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Items: 17

1.

A method for spatially resolved tissue transcriptomics applied to the mouse and lizard P. vitticeps brains

(Submitter supplied) We have developed an imaging-free framework to localize nucleic acids within a tissue by combining  a compressed sensing tissue-sampling strategy based on multi-angle-sectioning and an associated image reconstruction algorithm.  Initially, the tissue is cut into consecutive thin slices. Subsequently these are further sliced along an orthogonal plane at predefined orientations resulting in tissue strips that are subject to RNA sequencing. more...
Organism:
Mus musculus; Pogona vitticeps
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL28731 GPL13112
1200 Samples
Download data: TAB
Series
Accession:
GSE152989
ID:
200152989
2.

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens; Mus musculus
Type:
Expression profiling by high throughput sequencing; Other
6 related Platforms
871 Samples
Download data: DCC
Series
Accession:
GSE190089
ID:
200190089
3.

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human kidney]

(Submitter supplied) Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene or protein expression. Here we describe expanded chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probe pools targeting the protein-coding genes in the human and mouse transcriptomes, hereafter referred to as the human or mouse Whole Transcriptome Atlas (WTA). more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL21697
273 Samples
Download data: DCC, TXT
Series
Accession:
GSE190088
ID:
200190088
4.

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human tonsil]

(Submitter supplied) Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene or protein expression. Here we describe expanded chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probe pools targeting the protein-coding genes in the human and mouse transcriptomes, hereafter referred to as the human or mouse Whole Transcriptome Atlas (WTA). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL30173
49 Samples
Download data: DCC, TXT
Series
Accession:
GSE188451
ID:
200188451
5.

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [mouse organ array]

(Submitter supplied) Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene or protein expression. Here we describe expanded chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probe pools targeting the protein-coding genes in the human and mouse transcriptomes, hereafter referred to as the human or mouse Whole Transcriptome Atlas (WTA). more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL13112
85 Samples
Download data: DCC, XLSX
Series
Accession:
GSE187013
ID:
200187013
6.

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [mouse cell pellet array]

(Submitter supplied) Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene or protein expression. Here we describe expanded chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probe pools targeting the protein-coding genes in the human and mouse transcriptomes, hereafter referred to as the human or mouse Whole Transcriptome Atlas (WTA). more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL24247
71 Samples
Download data: DCC, XLSX
Series
Accession:
GSE187000
ID:
200187000
7.

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human cell pellet array]

(Submitter supplied) Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene or protein expression. Here we describe expanded chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probe pools targeting the protein-coding genes in the human and mouse transcriptomes, hereafter referred to as the human or mouse Whole Transcriptome Atlas (WTA). more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
36 Samples
Download data: DCC, XLSX
Series
Accession:
GSE186714
ID:
200186714
8.

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [E13.5 mouse embryo]

(Submitter supplied) Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene or protein expression. Here we describe expanded chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probe pools targeting the protein-coding genes in the human and mouse transcriptomes, hereafter referred to as the human or mouse Whole Transcriptome Atlas (WTA). more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30172
357 Samples
Download data: DCC, XLSX
Series
Accession:
GSE186594
ID:
200186594
9.

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: FPKM_TRACKING
Series
Accession:
GSE67685
ID:
200067685
10.

Three-dimensional molecular cartography of human cerebral organoids revealed by double-barcoded spatial transcriptomics

(Submitter supplied) Spatially-resolved transcriptomics methodologies are revolutionizing our understanding of complex tissues, but their elevated costs represent still a bottle-neck for their democratization. In this work we present a low-cost strategy for manufacturing molecularly double-barcoded DNA arrays, enabling large-scale spatially-resolved transcriptomics studies. We applied this technique to spatially resolve gene expression in several human brain organoids, including the reconstruction of a 3-dimensional view from multiple consecutive sections, revealing gene expression divergencies throughout the tissue.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
15 Samples
Download data: TSV
Series
Accession:
GSE223020
ID:
200223020
11.

Spatial Transcriptomics Using Multiplexed Deterministic Barcoding in Tissue

(Submitter supplied) In this study, we present a multiplexed version of Deterministic Barcoding in Tissue (xDBiT) to acquire spatially resolved transcriptomes of nine tissue sections in parallel. New microfluidic chips were developed to spatially encode mRNAs over a total tissue area of 1.17 cm2 with spots of 50 µm×50 µm. Optimization of the biochemical protocol increased read and gene counts per spot by one order of magnitude compared with previous reports. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL24247
26 Samples
Download data: H5AD, TAR
Series
Accession:
GSE207843
ID:
200207843
12.

Genome-wide RNA tomography in the zebrafish embryo

(Submitter supplied) Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome-wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes, they are unable to yield spatially resolved information in embryos or tissues. Microscopy-based approaches, using for example in situ hybridization, can provide spatial information about gene expression, but are limited to analyzing one or a few genes at a time. more...
Organism:
Danio rerio; Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL18413 GPL17021
34 Samples
Download data: TXT
Series
Accession:
GSE59873
ID:
200059873
13.

Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section

(Submitter supplied) We present a spatial omics approach that merges and expands the capabilities of independently performedin situassays on a single tissue section. Our spatial multimodal analysis combines histology, mass spectrometry imaging, and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular weight metabolites across tissue regions. We demonstrate the potential of our method using murine and human brain samples in the context of dopamine and Parkinson’s disease.
Organism:
Mus musculus; Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL30173 GPL30172
19 Samples
Download data: CSV, H5, JPG, JSON, PNG
Series
Accession:
GSE232910
ID:
200232910
14.

Gene expression profiling of the whole mouse brain using transcriptome tomography

(Submitter supplied) We developed a novel framework to assess comprehensive endogenous gene expression maps in a broad and isotropic 3D-anatomical context using a relatively small number of original data points: transcriptome tomography. Using this method, we produced a dataset of gene expression maps of the whole mouse brain, computationally reconstructed from fraction data.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL7202
61 Samples
Download data: TXT
Series
Accession:
GSE36408
ID:
200036408
15.

RNA-seq of laser-capture microdissected 50x50x50 um tissue cubes from the medial ganglionic eminence of wild-type and GFRa1 mutant mice

(Submitter supplied) Cortical interneurons originating from the medial ganglionic eminence (MGE) are among the most diverse cells within the CNS. Different pools of proliferating progenitor cells are thought to exist in the ventricular zone of the MGE, but whether the underlying subventricular and mantle regions of the MGE are spatially patterned has not yet been addressed. Here, we combined laser-capture microdissection and multiplex RNA-sequencing to map the transcriptome of MGE cells at a spatial resolution of 50 µm. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
312 Samples
Download data: TAB
Series
Accession:
GSE60402
ID:
200060402
16.

Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples

(Submitter supplied) Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of unbiased SRT methods targeting the polyA tail of mRNA, relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available SRT assays requires a careful sample screening process to increase the chance of obtaining high-quality data. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL30172
14 Samples
Download data: CSV, H5, JSON, PNG
Series
Accession:
GSE221571
ID:
200221571
17.

Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain

(Submitter supplied) Despite wide applications in tissue mapping and vastly improved imaging and omics technologies, spatial, genome-wide assays of gene expression are yet to reliably achieve the resolution and sensitivity approaching dissociative single-cell RNA sequencing. Here, we introduce Pixel-seq, a spatial barcoding method using “continuous” polony gels of ≤ 1 µm feature resolution for capturing tissue RNAs and precise aggregation of mapped transcripts into individual cells. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL24247
4 Samples
Download data: FA, RDS, TAB
Series
Accession:
GSE186097
ID:
200186097

Supplemental Content

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