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The Multi-Layered Transcriptional Architecture of Glioblastoma Ecosystems [smart-seq2]

ABSTRACT: The Multi-Layered Transcriptional Architecture of Glioblastoma Ecosystems [smart-seq2]

PROVIDER: PRJNA1147183 | ENA |

REPOSITORIES: ENA

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The Multi-Layered Transcriptional Architecture of Glioblastoma Ecosystems [smart-seq2]

Project description:To comprehensively define the cellular heterogeneity of glioblastoma (GBM), the GBM CARE (Cellular Analysis of Resistance and Evolution) consortium set out to profile 121 GBMs with extensive clinical annotation, by single-nucleus RNA-sequencing and bulk tumor DNA sequencing. The resulting dataset enabled us to characterize GBM heterogeneity at three levels. First, GBMs are classified by their cellular composition, encompassing malignant, immune, neuronal and glial cell types. Second, within each cell type, and particularly among the malignant cells, we describe the diversity of cellular states and their pathway-based functional activities. Third, after controlling for the frequencies of cellular states, we find that the remaining variation between GBMs highlights three baseline gene expression programs which we labeled Neuronal, Glial, and Extracellular Matrix. These three layers of heterogeneity are inter-related and partially associated with specific genetic aberrations, thereby defining three stereotypic ecosystems in GBM. This work provides an unparalleled view of the multi-layered transcriptional architecture of GBM.

2025-01-01 | GSE274548 | GEO

The Multi-Layered Transcriptional Architecture of Glioblastoma Ecosystems [10X]

Project description:The Multi-Layered Transcriptional Architecture of Glioblastoma Ecosystems [10X]

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High Resolution Mapping of Mouse Embryonic Genome Activation using SMART-seq2

Project description:Single-embryo SMART-seq2 of mouse 2-cell stage embryos. The embryos have been generated with in vitro fertilization (IVF) and are staged as hours post-IVF.

2026-06-24 | E-MTAB-15452 | biostudies-arrayexpress

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Project description:Smart-seq2 scRNA-seq of liver non-parenchymal cells from 3 high-fat diet and 3 control mice.

2023-04-29 | GSE230440 | GEO

Smart-seq2 single-cell RNA sequencing of human pancreatic islets

Project description:Previous study (Segerstolpe Å et.al., Cell Metab . 2016) has revealed the single-cell landscape of human pancreatic islets from 10 human individuals. Here, we have performed Smart-seq2 scRNA-seq of additional 4 healthy and 6 T2D individuals.

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SMART-seq2 of Kdm5b Overexpression in Fully Grown Oocytes

Project description:RNA-seq of single Fully Grown Oocytes using SMART-seq2. The oocytes were collected from female FVB mice, approximately. 44-48 h post-PMSG injection. The oocytes were microinjected with 1.3-1.7 μg/μL Kdm5b wild-type (WT) or catalytic mutant (CM) mRNA. Noninjected oocytes are denoted as “Noninj”. The oocytes were cultured overnight for approximately 16 h in M2 containing 20 μM Milrinone and 5% FBS and collected for sequencing.

2026-06-24 | E-MTAB-15453 | biostudies-arrayexpress

In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells (Smart-Seq2 scRNA-seq)

Project description:Single-cell RNA-seq (Smart-Seq2) to profile of cardiac progenitor cells

2018-09-12 | GSE114279 | GEO

Single-cell RNAseq (SMART-seq2) of wild-type (TLAB) and MZoep (tz57) zebrafish embryos at 50% epiboly stage

Project description:SMART-seq2 was performed on single cells isolated from visually staged zebrafish embryos.

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Smart-seq2 analysis of P17 FACS sorted retinal cells from the Kcng4-cre;stop-YFP X Thy1-stop-YFP Line#1 mice

Project description:Four Kcng4-cre;stop-YFP mouse retinas from two mice were dissected, dissociated and FACS sorted, and single cell RNA-seq libraries were generated for 384 single cells using Smart-seq2. Aligned bam files are generated for 383 samples as one failed to align. Four mouse retinas (labeled 1la, 1Ra, and 2la, 2Ra respective from the two mice) were used, and 96 single cells from each were processed using Smart-seq2. Total 384 cells Smart-seq2 analysis of P17 FACS sorted retinal cells from the Kcng4-cre;stop-YFP mice (Kcng4tm1.1(cre)Jrs mice [Duan et al., Cell 158, 793-807, 2015] crossed to the cre-dependent reporter Thy1-stop-YFP Line#1 [Buffelli et al., Nature 424, 430-434, 2003])

2016-08-25 | E-GEOD-81903 | biostudies-arrayexpress

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