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Single Cell RNA-Seq

ABSTRACT: 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. Single GM12878 cells were picked and RNA-seq libraries were generated using the SMART-seq protocol. We also carried out RNA-seq experiments on pools of 10, 30 and 100 cells, on 100pg and 10ng of total RNA.

ORGANISM(S): Homo sapiens

SUBMITTER: Diane Trout

PROVIDER: E-GEOD-44618 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Single Cell RNA-Seq

Project description: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.

2013-11-21 | GSE44618 | GEO

Genome-wide mapping of RNA Pol II binding site (GM12878)

Project description:We report the results of chromatin immunoprecipitation following by high-thoughput sequencing (ChIP-Seq) using the GA II platform from Illumina for the human RNA Polymerase II in GM12878 cells. We have also generated a sequenced input DNA datasets for GM12878 cells. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Map binding sites of RNA Polymerase II in the genome of GM12878 cells. The GM12878 input data has been deposited in GEO as GSM487430.

2009-12-31 | E-GEOD-19550 | biostudies-arrayexpress

Genome-wide mapping of RNA Pol III binding site (GM12878)

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2009-12-31 | E-GEOD-19549 | biostudies-arrayexpress

Single-cell RNA-seq of mouse developing spinal cord

Project description:12 cervicothoracic sections of mouse embryos were dissected at E9.5 (2 replicates), E10.5 (2 replicates), E11.5 (2 replicates), E12.5 (3 replicates), E13.5 (3 replicates). Single-cell RNA-seq libraries were encapsulated, sequenced, aligned, and counted with the 10X Genomics’ Chromium platform and Illumina’s HiSeq 4000 platform.

2018-11-29 | E-MTAB-7320 | biostudies-arrayexpress

Single cell RNA-seq atlas of human NSCLC lesions and non-involved tissue

Project description:We performed single cell RNA sequencing (scRNA-seq) of NSCLC tumours and matched, adjacent, non-involved lung tissue from 24 patients. The data set is composed of approximately 900,000 cells from two different populations: CD235- (haematopoietic and non-haematopoietic cells depleted of erythrocytes), and CD45+ (all haematopoietic cells).

2024-04-29 | E-MTAB-13526 | biostudies-arrayexpress

Single-cell RNA counting at allele- and isoform-resolution using Smart-seq3

Project description:Large-scale sequencing of RNAs from individual cells can reveal patterns of gene, isoform and allelic expression across cell types and states. However, current single-cell RNA-sequencing (scRNA-seq) methods have limited ability to count RNAs at allele- and isoform resolution, and long-read sequencing techniques lack the depth required for large-scale applications across cells. Here, we introduce Smart-seq3 that combines full-length transcriptome coverage with a 5’ unique molecular identifier (UMI) RNA counting strategy that enabled in silico reconstruction of thousands of RNA molecules per cell. Importantly, a large portion of counted and reconstructed RNA molecules could be directly assigned to specific isoforms and allelic origin, and we identified significant transcript isoform regulation in mouse strains and human cell types. Moreover, Smart-seq3 showed a dramatic increase in sensitivity and typically detected thousands more genes per cell than Smart-seq2. Altogether, we developed a short-read sequencing strategy for single-cell RNA counting at isoform and allele-resolution applicable to large-scale characterization of cell types and states across tissues and organisms.

2020-04-14 | E-MTAB-8735 | biostudies-arrayexpress

Single cell RNA sequencing of healthy and trisomy 21 (Down's syndrome) foetal liver and foetal bone marrow

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2024-07-22 | E-MTAB-13067 | biostudies-arrayexpress

Ro60-knockout cells

Project description:RNA-seq of Ro60-null GM12878 cell lines in order to determine the gene expression changes resulting from loss of Ro60. 3 separate clones of Ro60(Trove2)-null cells derived from zinc finger nuclease targeting of exon 2, two wildtype biological replicates, +/- IFNa for 6 hours.

2015-09-16 | E-GEOD-72501 | biostudies-arrayexpress

A single-cell transcriptome atlas of the human pancreas

Project description:To understand organ (dys)function it is important to have a complete inventory of its cell types and the corresponding markers that unambiguously identify these cell types. This is a challenging task, in particular in human tissues, because unique cell-type markers are typically unavailable, necessitating the analysis of complex cell type mixtures. Transcriptome-wide studies on pancreatic tissue are typically done on pooled islet material. To overcome this challenge we sequenced the transcriptome of thousands of single pancreatic cells from deceased organ donors with and without type 2 diabetes (T2D) allowing in silico purification of the different cell types. We identified the major pancreatic cell types resulting in the identification of many new cell-type specific and T2D-specific markers. Additionally we observed several subpopulations within the canonical pancreatic cell types, which we validated in situ. This resource will be useful for developing a deeper understanding of pancreatic biology and diabetes mellitus. Human cadaveric pancreata were used to extract islets of Langerhans, which were kept in culture until single-cell dispersion and FACS sorting. Single-cell transcriptomics was performed on live cells from this mixture using CEL-seq or on cells stained for CD63, CD13, TGFBR3 or CD24 and CD44. The RaceID algorithm was used to identify clusters of cells corresponding to the major pancreatic cell types and to mine for novel cell type-specific genes as well as subpopulations within the known pancreatic cell types.

2016-06-24 | E-GEOD-81076 | biostudies-arrayexpress

Schmidtea polychroa high resolution developmental transcriptomic time-course

Project description:Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This âphylotypic stageâ has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a âzootypicâ stage, however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum, including a segmented worm, a flatworm, a roundworm, a water bear, a fruitfly, a sea urchin, a zebrafish, a sea anemone, a sponge, and a comb jelly. For each species, we collected the embryonic transcriptomes at ~100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly, we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation, and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes, also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. 132 single embryo samples.

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