time-series of dexamethasone treatment, as well as to 11,233 cells from the mouse kidney.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19415 GPL19057

6 Samples

Download data: CSV, TXT

(Submitter supplied) We report a new technology for the parallel bimodal analysis of RNA-seq and ATAC-seq within a single-cell, known as ASTAR (Assay for Single-cell Transcriptome and Accessibility Regions).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

40 Samples

Download data: TXT

(Submitter supplied) We report a new technology for the parallel bimodal analysis of RNA-seq and ATAC-seq within a single-cell, known as ASTAR (Assay for Single-cell Transcriptome and Accessibility Regions).

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

40 Samples

Download data: BEDGRAPH