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Links from GEO DataSets

Items: 20

1.

Single-cell transcriptomics reveals widespread heterogeneity in gene regulation and RNA processing in stimulated immune cells

(Submitter supplied) Here, we used single-cell RNA-Seq to discover extensive cell-to-cell variability – in transcript expression levels, cell state, circuit usage, and alternative splicing – between stimulated immune cells
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
24 Samples
Download data:
GEO (TXT), SRA SRP015959
Series
Accession:
GSE41265
ID:
200041265
2.

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(Submitter supplied) Here, we use a microfluidics-based approach to prepare single-cell RNA-Seq libraries from over 1,700 primary mouse dendritic cells (DCs) stimulated with three pathogenic components and examine variation between individual cells exposed to the same stimulus and general strategies that multicellular populations use to establish complex dynamic responses.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL13112 GPL17021
2425 Samples
Download data:
GEO (TXT), SRA SRP027537
Series
Accession:
GSE48968
ID:
200048968
3.

Saccharomyces cerevisiae Transcript Isoform mapping

(Submitter supplied) Extensive transcriptional heterogeneity revealed by isoform profiling
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13821
18 Samples
Download data:
GEO (TXT), SRA SRP014137
Series
Accession:
GSE39128
ID:
200039128
4.

Single-Cell mRNA Sequencing Reveals Rare Intestinal Cell Types

(Submitter supplied) Understanding the development and function of an organ requires the characterization of all of its cell types. Traditional methods for visualizing and isolating sub-populations of cells are based on mRNA or protein expression of only few known marker genes. The unequivocal identification of a specific marker gene, however, poses a major challenge, particularly if this cell type is rare. Identifying rare cell types, such as stem cells, short-lived progenitors, cancer stem cells, or circulating tumor cells is crucial to acquire a better understanding of normal or diseased tissue biology. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19057 GPL17021
35 Samples
Download data:
GEO (TXT), SRA SRP048838
Series
Accession:
GSE62270
ID:
200062270
5.

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-/- Retinal Transcriptomes

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11002
6 Samples
Download data:
GEO (BAM, TXT, XLS), SRA SRP009096
Series
Accession:
GSE33141
ID:
200033141
6.

Single Cell RNA-Seq

(Submitter supplied) RNA-seq transcriptome measurements are typically performed by isolating RNA from large numbers of cells in culture or tissues. While highly informative, such experiments mask the variability in gene expression patterns that exists between individual cells. To gain insight into the dynamics of gene expression on the level of single-cells, we have carried out the transcriptomes of single-cells from the GM12878 cell line using RNA-seq.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
62 Samples
Download data:
GEO (FPKM_TRACKING, TXT), SRA SRP018838
Series
Accession:
GSE44618
ID:
200044618
7.

Microfluidic single-cell whole-transcriptome sequencing

(Submitter supplied) Single-cell whole-transcriptome analysis is a powerful tool for quantifying gene expression heterogeneity in populations of cells. Many techniques have, thus, been recently developed to perform transcriptome sequencing (RNA-Seq) on individual cells. To probe subtle biological variation between samples with limiting amounts of RNA, more precise and sensitive methods are still required. We adapted a previously developed strategy for single-cell RNA-Seq that has shown promise for superior sensitivity and implemented the chemistry in a microfluidic platform for single-cell whole transcriptome analysis. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
102 Samples
Download data:
GEO (TXT), SRA SRP025171
Series
Accession:
GSE47835
ID:
200047835
8.

Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation

(Submitter supplied) We present high quality deep read-depth single cell RNA sequencing for 91 cells from five mouse tissues and 18 cells from two rat tissues, along with 30 control samples of bulk RNA diluted to single-cell levels. We find that transcriptomes differ globally across tissues with regard to the number of genes expressed, the average expression patterns, and within cell-type variation patterns. We develop methods to filter genes for reliable quantification and to calibrate biological variation. more...
Organism:
Mus musculus; Rattus norvegicus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL17021 GPL14844 GPL13112
137 Samples
Download data:
GEO (TXT), SRA SRP041119
Series
Accession:
GSE56638
ID:
200056638
9.

[E-MTAB-5] Dynamic repertoire of a eukaryotic transcriptome surveyed at single nucleotide resolution

(Submitter supplied) Recent data from several organisms indicate that the transcribed portions of genomes are larger and more complex than expected, and many functional properties of transcripts are not based on coding sequences but on regulatory sequences in untranslated regions or non-coding RNAs. Alternative start and polyadenylation sites and regulation of intron splicing add additional dimensions to the rich transcriptional output. more...
Organism:
Schizosaccharomyces pombe
Type:
Expression profiling by high throughput sequencing
Platform:
GPL9854
31 Samples
Download data:
GEO (TXT)
Series
Accession:
GSE25003
ID:
200025003
10.

Effect of LMP7 and MECL1-immunoproteasome subunits deficiency on the transcriptome of mouse bone marrow-derived dendritic cells

(Submitter supplied) As regulators of protein degradation, proteasomes regulate practically all cellular functions. It is therefore logical to assume that replacement of the constitutive proteasome (CP) by its IFN- inducible homolog immunoproteasome (IP) could have far reaching effects on cell function. Accordingly, recent studies have revealed important roles for IPs in immune cells beyond MHC I-peptide processing. Moreover, the expression of IPs in non-immune cells from non-inflamed tissues suggests that the involvement of IPs is not limited to the immune system. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
32 Samples
Download data:
GEO (TXT), SRA SRP033235
Series
Accession:
GSE52616
ID:
200052616
11.

Combined genome-wide expression profiling and targeted RNA interference in primary mouse macrophages

(Submitter supplied) Here we have used targeted RNA interference to suppress the expression of a number of key genes associated with IFN signalling in murine macrophages prior to activation. Genome-wide changes in transcript abundance caused by siRNA activity were measured using Affymetrix exon-arrays in the presence or absence of IFNγ stimulation. Transfection of murine bone-marrow derived macrophages (BMDMs) with non-targeting (control) siRNA and 11 sequence-specific siRNAs was performed using a cationic lipid transfection reagent (Lipofectamine2000) prior to stimulation with IFNγ. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6096
90 Samples
Download data:
GEO (CEL, CHP)
Series
Accession:
GSE14534
ID:
200014534
12.

Spatially resolved, highly multiplexed RNA profiling in single cells

(Submitter supplied) Knowledge of the expression profile and spatial landscape of the transcriptome in individual cells is essential for understanding the rich repertoire of cellular behaviors. Here we report multiplexed error-robust fluorescence in situ hybridization (MERFISH), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15520
1 Sample
Download data:
GEO (FPKM_TRACKING), SRA SRP056989
Series
Accession:
GSE67685
ID:
200067685
13.

RNA-Seq based characterization of long non-coding RNA involved in respiratory viruses pathogenesis

(Submitter supplied) We aimed at systematically inferring the regulatory functions of host lncRNAs in response to influenza A virus (IAV) and severe acute respiratory syndrome coronavirus (SARS-CoV) in the mouse model, using a ‘guilt-by-association’ approach which relies on finding which lncRNAs have similar expression profiles to protein-coding genes of known function. To build a large panel of diverse host responses to viral infection, we took advantage of the genetic diversity present in the 8 founder strains of the Collaborative Cross (CC) mouse resource. more...
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL11002
123 Samples
Download data:
GEO (TXT), SRA SRP033021
Series
Accession:
GSE52405
ID:
200052405
14.

Integrated genome and transcriptome sequencing from the same cell

(Submitter supplied) Single-cell genomics and single-cell transcriptomics have recently emerged as powerful tools to study the biology of single cells at a genome-wide scale. Here we describe a method that allows the integration of genomic DNA and mRNA sequencing from the same cell. We use this method to correlate DNA copy number variation to transcriptome variability among individual cells.
Organism:
Homo sapiens; Mus musculus
Type:
Genome variation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL16791 GPL17021
20 Samples
Download data:
GEO (CSV, TXT), SRA SRP049500
Series
Accession:
GSE62952
ID:
200062952
15.

Dynamic profiling of the protein life cycle in response to pathogens

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Protein profiling by Mass Spec
Platforms:
GPL18998 GPL17021
116 Samples
Download data:
GEO
Series
Accession:
GSE59793
ID:
200059793
16.

Dynamic profiling of the protein life cycle in response to pathogens (protein)

(Submitter supplied) Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. more...
Organism:
Mus musculus
Type:
Protein profiling by Mass Spec
Platform:
GPL18998
88 Samples
Download data:
GEO (TXT)
Series
Accession:
GSE59792
ID:
200059792
17.

Dynamic profiling of the protein life cycle in response to pathogens (RNA-seq)

(Submitter supplied) Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
28 Samples
Download data:
GEO (TXT), SRA SRP044873
Series
Accession:
GSE59784
ID:
200059784
18.

Gene expression profiling of BM-derived dendritic cells reveals important mechanisms associated with predisposition to Staphylococcus infections

(Submitter supplied) Background: Staphylococcus aureus is a major pathogen of humans and animals and rapidly emerging antibiotic-resistant strains have further increased the severity of this health issue. Host genetics influence susceptibility to S. aureus infections, and genes determining infection outcome should be identified to analyze immune-based therapies as an alternative to antibiotics. Here, we used outbred animals from a divergent selection on susceptibility towards Staphylococcus infection to explore host immunogenetics. more...
Organism:
Ovis aries
Type:
Expression profiling by array
Platform:
GPL10427
44 Samples
Download data:
GEO
Series
Accession:
GSE24448
ID:
200024448
19.

Deep sequencing the circadian and light-dependent transcriptome of Drosophila brain

(Submitter supplied) Eukaryotic circadian clocks include transcriptional/translational feedback loops that drive 24-hour rhythms of transcription.These transcriptional rhythms underlie oscillations of protein abundance, thereby mediating circadian rhythms of behavior, physiology, and metabolism. Numerous studies over the last decade have employed microarrays to profile circadian transcriptional rhythms in various organisms and tissues. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13304
24 Samples
Download data:
GEO (BED, BEDGRAPH, TXT), SRA SRP011074
Series
Accession:
GSE36108
ID:
200036108
20.

Deep sequencing the circadian transcriptome of Drosophila brain

(Submitter supplied) RNAseq transcriptional profiling of Drosophila brains from wildtype, and period loss-of-function animals with time points taken over two days.
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL11203
24 Samples
Download data:
GEO (BED, BEDGRAPH, TXT), SRA SRP007416
Series
Accession:
GSE29972
ID:
200029972
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