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| Status |
Public on Aug 02, 2020 |
| Title |
A method for spatially resolved tissue transcriptomics applied to the mouse and lizard P. vitticeps brains |
| Organisms |
Mus musculus; Pogona vitticeps |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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. We implemented this framework to transform a single-cell RNA sequencing protocol into an imaging-free spatial transcriptomics technique. The method was validated by profiling the transcriptome of the Murine brain, and used to spatially profile the brain transcriptome of the Australian Central bearded dragon, Pogona vitticeps.
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| |
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| Overall design |
One Mus musculus and one Pogona vitticeps brain in thin coronal sections, cut into stripes at several alternating angles
Please note that the 'GSE152989_new_suppl_files.tar.gz' contains the expression data formatted in ".cef" format. The "cef" is a tab delimited file format described at: https://github.com/linnarsson-lab/ceftools
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| |
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| Contributor(s) |
Schede HH, LaManno G |
| Citation(s) |
33875865 |
| |
| Submission date |
Jun 22, 2020 |
| Last update date |
Sep 25, 2021 |
| Contact name |
Sten Linnarsson |
| Organization name |
Karolinska Institutet
|
| Department |
Medical Biochemistry and Biophysics
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| Lab |
Molecular Neurobiology
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| Street address |
Scheeles väg 1
|
| City |
Stockholm |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL28731 |
Illumina HiSeq 2000 (Pogona vitticeps) |
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| Samples (1200)
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|
| Relations |
| BioProject |
PRJNA641126 |
| SRA |
SRP268323 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE152989_LizardA_expression.tab.gz |
945.2 Kb |
(ftp)(http) |
TAB |
| GSE152989_LizardB_expression.tab.gz |
1.1 Mb |
(ftp)(http) |
TAB |
| GSE152989_LizardC_expression.tab.gz |
1.1 Mb |
(ftp)(http) |
TAB |
| GSE152989_LizardD_expression.tab.gz |
836.4 Kb |
(ftp)(http) |
TAB |
| GSE152989_LizardE_expression.tab.gz |
988.8 Kb |
(ftp)(http) |
TAB |
| GSE152989_Mouse10_expression.tab.gz |
1.0 Mb |
(ftp)(http) |
TAB |
| GSE152989_Mouse1_expression.tab.gz |
821.1 Kb |
(ftp)(http) |
TAB |
| GSE152989_Mouse2_expression.tab.gz |
918.2 Kb |
(ftp)(http) |
TAB |
| GSE152989_Mouse3_expression.tab.gz |
821.8 Kb |
(ftp)(http) |
TAB |
| GSE152989_Mouse4_expression.tab.gz |
946.0 Kb |
(ftp)(http) |
TAB |
| GSE152989_Mouse5_expression.tab.gz |
892.0 Kb |
(ftp)(http) |
TAB |
| GSE152989_Mouse6_expression.tab.gz |
1.0 Mb |
(ftp)(http) |
TAB |
| GSE152989_Mouse7_expression.tab.gz |
592.5 Kb |
(ftp)(http) |
TAB |
| GSE152989_Mouse8_expression.tab.gz |
1.2 Mb |
(ftp)(http) |
TAB |
| GSE152989_Mouse9_expression.tab.gz |
747.4 Kb |
(ftp)(http) |
TAB |
| GSE152989_new_suppl_files.tar.gz |
5.9 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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