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Dataset results
39 results for “In situ sequencing”
Development of Multiomics in situ Pairwise Sequencing (MiP-Seq) for Single-cell Resolution Multidimensional Spatial Omics
<p>The original data used in the article: Development of Multiomics in situ Pairwise Sequencing (MiP-Seq) for Single-cell Resolution Multidimensional Spatial Omics</p> <p>Delineating the spatial multiomics landscape will pave the way to understanding the molecular basis of physiology and pathology. However, current spatial omics technology development is still in its infancy. Here, we developed a high-throughput targeted in situ sequencing strategy, multiomics in situ pairwise sequencing (MiP-Seq), to efficiently decipher multiplexed DNAs, RNAs, proteins, and small biomolecules at subcellular resolution. MiP-Seq simultaneously sequenced the dual barcode base of padlock probes, dramatically increasing the detection capacity to 10N by N rounds of sequencing. We delineated spatial gene profiles in the hypothalamus using MiP-Seq. Moreover, MiP-Seq was unitized to detect tumor gene mutations and allele-specific expression of parental genes and to differentiate sites with and without the m6A RNA modification at specific sites. MiP-Seq was combined with in vivo Ca2+ imaging and Raman imaging to obtain a spatial multiomics atlas correlated to neuronal activity and cellular biochemical fingerprints. Importantly, we proposed a “signal dilution strategy” to resolve the crowded signals that challenge the applicability of in situ sequencing. Together, our method improves spatial multiomics and precision diagnostics, and facilitates analyzing cell function in connection with gene profiles.</p>
Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue
<p>You can find here the Direct RNA In Situ Sequencing (HybISS-based) maps generated using the Hight Sensitivity kit from CARTANA AB. They include half a mouse brain coronal section, targeting 50 genes. Genes were targeted in a sequential manner. Both reads, DAPI staining and segmented cells are included. The analysis of the same cells, but using 10X magnification are also provided in an anndata object.</p>
Liu_et_al_DMG_In Situ Sequencing_expression_maps
<p>This repository includes the In Situ Sequencing datasets (HybISS) generated for Liu et al. 2022. Both gene expression maps (reads.zip) as well as cell type maps (this is, after segmenting individual cells) are included. Malignant cell types were assigned based on probabilistic cell typing by ISS (Qian et al. 2020) and can be found at celltyping_malignant.zip. Healthy cells, in addition to the described malignant ones, were included in celltyping_malignant_and_healthy.zip. In addition annotated data objects (anndata) were generated for all 16 samples (anndata_objects)</p>
Mini In Situ Sequencing mouse brain dataset using Cartana technology
<div> <div> <div> <p>A subset of an ISS dataset is being utilized here to showcase the data format without replicating the ISS decoding procedure (for this first version).</p> <p>There are in total 3 data objects:</p> <ol> <li>A 5-channel raw microscope image</li> <li>The corresponding single cell segmentation image (label image)</li> <li>The correspdoning single-cell gene expression data object (.h5ad)</li> </ol> </div> </div> </div>
Expansion in situ genomic sequencing datasets
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Automated identification of the mouse brain's spatial compartments from in situ sequencing data
<p>Example data [1] for testing in situ sequencing graph-based decoding pipeline and decoding results for reproducing publication analyses. Image decoding pipeline and notebooks are available at: <a href="https://github.com/wahlby-lab/graph-iss">https://github.com/wahlby-lab/graph-iss</a></p> <p>------------</p> <p>[1] Ke, Rongqin, et al. "In situ sequencing for RNA analysis in preserved tissue and cells." <em>Nature methods</em> 10.9 (2013): 857.</p>
Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing - Image and In SItu Sequencing data
<p>Image and ISS data for Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing reveals a biologically relevant zonation of the desmoplastic rim.</p><p>Image data consists of:</p><ul><li>Nucler stain (DAPI)</li><li>Masks for liver, rim and tumor regions</li><li>H&E images of parallel tissue sections</li></ul><p>Gene and cluster marker data is collected in the <i>markers.h5ad</i> file which can be read using AnnData (<a href="https://anndata.readthedocs.io/en/latest/">https://anndata.readthedocs.io/en/latest/)</a>. </p><p> </p>
Supplementary data for paper "RNA in situ conformation sequencing reveals novel long-range RNA interactions that impact splicing"
<p>Supplementary data for paper "RNA in situ conformation sequencing reveals novel long-range RNA structures with impact on splicing".</p> <p>Data showing support for PCCR (<a href="https://www.nature.com/articles/s41467-021-22549-7">paper</a>) in RIC-seq data (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190214">archive</a>).</p> <p> </p> <p>S1: for each supported PCCR lists numbers of experiments with inner and outer support and number of supporting reads in each experiment</p> <p>S2: for select PCCR lists supporting and non-supporting cell lines, total number of supporting reads and mean PSI in each group, and difference in mean PSI between the groups</p>
In situ hybridization probe sequences for mouse Alx3, Fgf8, Msx1, Shh, Six3
<p><span><span><span><span><span><span><span><span><span><span><span>Serum response factor (SRF) is an essential transcription factor that influences many cellular processes including cell proliferation, migration, and differentiation. SRF directly regulates and is required for immediate early gene (IEG) and actin cytoskeleton-related gene expression. SRF coordinates these competing transcription programs through discrete sets of cofactors, the Ternary Complex Factors (TCFs) and Myocardin Related Transcription Factors (MRTFs). The relative contribution of these two programs to <i>in vivo</i> SRF activity and mutant phenotypes is not fully understood. To study how SRF utilizes its cofactors during development, we generated a knock-in <i>Srf</i><i><sup>a</sup></i><i><sup>I</sup></i> allele in mice harboring point mutations that disrupt SRF-MRTF-DNA complex formation but leave SRF-TCF activity unaffected. Homozygous <i>Srf</i><i><sup>a</sup></i><i><sup>I/</sup></i><i><sup>a</sup></i><i><sup>I</sup></i> mutants die at E10.5 with notable cardiovascular phenotypes, and neural crest conditional mutants succumb at birth to defects of the cardiac outflow tract but display none of the craniofacial phenotypes associated with complete loss of SRF in that lineage. Our studies further support an important role for MRTF mediating SRF function in cardiac neural crest and suggest new mechanisms by which SRF regulates transcription during development.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Efficient in situ barcode sequencing using padlock probe-based BaristaSeq
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In situ hybridization probe sequences for mouse Alx3, Fgf8, Msx1, Shh, Six3
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DSBCapture: in situ capture and direct sequencing of dsDNA breaks
GEO Series GSE78172. Homo sapiens. 11 samples. Type: Other; Expression profiling by high throughput sequencing.
DEEP SEQUENCING OF MODELS OF BREAST DUCTAL CARCINOMA IN SITU REVEALS ALDH5A1 AS A NOVEL POTENTIAL THERAPEUTIC TARGET
GEO Series GSE36863. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
In situ tumor arrays reveal early environmental control of cancer immunity [Whole Exome Sequencing]
GEO Series GSE222540. Mus musculus. 11 samples. Type: Other.
Image-seq: spatially-resolved single cell sequencing guided by in situ and in vivo imaging
GEO Series GSE188902. Mus musculus. 153 samples. Type: Expression profiling by high throughput sequencing.
Single-nucleus total RNA-sequencing of C2C12 myoblasts via in situ polyadenylation
GEO Series GSE209780. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Light-Seq: Light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing
GEO Series GSE208650. Homo sapiens; Mus musculus. 14 samples. Type: Expression profiling by high throughput sequencing.
Paradise fish (Macropodus opercularis) in situ probe sequences, whole mount in situ hybridization and phalloidin staining protocol
<p>Detailed whole-mount <em>in situ </em>hybridization and phalloidin staining for paradise fish (<em>Macropodus opercularis</em>). Sequencing results of the paradise fish coding DNA sequence (CDS) fragments cloned into pGEMT plasmid and used for the <em>in situ</em> hybridization probe synthesis experiments described in the paper.</p>
Role of Next Generation Sequencing in the Etiological Diagnosis of Permanent Congenital Hypothyroidism with in Situ Thyroid
ClinicalTrials.gov study NCT06728735. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing
GEO Series GSE141018. Escherichia coli; Staphylococcus aureus. 18 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.